From 3038d61d379f1ae9dfbf9d5e825494a45e3bdd0f Mon Sep 17 00:00:00 2001 From: admin Date: Wed, 20 Nov 2024 04:21:13 +0000 Subject: [PATCH] Jenkins update build 220. --- automated_tool_installation_log.tsv | 29 ++ staging.gvl.org.au/annotation.yml | 124 ++++---- staging.gvl.org.au/assembly.yml | 266 ++++++++-------- staging.gvl.org.au/bacterial_typing.yml | 12 +- staging.gvl.org.au/bb_tools.yml | 9 +- staging.gvl.org.au/bed.yml | 12 +- staging.gvl.org.au/blast.yml | 14 +- staging.gvl.org.au/chemicaltoolbox.yml | 60 ++-- staging.gvl.org.au/chip_seq.yml | 12 +- staging.gvl.org.au/collection_operations.yml | 14 +- staging.gvl.org.au/convert_formats.yml | 42 +-- staging.gvl.org.au/deeptools.yml | 118 +++---- staging.gvl.org.au/dna_metabarcoding.yml | 10 +- staging.gvl.org.au/emboss.yml | 4 +- staging.gvl.org.au/epigenetics.yml | 6 +- staging.gvl.org.au/fastafastq.yml | 147 ++++----- staging.gvl.org.au/fastq_quality_control.yml | 32 +- .../fetch_alignmentssequences.yml | 2 +- staging.gvl.org.au/filter_and_sort.yml | 2 +- staging.gvl.org.au/gemini_tools.yml | 20 +- staging.gvl.org.au/genome_editing.yml | 4 +- staging.gvl.org.au/get_data.yml | 40 +-- staging.gvl.org.au/graphdisplay_data.yml | 81 ++--- staging.gvl.org.au/hca_single_cell.yml | 30 +- staging.gvl.org.au/hicexplorer.yml | 28 +- staging.gvl.org.au/imaging.yml | 66 ++-- staging.gvl.org.au/ivar.yml | 80 ++--- .../join_subtract_and_group.yml | 8 +- staging.gvl.org.au/machine_learning.yml | 56 ++-- staging.gvl.org.au/mapping.yml | 54 ++-- staging.gvl.org.au/metabolomics.yml | 58 ++-- staging.gvl.org.au/metagenomic_analysis.yml | 169 +++++----- staging.gvl.org.au/mothur.yml | 4 +- staging.gvl.org.au/multiple_alignments.yml | 66 ++-- staging.gvl.org.au/nanopore.yml | 64 ++-- staging.gvl.org.au/none.yml | 61 ++-- staging.gvl.org.au/phylogenetics.yml | 92 +++--- staging.gvl.org.au/picard.yml | 12 +- staging.gvl.org.au/proteomic_ai.yml | 12 +- staging.gvl.org.au/proteomics.yml | 230 +++++++------- staging.gvl.org.au/qiime_2.yml | 2 +- staging.gvl.org.au/rad_seq.yml | 66 ++-- staging.gvl.org.au/rna_seq.yml | 156 +++++----- staging.gvl.org.au/rseqc.yml | 2 +- staging.gvl.org.au/sambam.yml | 80 ++--- staging.gvl.org.au/send_data.yml | 10 +- staging.gvl.org.au/single_cell.yml | 240 +++++++------- staging.gvl.org.au/statistics.yml | 32 +- staging.gvl.org.au/text_manipulation.yml | 52 ++-- staging.gvl.org.au/variant_calling.yml | 45 +-- staging.gvl.org.au/vcfbcf.yml | 294 +++++++++--------- staging.gvl.org.au/viral_tools.yml | 2 +- usegalaxy.org.au/annotation.yml | 107 +++---- usegalaxy.org.au/assembly.yml | 251 ++++++++------- usegalaxy.org.au/bacterial_typing.yml | 8 +- usegalaxy.org.au/bb_tools.yml | 9 +- usegalaxy.org.au/bed.yml | 18 +- usegalaxy.org.au/blast.yml | 14 +- usegalaxy.org.au/chemicaltoolbox.yml | 60 ++-- usegalaxy.org.au/chip_seq.yml | 14 +- usegalaxy.org.au/collection_operations.yml | 14 +- usegalaxy.org.au/convert_formats.yml | 46 +-- usegalaxy.org.au/deeptools.yml | 128 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 10 +- usegalaxy.org.au/emboss.yml | 4 +- usegalaxy.org.au/epigenetics.yml | 8 +- usegalaxy.org.au/fastafastq.yml | 121 +++---- usegalaxy.org.au/fastq_quality_control.yml | 36 +-- .../fetch_alignmentssequences.yml | 2 +- usegalaxy.org.au/filter_and_sort.yml | 8 +- usegalaxy.org.au/gemini_tools.yml | 28 +- usegalaxy.org.au/genome_editing.yml | 10 +- usegalaxy.org.au/get_data.yml | 30 +- usegalaxy.org.au/graphdisplay_data.yml | 71 ++--- usegalaxy.org.au/hca_single_cell.yml | 30 +- usegalaxy.org.au/hicexplorer.yml | 28 +- usegalaxy.org.au/imaging.yml | 54 ++-- usegalaxy.org.au/ivar.yml | 70 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 10 +- usegalaxy.org.au/machine_learning.yml | 40 +-- usegalaxy.org.au/mapping.yml | 44 +-- usegalaxy.org.au/metabolomics.yml | 48 ++- usegalaxy.org.au/metagenomic_analysis.yml | 183 +++++------ usegalaxy.org.au/mothur.yml | 8 +- usegalaxy.org.au/multiple_alignments.yml | 62 ++-- usegalaxy.org.au/nanopore.yml | 54 ++-- usegalaxy.org.au/none.yml | 51 +-- usegalaxy.org.au/phylogenetics.yml | 102 +++--- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 14 +- usegalaxy.org.au/proteomics.yml | 220 ++++++------- usegalaxy.org.au/rad_seq.yml | 70 ++--- usegalaxy.org.au/rna_seq.yml | 176 +++++------ usegalaxy.org.au/rseqc.yml | 4 +- usegalaxy.org.au/sambam.yml | 82 ++--- usegalaxy.org.au/send_data.yml | 6 +- usegalaxy.org.au/single_cell.yml | 242 +++++++------- usegalaxy.org.au/statistics.yml | 30 +- usegalaxy.org.au/text_manipulation.yml | 42 +-- usegalaxy.org.au/variant_calling.yml | 37 +-- usegalaxy.org.au/vcfbcf.yml | 276 ++++++++-------- 101 files changed, 3098 insertions(+), 3023 deletions(-) diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index efb8add8d..4a7dacd28 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -8110,3 +8110,32 @@ Update 219 13/11/24 04:02:33 trycycler_consensus False Installed iuc a7ed21de23f Update 219 13/11/24 04:03:11 trycycler_partition False Installed iuc 7673a6c920b2 7673a6c920b2 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_219/install_log.txt Update 219 13/11/24 04:03:52 trycycler_reconcile_msa False Installed iuc ed312479d9eb ed312479d9eb Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_219/install_log.txt Update 219 13/11/24 04:04:36 trycycler_subsample False Installed iuc b9b0246a2be3 b9b0246a2be3 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_219/install_log.txt +Update 220 20/11/24 01:36:44 abyss False Tests failed iuc db9b10824c61 db9b10824c61 Staging Testing 0/3 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 01:42:53 bbtools_bbduk False Installed iuc d58c27d2c5a7 d58c27d2c5a7 3/3 BB Tools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 01:48:03 bbtools_bbmerge False Installed iuc 1bb2b5b52030 1bb2b5b52030 3/3 BB Tools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 01:53:08 bbtools_tadpole False Installed iuc ce13b4678f18 ce13b4678f18 3/3 BB Tools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 01:53:48 blobtoolkit False Installed bgruening 392811378515 392811378515 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 01:58:18 data_manager_build_kraken2_database False Installed iuc e9ee4d074d5d e9ee4d074d5d 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:12:29 fastp False Installed iuc a626e8c0e1ba a626e8c0e1ba 15/15 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:22:08 infernal False Tests failed bgruening 1d74ed49cf41 1d74ed49cf41 Staging Testing 6/12 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:22:50 matchms_add_key False Installed recetox a5d41764722d a5d41764722d Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:23:32 matchms_convert False Installed recetox 9e83636da9d3 9e83636da9d3 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:24:15 matchms_filtering False Installed recetox 83c4b4359ac4 83c4b4359ac4 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:24:57 matchms_fingerprint_similarity False Installed recetox fd890f162ce6 fd890f162ce6 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:25:49 matchms_formatter False Installed recetox a5a5b147da70 a5a5b147da70 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:26:28 matchms_metadata_export False Installed recetox 8832425b1ff6 8832425b1ff6 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:27:11 matchms_metadata_match False Installed recetox 330b0dfae8da 330b0dfae8da Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:27:53 matchms_metadata_merge False Installed recetox 1fd950c5586a 1fd950c5586a Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:28:32 matchms_networking False Installed recetox f04b378325e5 f04b378325e5 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:29:15 matchms_remove_key False Installed recetox fbdb2ae524df fbdb2ae524df Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:29:55 matchms_remove_spectra False Installed recetox d50ce2f51fc0 d50ce2f51fc0 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:30:35 matchms_spectral_similarity False Installed recetox 7ba589b01dbc 7ba589b01dbc Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:31:13 matchms_split False Installed recetox ea6c5636c0cf ea6c5636c0cf Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 02:31:57 matchms_subsetting False Installed recetox 5bbd1a8404f5 5bbd1a8404f5 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 03:02:46 polypolish False Installed iuc 915637bd1d1a 915637bd1d1a 13/13 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 03:03:25 pretext_map False Installed iuc c6cec5ab35c1 c6cec5ab35c1 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 03:04:04 pretext_snapshot False Installed iuc 26f2fe7e53a1 26f2fe7e53a1 Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 03:19:15 quast False Tests failed iuc a3b35edea53a a3b35edea53a Staging Testing 11/13 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 03:45:35 sniffles False Installed iuc ceff2f6a5368 ceff2f6a5368 6/6 Variant Calling toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 03:46:17 snpeff False Installed iuc c7275bd8b4d6 c7275bd8b4d6 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt +Update 220 20/11/24 04:20:43 tbprofiler False Installed iuc 8cb134b8c1a5 8cb134b8c1a5 4/4 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_220/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index a59671848..8f0340122 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 6e9aea89e388 - 3f3e247c053d - - 78c75f134c16 - - 4efdca267d51 + - 6e9aea89e388 - c2ef298da409 + - 4efdca267d51 + - 78c75f134c16 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -19,37 +19,37 @@ tools: - name: aegean_gaeval owner: iuc revisions: - - 8dc7512c9dc9 - 1dd7adc21b6d + - 8dc7512c9dc9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval owner: iuc revisions: - - d6c074a93c51 - 1b52f0c8ad7f + - d6c074a93c51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - 4f2967b27e67 - 133f36c29579 - fe3ca740a485 - b5d8e5475247 - - 1aae04680c4b - - 44018dd6b447 - 3e1f6f6d557e + - 44018dd6b447 - cd2480f35935 - - f29602ae449e - a79ee60b6926 + - 4f2967b27e67 + - f29602ae449e + - 1aae04680c4b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,26 +62,26 @@ tools: - name: augustus_training owner: bgruening revisions: - - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 + - 6519ebe25019 - f1e653756174 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - bd0e53f3a891 - - ca6d970d931c + - 09855551d713 - 28433faa6e42 + - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - da5f1924bb2e - d77802fe76f7 + - da5f1924bb2e - 728dacaf08a9 - 92eee5f31117 tool_panel_section_label: Annotation @@ -89,9 +89,9 @@ tools: - name: barrnap owner: iuc revisions: - - 8fd427007e93 - 7355bbf5e05f - fe48aa4ccd5e + - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -103,8 +103,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -116,9 +116,9 @@ tools: - name: cpat owner: bgruening revisions: + - 8e9e228c54c4 - 7ccc6234b54e - 1ac12c0cc7a0 - - 8e9e228c54c4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper @@ -156,60 +156,60 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 3bbe70fef6df - - 582fd74dc2a1 - - 9f2455341fac - - 9c15ca7e764e - - b6b5cd37f2a2 - 14f588312c56 - 756376aeb1ae + - b6b5cd37f2a2 + - 9f2455341fac + - 9c15ca7e764e + - 3bbe70fef6df + - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 30fb23d4c31c - a230ea445788 + - 0ffe5be70caf + - 1691af4a0d17 - 73428a792541 - - 8e1ace8f77c6 - 989f7c061f35 - - 1691af4a0d17 - - 0ffe5be70caf + - 8e1ace8f77c6 + - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 563a19373357 - - 494f0bb4a993 - - 5a5ae61da69c - 0418d28136de + - 5a5ae61da69c + - 30f08d74024f + - 494f0bb4a993 + - 563a19373357 - e94187d661df - 57c6718cbfcc - - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 1bc5a03faf2e - - f77d7b685bb3 - d6c7106b7b2e - - 4b96ced19f75 + - f77d7b685bb3 + - f31125bb85ea - 2bba2ff070d9 + - 4b96ced19f75 + - 1bc5a03faf2e - 7abc5f6dd595 - - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 54961e026fe4 - fed64e676186 + - d77fdcca400e + - 54961e026fe4 - b3cf4684e9c7 - - 52af33194019 - d3af38b9c7e1 - - d77fdcca400e + - 52af33194019 - 520e30695ec3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -222,9 +222,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 07d7991bf205 - - 79261884facd - 2aea122fbd25 + - 79261884facd + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -236,10 +236,10 @@ tools: - name: goseq owner: iuc revisions: - - ef2ad746b589 - - 8b3e3657034e - - 43798b4caee0 - 602de62d995b + - 43798b4caee0 + - 8b3e3657034e + - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -263,16 +263,16 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: + - 74810db257cc - c55643c3d813 - 98cafcbd2578 - - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -297,19 +297,19 @@ tools: - name: maker owner: iuc revisions: - - d46d803ca6cc - 370c210d9541 + - d46d803ca6cc - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - c8ac28e8ac44 - - 624606f7c996 - 033755194fe9 - b815ec682418 + - c8ac28e8ac44 - e95d52d295d7 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -351,11 +351,11 @@ tools: - name: prokka owner: crs4 revisions: - - a17498c603ec - 8a22554cdde2 - eaee459f3d69 - - d643e3b03500 - bf68eb663bc3 + - a17498c603ec + - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -374,8 +374,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -399,22 +399,23 @@ tools: - name: snpeff owner: iuc revisions: - - 5c7b70713fb5 + - 8f92c2b26e6d + - ca2b512e8d7c + - c7275bd8b4d6 - 268d162b9c49 + - 68693743661e - cfcf33df7fc0 - 6322be79bd8e - - 8f92c2b26e6d - - 68693743661e - - ca2b512e8d7c - 5a29ab10dba6 - 5b80f544c67f + - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - 2b3e65a4252f + - 5fab4f81391d - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -427,8 +428,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -440,15 +441,16 @@ tools: - name: tbprofiler owner: iuc revisions: - - 45083d070fb8 - 51dd22484644 + - 45083d070fb8 - 37213cf56392 - - 037a11682176 + - ac8250086ac3 + - e1a9d6fd258d - d03af1c7002c + - 8cb134b8c1a5 + - 037a11682176 - 809dfc93d593 - - e1a9d6fd258d - 200c378d85f3 - - ac8250086ac3 - 4839e590cb26 - ba6f87115e13 tool_panel_section_label: Annotation @@ -456,8 +458,8 @@ tools: - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index e4609446e..14bc5c417 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,27 +2,27 @@ tools: - name: abyss owner: iuc revisions: - - a929ce596a34 - - 7547fcab5d19 + - 0124fce4654a - 890b794c997d + - fa5259cc561b + - 7547fcab5d19 - 8f1b150a2487 + - d6d5ccc2c581 - 841084c5fc46 - - fa5259cc561b - - 0124fce4654a - 553bfe8bd0b5 - - d6d5ccc2c581 + - a929ce596a34 - 0e93176640ac tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - 94fe43e75ddc + - b2860df42e16 - 067592b6b312 - - ddddce450736 - 21e491ad532a + - ddddce450736 - b9e31c5c01c7 - - b2860df42e16 - - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -35,9 +35,9 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - 3371c5bdc17a - 5258e18bbe23 + - 22286dab5aa1 - a7f16f24e9a1 - faee8629b460 tool_panel_section_label: Assembly @@ -46,38 +46,39 @@ tools: owner: bgruening revisions: - 53dd00a4ab68 + - '392811378515' - 8c2167481e72 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 41030a6c03b7 + - 1e62c28ba91d + - 1440ae06552f - e824f5d958d0 - - e4bd1e99bacf - - 46ae58b1d792 - - 4048d82f0c88 - - 5ecdeca79a0d - - 2dd755c1c6ff - ea8146ee148f - - bb935709506a - - cf13a1e03e5b - e5c372c91e46 - - 2babe6d5c561 - - 94170eee0ad8 + - bb935709506a + - 41030a6c03b7 + - 46ae58b1d792 + - 0d243f458b53 + - 2dd755c1c6ff - 602fb8e63aa7 + - 5ecdeca79a0d + - 94170eee0ad8 + - 2babe6d5c561 - f18f0b887c31 - - 1e62c28ba91d - - 1440ae06552f - - 0d243f458b53 + - cf13a1e03e5b + - e4bd1e99bacf + - 4048d82f0c88 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 5732f959936a - c5b7390290b1 - 86f150c8019d - - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -89,44 +90,44 @@ tools: - name: flye owner: bgruening revisions: - - e27815e82dd4 - - 3ee0ef312022 - 8d4f03b5fe9d + - 3e4f8642c77e + - 1ce9b1d72ec3 - 276f5d8712d5 + - e27815e82dd4 + - 3ee0ef312022 - 291923e6f276 - - cb8dfd28c16f - - 3e4f8642c77e - 1f0769f0b56b - - 1ce9b1d72ec3 + - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 01210c4e9144 - - 460fad600dce - 3169a38c2656 + - 01210c4e9144 - b2f674562a18 + - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 7348b69e5109 - 8b330a577046 - - ba88bc5a6446 + - 7348b69e5109 - 06bcf65179fb + - ba88bc5a6446 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 690c2caa367e - - 6ec1b853c8fd - 5127a713de83 + - 690c2caa367e - 3ef480892a9f - - 3fba9c77550a - f4a3eff8ab85 + - 3fba9c77550a + - 6ec1b853c8fd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -138,24 +139,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - 045c7c3d8e59 + - 366a11d316a7 + - da9d8bf98802 - 6505bd37670d - - 0ee0c3089254 - - 284a1cb82b61 - - 5161f204ba63 - 3f7be05a1597 - - df25d4fb79b7 - - ec9e21e9c71b + - 60024a528cbd + - 5bec28269d95 - 2061fb3b81b4 - 5f625c63b8bc - - 366a11d316a7 - 9ef6920c3089 - - 60024a528cbd - - da9d8bf98802 + - 284a1cb82b61 + - 41cea2aa2dce - f3c89da3af16 + - ec9e21e9c71b - 71740308d412 - - 5bec28269d95 - - 41cea2aa2dce + - 0ee0c3089254 + - 045c7c3d8e59 + - 5161f204ba63 + - df25d4fb79b7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -173,43 +174,43 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - de387b2b2803 - - 7518ee87b53d - a96f3ad4e0d8 + - 14ddfc8ffb93 + - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 9d79beb19ac3 - - d7edbc9c3a07 + - 09c589057ee8 - eb7b00ec347d - 39edec572bae - - 09c589057ee8 + - 9d79beb19ac3 - f8113c25bc6b + - d7edbc9c3a07 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - - eadfd71dde37 - 29dabd8db6f2 + - eadfd71dde37 + - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - f369ef5f210b + - fd128c111ab0 - 3ca2d2a9068c - f338e9942b27 - - eb7a370f6588 - - fd128c111ab0 - - e731ea24e48d - - 606b09cc9860 - 2ecf5a570907 - 99ecfdafc64f + - f369ef5f210b + - e731ea24e48d + - 606b09cc9860 + - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -221,11 +222,11 @@ tools: - name: miniasm owner: iuc revisions: - - 73a3846701e1 - b799a615995d - - a7b889b90140 - 8dee0218ac7d - 8b6d0d85252b + - 73a3846701e1 + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -243,8 +244,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - 64a1c751d99b + - 7c2f5268d01c - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -258,45 +259,46 @@ tools: owner: iuc revisions: - dfb8a4497339 - - bbe19ef04a74 + - c6cec5ab35c1 - 2b16ba799da9 - 8fef980d48b5 - 02831bf9e95f - - 79b48f02db49 - d256a51a656b + - 79b48f02db49 + - bbe19ef04a74 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - a315c25dc813 - - 76d4cbefff85 - e9bd16ba5ebd + - 76d4cbefff85 + - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 7594365c546b - - 342a1d1fed7b - - 72472698a2df - 875d0f36d66f - - 3061c8b029e5 - - ebb0dcdb621a - - 6fcbee531de6 + - 72472698a2df + - 342a1d1fed7b - 675488238c96 + - 6fcbee531de6 + - 3061c8b029e5 - 59db8ea8c845 + - 7594365c546b + - ebb0dcdb621a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 39bed8de8017 - cd06929b224b - aa39b19ca11e - - a199cd7ac344 + - 39bed8de8017 - 78c533842eeb - d865b62f501c + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -314,31 +316,31 @@ tools: - name: raven owner: iuc revisions: - - 2b2a352488fa - - f11b994b7eb2 - - 3edba9afc9bc - 5c55448d0f33 - 33b7d8481a76 - f8564b2d7f63 + - 3edba9afc9bc + - 2b2a352488fa + - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - 8e66f695d859 - f73ab5187eed + - 8e66f695d859 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - e122f9101584 + - 1d06c8b38e77 - 378e55aeeb25 - 53c2bc8c2ae3 + - e122f9101584 - ef69617ecb42 - 5fc94b3a4704 - 28189050e437 - - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -350,195 +352,195 @@ tools: - name: shovill owner: iuc revisions: + - ad80238462c1 + - d9f6a00b6db7 - ee17a294d3a3 - 83ead2be47b2 - - 196a599ec43d - - d9f6a00b6db7 - f698c7604b3b + - 196a599ec43d - 865119fcb694 - - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 015283de3004 - - 5e0825476fb7 - 24e471d13fe9 + - 5e0825476fb7 + - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 7490b213baa9 + - 1fc82fe7ebef + - 904bf932cf78 - 1bb12736175c - - 604782a8a53a - 051fd2db8a27 - c33a476f4001 - - 1fc82fe7ebef - - 904bf932cf78 + - 604782a8a53a + - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 9678993ca5bd - - 34305b013402 - - 655fa188c3cc - fee85957cebe + - 34305b013402 + - 9678993ca5bd + - d6e617c4e338 - 808b3a0a6716 - ad8b536d1caa - - d6e617c4e338 + - 655fa188c3cc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - e5a3b75a271f - - b8002c3f7141 + - 6b5a5842531e - 8d4b90bf9caf - 037f9927c4ff - 21da31ed41a1 - - 6b5a5842531e - 7e27faaad80e + - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - f1532cb33c75 - - 7922870efcca - - 328aa71f0f3c - - 86f66ab58e14 - 9de69775f512 - 2a10645aeadd + - f1532cb33c75 - 5b26685e5d3b + - 86f66ab58e14 + - 7922870efcca + - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 8cc856b935ee - - 85fb02c43042 + - e41dcb0e913b - 340bc17f49cf - - 1708851f8804 + - 85fb02c43042 + - 8cc856b935ee - 6aad515a5270 - - e41dcb0e913b + - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - de1260f8a300 - d5fb354f745d + - b3490b036c5a + - b65a43f70b99 - d159735a6a9f - 6357b127161e - - b65a43f70b99 - - b3490b036c5a - - de1260f8a300 - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - dd7ad84f3943 - - b7829778729f - - a90db5dbaaf3 - d5887ace0dd4 - d2d1df21dfb9 + - b7829778729f - 7897763d14ec + - dd7ad84f3943 - 33368fec3b70 - 9006e5836729 + - a90db5dbaaf3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ed2425b9fd27 - - 8f631679571f - - 189e837009c9 - - 505a9833ab5d - - 0368ac680e70 - ced385aa976d + - 505a9833ab5d + - 189e837009c9 - 6f4c8ad6ea01 + - ed2425b9fd27 + - 0368ac680e70 + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - - 19bdfd1e6fe3 - - f31d376ce725 + - 356afed970b4 - 9ded6109434a + - d40ed4eb0c0e - a7ed21de23fe + - f31d376ce725 - e59bee4565b3 - - 356afed970b4 + - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 4688ae3b49b5 - 80a17897564d + - 7673a6c920b2 - 6dd935e4984b - ebd801e712bc - b23249f81bc4 - - 7673a6c920b2 - - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - ed312479d9eb - cb1e3db43020 + - bb11fefb23a3 - b64696992ee9 - - 59bd28f6265d - - ed312479d9eb - 937ea677d437 - b5e35a2ca4f3 - - bb11fefb23a3 + - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 05bd7504fdb2 + - b9b0246a2be3 + - 2628f6790eda - 6015aa0303f2 - cb4768eeca3b - 6bfab4a4a988 - - 2628f6790eda - - b9b0246a2be3 - 383bb5ad32e2 + - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - 9e3e80cc4ad4 - 8f9f06995f98 - - e92675014ac9 - - 6e26c9afd301 + - e022dff952df - 3e44ef016b45 + - e92675014ac9 - 0a3a602cd1e3 - - 9e3e80cc4ad4 - - e022dff952df + - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 920677cd220f - 5da9a0e2fb2d - 08256557922f - 8d09f8be269e + - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: + - 0e2b4e3f9ca1 - 4a53b89fa703 + - 82398ba86ba7 - 37d88f41c810 - d81360ea69d8 - - 0e2b4e3f9ca1 - - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index c644ae5cb..7303e3df5 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: - - bfd290fe1588 - - 392f100eebcd - 1ae00120dd24 + - 392f100eebcd - 4768f7f8e93f + - bfd290fe1588 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - - ded48b36f3b7 - - 1f5641a52664 - 31812e7a1315 + - 1f5641a52664 + - ded48b36f3b7 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - 24a7a95867b0 - 17fcac7ddf54 + - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 66c3bf9c9..b2eeb315e 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -3,23 +3,26 @@ tools: owner: iuc revisions: - 159b04e36791 - - 1c427e24fb79 - - 7beb76ffbc0f + - a9c9d768b751 - 204a131e47db + - 1c427e24fb79 - 0840ba83860c - - a9c9d768b751 + - 7beb76ffbc0f - d1f62024a08b + - d58c27d2c5a7 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge owner: iuc revisions: - cab19c0452c4 + - 1bb2b5b52030 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_tadpole owner: iuc revisions: - 0ddf147d1897 + - ce13b4678f18 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index efe967f63..3aa4c16c2 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - dde39ba9c031 - 589e7e57fd6d - - e19bebe96cd2 - - a68aa6c1204a + - dde39ba9c031 - 87ee588b3d45 - - ce3c7f062223 - - a8eabd2838f6 - - b28e0cfa7ba1 - 64e2edfe7a2c - 0a5c785ac6db - a1a923cd89e8 + - a68aa6c1204a + - e19bebe96cd2 + - a8eabd2838f6 + - b28e0cfa7ba1 - 07e8b80f278c + - ce3c7f062223 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index 0f87b4301..c5e1c8c39 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,9 +8,9 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 - f921014aba5a - 54f751e413f4 + - e8ac2b53f262 - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 6f386c5dc4fb - - 2889433c7ae1 - - 5edc472ec434 - - 0e3cf9594bb7 - a52d2d93e595 + - d999e774072a - acf4e47b734c - - e25d3acf6e68 + - 0e3cf9594bb7 + - 2889433c7ae1 - cbf3f518b668 - - d999e774072a + - e25d3acf6e68 + - 5edc472ec434 + - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 2bd143e42..bb52084eb 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - c8cdde00b105 - - f4230f116196 - - 710301bc46fa - - 6ca543ec1bf8 + - 095ad4d096d1 - 27ee142314a9 + - 6ca543ec1bf8 + - 710301bc46fa - da6bd1975a71 - - 095ad4d096d1 + - f4230f116196 + - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -130,73 +130,73 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - bfb65cb551d8 - - 0fac8e2afc13 - 3b8a9d5ced85 - 88076940fa94 + - bfb65cb551d8 + - 0fac8e2afc13 - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - eb6564a60136 - 55918daa5651 - - b46d4b4d995c + - f5d979cb4b54 - d532b7e5f64b + - b46d4b4d995c - 715cd0e87781 - - f5d979cb4b54 + - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - f26afd1b7104 - - 97872d87ba80 - 5579659312e6 - - d2f955aea23a - fdf2cc80adb5 + - 97872d87ba80 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: + - d1d0efda35c0 - bc31d02be922 - 319a28774da9 - - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 4da9ee404eab + - 070e3ecc3fda + - cac1886249a2 - ed736e6eee39 + - 4da9ee404eab - 2c349b027a01 - - cac1886249a2 - - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - 73008ef1f487 + - c0c9a5024177 + - d1f803b5943c + - da8753545526 - 807aa4c9293d + - f197e34c33a9 - 525ca7c8065f - 2e219a2d9327 - - da8753545526 - - d1f803b5943c - - 73008ef1f487 - - f197e34c33a9 - - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 7568ae18908a - 61094e01eff9 - 1809414a9454 - - 27ea4e1a3f95 + - 7568ae18908a - c4fbab8e03c5 + - 27ea4e1a3f95 - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: + - 730ef07b90ae - 79e8ab8f1e81 - d7ec25187599 - - 730ef07b90ae - - ccfbd956a2d3 - ba83f0923369 + - ccfbd956a2d3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -283,15 +283,15 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 7672039a0bb0 - 75ee9c410951 + - 7672039a0bb0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres owner: recetox revisions: - - 53dce0e49af7 - 89b026d67e9f + - 53dce0e49af7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_neutral_run @@ -304,8 +304,8 @@ tools: - name: qcxms_production_run owner: recetox revisions: - - 356f7916ac07 - e97bfe7ac906 + - 356f7916ac07 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: rem_complex @@ -341,10 +341,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 9b48456a96fe - d4c67ced6abc - 85fad59f8168 - bf99565cec1f - - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 569b99d6e..af06e8f9c 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: + - fa56d93f7980 + - c97a786e8fb5 - 163688bb8f73 - f907216064f6 - - c97a786e8fb5 - - fa56d93f7980 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -30,11 +30,11 @@ tools: - name: macs2 owner: iuc revisions: + - f5d67c722d67 + - 424aefbd7777 - 640d3af5d833 - 495a4173006f - 86e2413cf3f8 - - f5d67c722d67 - - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -53,9 +53,9 @@ tools: - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - - 4a14714649b4 - 74c9214cc8e6 + - 4a14714649b4 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index 9354088e2..42d913203 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: + - 33151a38533a - 830961c48e42 - - 25136a2b0cfe - 90981f86000f - - 33151a38533a + - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: + - 0046692724f9 + - baabc30154cd - 2dae863c8f42 - 6cbe2f30c2d7 - - baabc30154cd - - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 81744e5d7..8fa70754e 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - ab9350a8ab4d + - 6ef0b5664c69 + - 367b1ed91207 - 3b6f97e7094c - 5e1240a87bcb - - 367b1ed91207 - - 0b3c3ad92827 - - 6ef0b5664c69 + - a3b86937ead6 - e3cbd2287f63 - - 4a6ee918c13a + - ab9350a8ab4d + - 0b3c3ad92827 - f3a19509108a - - a3b86937ead6 + - 4a6ee918c13a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 33c99804a32f - 501c21cce614 - - 091bb5922a82 - - d4d4e9febf5c + - 584008e574b2 + - bd46669113b9 + - 1b5fc03380d4 - 72ed72122deb - - e177a8ea0bf1 - e525f9ffb9ac - - 1b5fc03380d4 - - bd46669113b9 - - 584008e574b2 - 54ccb7e1f49a + - 33c99804a32f + - e177a8ea0bf1 + - d4d4e9febf5c + - 091bb5922a82 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -68,8 +68,8 @@ tools: owner: devteam revisions: - 8979c288aefb - - 186b8d913e6c - 77b41c89d856 + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -102,9 +102,9 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - - 3e436657dcd0 - 154d00cbbf2d + - 3e436657dcd0 + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -144,19 +144,19 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - 78fb18899c99 + - 68f57cc8fad0 - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 19e45916daf9 - 63769c4217a7 - - 92ac8e086317 - 26c6706bfb07 + - 92ac8e086317 - b9b385097f13 + - 19e45916daf9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -168,17 +168,17 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - 8067dfa00ed2 - e9bbe2f71784 - 3c6f9e8a4c17 + - 8067dfa00ed2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - fa49730d1d4b - 98704d357ede - a2f83a375bf2 + - fa49730d1d4b tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 59d8dfb9a..e431f54a2 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,71 +2,71 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - e821645ef8fc - - de72ba3ed6f2 + - 5f6d123679f4 - a1ca9bccc7f2 + - e821645ef8fc + - 268e91e540ee - 29451af70c52 + - de72ba3ed6f2 - c929a006727f - - 268e91e540ee - - 5f6d123679f4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 12af64f93288 + - 0e49b109abc2 + - bb1e4f63e0e6 + - 0e143b4c3987 - 2d2cf5c1ea8a - 5d11599b8a7d + - 12af64f93288 - 7a7fd0f5f15d - - bb1e4f63e0e6 - - 0e143b4c3987 - - 0e49b109abc2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 195e98217334 - - 81b1e3e1fc6c - - c06951d10364 - dc059492a995 - 7c1beb6d6eca + - 195e98217334 + - c06951d10364 + - 81b1e3e1fc6c - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 93eb012d9eed + - 07418a30ed01 + - a67ac707496a + - bfff7454b59a - 3d211717a775 - 26e7304d6737 - - 07418a30ed01 - 71aa86af6762 - - bfff7454b59a - - a67ac707496a + - 93eb012d9eed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 2bc10a9ca58b - dd0b7398bb96 + - b8858746dc1f - 29fcfd36e90a - 26983857c91a - 56d5b797ce84 - - b8858746dc1f - 5be24eba848d + - 2bc10a9ca58b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - e6d0bff01239 - 7e6bcd2e5128 - - 7ef978dc1b8a + - e6d0bff01239 - 9384cd033f30 - - ee3a1b0f45f1 - c3e012dfe21f + - 7ef978dc1b8a + - ee3a1b0f45f1 - 72bfafe3330b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -74,98 +74,98 @@ tools: owner: bgruening revisions: - b73e213add0c - - fd1275e01605 - - 514fa53b5efb - 9470f29702f8 + - d9a637e83828 - a60c359ec43c + - 514fa53b5efb - 167788df3b46 - fb9cf9c97ec4 - - d9a637e83828 + - fd1275e01605 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: + - 5bffaa8354a1 - e479c7ca5570 - 2c37ce318bc3 - - c34d11ea4ba6 - 86febdcc4283 - ca0616bb2cdf + - c34d11ea4ba6 - a02cfa31e9cb - - 5bffaa8354a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - 192ef85c0b0b - - 69a8621ca2f0 - 2d466b530754 - 78f405266706 - 004aea905d4d - - 01fb6a7654e6 - 1fcb7adc39b8 + - 69a8621ca2f0 + - 01fb6a7654e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 3c9f0c486cca - - db940c262830 - d9ce4897dbb2 - - d580d6acd1df - - 2f9e4843f480 - - 459cfa861f0b - 9ecba5e225a6 - 137c4beed34b + - db940c262830 + - 459cfa861f0b + - 3c9f0c486cca + - 2f9e4843f480 + - d580d6acd1df tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 2c66e43f1c86 - - fbe773640707 - - bd7db9e2f2cb - - fd408d755394 - 32e451def88c + - 2c66e43f1c86 - f264afa9fa6f + - fd408d755394 + - fbe773640707 - bad3ca889618 + - bd7db9e2f2cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 4e12ea27f788 + - 9368fbc49c8b + - 3b9d990a0a0e + - 7fda5607e777 + - 7e361d147872 - 56bce3c82278 + - 4e12ea27f788 - 231994413f89 - - 7e361d147872 - - 7fda5607e777 - - 3b9d990a0a0e - - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - d9114ef1c8a5 + - ce4ce3316f74 + - b1779366c8e9 + - 4431f39ede55 - c03c3384cd81 - 94ca68515826 - - b1779366c8e9 + - d9114ef1c8a5 - e65d16fb2724 - - ce4ce3316f74 - - 4431f39ede55 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - b88ebb3672a1 - - 23f7c5f1fdaf - 4ed32329e0ed + - 23f7c5f1fdaf + - b88ebb3672a1 + - f8fc4e5aff9d - 793665fff0f8 - - 2da482e408b8 - d57251071381 - - f8fc4e5aff9d + - 2da482e408b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap @@ -173,34 +173,34 @@ tools: revisions: - 010e58e9d822 - 512155688d98 - - c60570fa602f - - a7849312d328 - ba6efa77fb79 - e4c7985d4585 - - a4dfb122e52b + - c60570fa602f + - a7849312d328 - 25d830337d31 + - a4dfb122e52b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 443d9a9d6d11 - - c899e0ccff8c - - 69264da0ce77 - 4d678170d29b - - 00d869ea03a1 + - 443d9a9d6d11 - 38e3f226248b + - 00d869ea03a1 - aa200e4f3939 + - c899e0ccff8c + - 69264da0ce77 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a + - aac8444d6681 - d806504e96d9 + - a2d70c4fd406 - 6662b1a8d326 - - aac8444d6681 - 10301d137111 - - a2d70c4fd406 + - c361b12d207a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index bb804bbc9..79884cada 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -2,29 +2,29 @@ tools: - name: obi_annotate owner: iuc revisions: - - 3021b9f5809f - d50dc96e3ce9 + - 3021b9f5809f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean owner: iuc revisions: - - 08d873cdd5f6 - 7d16de45c021 + - 08d873cdd5f6 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert owner: iuc revisions: - - e328ced6cf0a - 4d705e3443a7 + - e328ced6cf0a tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - 02bab5ff7c37 + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 91a1ed0b486f + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index 9e65a9209..08bf8c016 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - ce385837c160 - - 832c20329690 - dba489bfcd62 - 63dd26468588 + - 832c20329690 + - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index e0c2bf6de..b7e7acbb2 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 6da3972210ee - cf1322aeb137 - - 29bdbc353f20 - - d82648ad25a3 - 62f5fab76dfb + - d82648ad25a3 + - 6da3972210ee + - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index f3b47e659..ad180d118 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 660cffd8d92a - - 49370cb85f0f - - 135b80fb1ac2 - - 48f587c13075 + - c053d4cad713 + - de6cebe3c043 - 288f97432497 + - 660cffd8d92a + - c4b82dce8335 - c5e2e5902201 - - de6cebe3c043 - - c053d4cad713 - - 8c0175e03cee + - b1c926deaa2d + - 5915ea1ec9b1 - 093678460093 - - 64172f1c1202 + - 8665bcc8b847 + - 135b80fb1ac2 + - 48f587c13075 + - 49370cb85f0f - 5eb7e84243f2 - - b1c926deaa2d - - 44e2cc14f75b - - fe74900d6dc7 + - 64172f1c1202 - 4e5056fefd88 - - 8665bcc8b847 - - 5915ea1ec9b1 - - c4b82dce8335 - e4691e1589d3 + - 8c0175e03cee + - fe74900d6dc7 + - 44e2cc14f75b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -39,8 +39,8 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: - - 9db07fd39f85 - f666895cbebd + - 9db07fd39f85 - 8889eb864cef tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -54,8 +54,8 @@ tools: owner: devteam revisions: - de2db1bdfbf8 - - 5cbde03c1103 - 7d37cfda8e00 + - 5cbde03c1103 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -67,8 +67,8 @@ tools: - name: fasta_concatenate_by_species owner: devteam revisions: - - 717aee069681 - 25b8736c627a + - 717aee069681 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -87,9 +87,9 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 9457a20156db - - 859422bcb689 - 516b97a23d7e + - 859422bcb689 + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -108,9 +108,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a - f81d4362b6c1 - f773e98b26cf + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -124,8 +124,8 @@ tools: revisions: - 0dbb995c7d35 - 56022eb50bbd - - cd0874854f51 - 9c620a950d3a + - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -137,27 +137,28 @@ tools: - name: fastp owner: iuc revisions: - - dbfc505896e9 - - c59d48774d03 - - ecb9f4854617 - - dbf9c561ef29 - - 65b93b623c77 - 1d8fe9bc4cb0 + - 65b93b623c77 + - dbf9c561ef29 + - a626e8c0e1ba + - ecb9f4854617 + - dbfc505896e9 - d60c3f704da0 + - c59d48774d03 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - ecb9f4854617 + - a626e8c0e1ba tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - 9115b978ce10 - - f1dc2a761c30 - b05e39b9c170 + - f1dc2a761c30 + - 9115b978ce10 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -169,9 +170,9 @@ tools: - name: fastq_filter owner: devteam revisions: + - 81a9090d6df3 - 10b75444feae - '144275714590' - - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -184,8 +185,8 @@ tools: owner: devteam revisions: - e9f8633db0a2 - - 8611b80a14d6 - 47e5dbc3e790 + - 8611b80a14d6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -197,9 +198,9 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - e30352e889fe - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 + - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -212,8 +213,8 @@ tools: owner: devteam revisions: - 4e1d64e6385f - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -225,9 +226,9 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 03d57fea6482 - - f3936d0632cb - 523c2aff0376 + - f3936d0632cb + - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -239,9 +240,9 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: + - b41c2c1bcfbf - 2ccb8dcabddc - 3e396e702cea - - b41c2c1bcfbf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -253,8 +254,8 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - 8d958759cf2a - c885369b207b + - 8d958759cf2a - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,10 +268,10 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 249c8393f2d4 - - 397dc333436b - e39cc71d3ed6 + - 249c8393f2d4 - 35e38452bb3f + - 397dc333436b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -282,9 +283,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 045f0e1043f7 - - 54053ea6c77e - 74db4cffab1f + - 54053ea6c77e + - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -296,9 +297,9 @@ tools: - name: fastq_stats owner: devteam revisions: + - b1cea1b2fcd0 - f86c27295151 - f0e7deab6518 - - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -310,9 +311,9 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - - f0b18efb97f1 - 33794bdb7fe0 + - f0b18efb97f1 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -331,10 +332,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: + - d5e9e83cd3d8 + - 567d5b3c52b1 - 09070cacefd8 - 529bccd5e4a1 - - 567d5b3c52b1 - - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -346,9 +347,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - - 0b7ec11b3c7c - 8abdedf55101 + - 0b7ec11b3c7c + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -360,10 +361,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - 90858c306551 + - 736b8f6ee456 - bdf1ce174e39 - cb1e251cac37 - - 736b8f6ee456 + - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -389,8 +390,8 @@ tools: - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 - 3599f5451ee2 + - b29d37ca9e41 - f984bb114520 - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ @@ -404,10 +405,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: + - e246088b6e34 + - 6027ef51ef91 - 0c2907307ba4 - 177f0621c266 - - 6027ef51ef91 - - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -420,9 +421,9 @@ tools: owner: devteam revisions: - 377ac2829eac - - 547e8d00f11c - - 73194cdd4f57 - 61b4cedc8934 + - 73194cdd4f57 + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -446,10 +447,10 @@ tools: - name: pear owner: iuc revisions: - - f69501361cec - 037f0acc7830 - - 2f804526f5fd - b4c6f054210a + - 2f804526f5fd + - f69501361cec tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -468,32 +469,32 @@ tools: - name: seqkit_sort owner: iuc revisions: + - fdc21382376d - 61eb4cfc7313 - 29ef2c5ec205 - - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: + - 795cd16de38f - 812705bcf39c - fe1ae2ebf63d - - 795cd16de38f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - a019807f4e67 - 4b494533146a - 3da72230c066 + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - a019807f4e67 - 4b494533146a + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: split_paired_reads @@ -505,16 +506,16 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - bf04bd405d5b - - 71f649c23021 - d3f58a0dc09d + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -526,12 +527,12 @@ tools: - name: umi_tools_count owner: iuc revisions: - - b557acca0b56 - e654095ab143 - - a535cf1e5da4 - - 8250ea3a1501 - 71ad4a56c40c + - b557acca0b56 - 24013bf85a6f + - a535cf1e5da4 + - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -543,21 +544,21 @@ tools: - name: umi_tools_dedup owner: iuc revisions: - - f1d33e4c7bd8 - c5a2ee07c4e1 + - f1d33e4c7bd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: - - f3759eec3018 + - 6a675c3aa610 + - 015cf18f4a15 - 7a7e33d28f62 - 7accf7407811 - - 015cf18f4a15 - 27ac32a22ad2 - 9fa7803d1c51 - 828dba98cdb4 - - 6a675c3aa610 + - f3759eec3018 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -569,15 +570,15 @@ tools: - name: umi_tools_group owner: iuc revisions: - - d6255614afd7 - 428735be9764 + - d6255614afd7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist owner: iuc revisions: - e4e12f0b3af1 - - 953b4821b183 - 4c8a1c7d3608 + - 953b4821b183 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 646af7856..cab5d247d 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - ce9cd02d5b88 - - 64e9a6afdd0c - 7b4468117008 + - 64e9a6afdd0c - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,14 +18,14 @@ tools: - name: fastqc owner: devteam revisions: + - 2b0c9d9fc6ca + - f2e8552cf1d0 + - ff9530579d1f + - 2c64fded1286 - e7b2202befea - 3d0c7bdf12f5 - - 9da02be9c6cc - - 2c64fded1286 - - ff9530579d1f - - f2e8552cf1d0 - - 2b0c9d9fc6ca - 5ec9f6bceaee + - 9da02be9c6cc tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -38,47 +38,47 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - - ad116ae3f4d9 - b6b54ba71bd8 + - ad116ae3f4d9 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - 59003d0543cd - - cc0fd298cc17 - 7306ec78632a + - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - 1f296803dfa3 - - 8880fb74ef56 - a72af9de6bf5 + - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: + - 75c93c70d094 + - f7e2f1eb3a16 - abfd8a6544d7 + - bf675f34b056 - 3d93dd18d9f8 - - 1c2db0054039 - 9a913cdee30e - - f7e2f1eb3a16 - - f7985e0479b9 - 5e33b465d8d5 - - bf675f34b056 - - 75c93c70d094 + - 1c2db0054039 - b2f1f75d49c4 + - f7985e0479b9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - 084bbd8ba7b8 - 949f01671246 + - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fetch_alignmentssequences.yml b/staging.gvl.org.au/fetch_alignmentssequences.yml index c01999d90..0dfc5355c 100644 --- a/staging.gvl.org.au/fetch_alignmentssequences.yml +++ b/staging.gvl.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index ab23c208f..b248d7a64 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -16,7 +16,7 @@ tools: owner: peterjc revisions: - 83a19df00eab - - 85ef5f5a0562 - 141612f8c3e3 + - 85ef5f5a0562 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 4452ea21e..a96c17603 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -9,16 +9,16 @@ tools: - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - 8f53b238a360 - 0c8f7322f8fc + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -31,8 +31,8 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -52,8 +52,8 @@ tools: - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: - - cf61daf064fe - 45296e47d565 - b2c25142267e + - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,8 +108,8 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,8 +122,8 @@ tools: - name: gemini_query owner: iuc revisions: - - 840fb4850be3 - da74170c55c7 + - 840fb4850be3 - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,8 +137,8 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -158,8 +158,8 @@ tools: - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index c5b84e945..aade5505c 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index bfe80056b..690f919dc 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -18,52 +18,52 @@ tools: owner: iuc revisions: - e063168e0a81 - - 1c58de56d587 - 28587613264f + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 653e89d73fc4 - - f8054ea1c365 - - 9a776b080193 + - 516a54ddf218 + - f5ea3ce9b9b0 - aad3885b3216 + - 734abc7ac21d + - 5e6237d58b0c + - 8848455c0270 + - 6591f049cf7e + - 9a776b080193 + - 7068f48d0ef9 - 1ec814014652 + - ba931a59dd59 + - 4317d3cb6cba + - 653e89d73fc4 + - 4df8de2d0e48 - c441583adae5 - - 6591f049cf7e - - 5e6237d58b0c - - 516a54ddf218 - - 734abc7ac21d - 1790dcf3c32d + - f8054ea1c365 + - 6ea73833cf67 + - e08a7ad4378b - 83c7d564b128 - - 7068f48d0ef9 - - 4317d3cb6cba - 69ebb7f46e45 - - f5ea3ce9b9b0 - - 6ea73833cf67 - - 4df8de2d0e48 - e407b9da183a - - e08a7ad4378b - - 8848455c0270 - - ba931a59dd59 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - - 34758ab8aaa4 - 9aaa46d45472 + - 75b3b3d0adbf - 21a560af5913 + - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 054483e27a35 - 468c71dac78a - - af5eccf83605 - bfdc6a7ffd3a + - 054483e27a35 + - af5eccf83605 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 61679356c..1a70aaa82 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 740057a5126d - - a64dc31ab7f2 - - fd59d783248a - - df7356989ac1 - - 290a11559985 - - ae9994cf526f - 4b519282a05b - 7f13dc906cb9 - c4bde687c846 + - df7356989ac1 + - fd59d783248a + - 740057a5126d + - 290a11559985 + - a64dc31ab7f2 + - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,8 +34,8 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 867ab348287d - f95284aa2946 + - 867ab348287d - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,24 +48,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - '566197475670' + - 53460afd5115 - 374e9062d874 + - '566197475670' - ca7cb0eaad62 + - 51c6ccaace7e - 3b37b1b1c3a7 - - 53460afd5115 - 48b42ee61bc5 - - 51c6ccaace7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 10515715c940 + - 3d059e9c2fba - d3a9e32672ec - da4c086cff5b - 391a4cc45fea - - 10515715c940 - 1a72f938213e - - 3d059e9c2fba tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -78,26 +78,26 @@ tools: - name: ggplot2_pca owner: iuc revisions: - - b1268b7544d3 - ae344ccf9d62 + - b1268b7544d3 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - d0fc8b746d57 - - 5298e06f14f9 - - 5fe1dc76176e - 1acf88921176 - 299307abd804 + - 5298e06f14f9 - e3a675da7fd0 + - 5fe1dc76176e + - d0fc8b746d57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 0e7290688b50 - 17b666467c32 + - 0e7290688b50 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -109,8 +109,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -123,8 +123,8 @@ tools: - name: histogram owner: devteam revisions: - - 6f134426c2b0 - cdb9e89e2970 + - 6f134426c2b0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse2 @@ -136,17 +136,17 @@ tools: - name: jbrowse owner: iuc revisions: + - 1cfc579079a6 + - 2bb2e07a7a21 - 6cd09d7b5f37 - 4542035c1075 - - 112eb40ba6cf - - a6e57ff585c0 + - 17359b808b01 - 667e17248bfe - - ca2def38369c - 836d1aa3e89a - - 1cfc579079a6 - - 17359b808b01 + - a6e57ff585c0 + - ca2def38369c + - 112eb40ba6cf - fd5dbf0f732e - - 2bb2e07a7a21 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -164,33 +164,33 @@ tools: - name: pathview owner: iuc revisions: + - 03c13085aecc - f1691de443a7 - fe154a7af404 - - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - 594b85e4237a - bd1416eea1f0 + - 594b85e4237a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plot_ragtag_paf owner: galaxy-australia revisions: - - 94e0834ae4ed - - 501dcf66c0ce - c1bed78b9ed5 + - 501dcf66c0ce + - 94e0834ae4ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 1c5dcef5ce0f - - 62e3a4e8c54c - 85da91bbdbfb - f234e2e59d76 + - 1c5dcef5ce0f + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -209,10 +209,11 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 + - 26f2fe7e53a1 - 6c571966cfb9 - - 44c66e8d21e6 + - 7c9417381ad5 - 326098bc19cc + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -224,23 +225,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 - - a1abfa420d9d - - 36b848d5f3ec - 4ac4e7083b7e - 326a3db8d9d1 + - 7dd841a32245 - 14e7c35f3d00 - - 2824d77cd8f8 + - 36b848d5f3ec + - a1abfa420d9d - 360df4999907 + - 2824d77cd8f8 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - - 73b8cb5bddcd - 2f557f6abbfb + - 44608d0193ed - 83c573f2e73c + - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 @@ -252,7 +253,7 @@ tools: - name: xy_plot owner: devteam revisions: - - 319fa5a9fc1b - ecb437f1d298 + - 319fa5a9fc1b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index aae3d618a..9274cfe21 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -21,15 +21,15 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells @@ -77,8 +77,8 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony @@ -91,8 +91,8 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 9a2f72d7dbd2 - 94697510d55f + - 9a2f72d7dbd2 - ff6decc0f432 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -106,29 +106,29 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 3027cb62adbd - 28b1546857b0 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 73d43034c860 - d4c9061c8fef + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 1be0fc4d8654 - 7d5c97823f8b + - 1be0fc4d8654 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 4a74b45c1ce4 - 6f5509cf3176 + - 4a74b45c1ce4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory @@ -141,22 +141,22 @@ tools: - name: scanpy_read_10x owner: ebi-gxa revisions: - - 078aa23c9374 - 287503c35cb4 + - 078aa23c9374 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable owner: ebi-gxa revisions: - - 0bab2ae44e7a - d18ed15697bb + - 0bab2ae44e7a tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 6a6364b488db - 79cc06a557b0 + - 6a6364b488db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -183,29 +183,29 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: - - 4428dba93375 - 0cf90e01d9f8 + - 4428dba93375 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - - 3fb53f5e46ea - abdb61e4afa3 + - 3fb53f5e46ea tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - ea91cfd0444e - 767a675b5254 - 0f98603d0116 + - ea91cfd0444e tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - 4cc9362782b4 - e2d0dc8a50ca + - 4cc9362782b4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 2c8fa949b..58b3331b4 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,56 +2,56 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - a4c13ddcc8ee - ed2cca6b5de4 - - 29f66c353bcb + - a4c13ddcc8ee - 921a2da49a0c - - 9edf8894a22d - 0f611e7d7858 + - 9edf8894a22d + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - 78fb5e286609 + - 755df866ad0c - 5746d61f0a91 - 11de0d28ab30 - ec4b948dc6f0 - d404277cc87a - - 78fb5e286609 - - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - f72063d9426b - - 4d511437b1e5 - 977dc15add20 + - 03dd3c16ae4e + - f72063d9426b - 9e357a8b2ec3 - 11fa44ee0603 - - 03dd3c16ae4e + - 4d511437b1e5 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 0ba4f56a3613 - - 3b5b54ed6392 - c3e5e2cf12b7 - - 1da5f169b491 - 77919cc3618e - 41dbf4d162a2 + - 3b5b54ed6392 + - 1da5f169b491 + - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 12d51d7be66f - - 7babd8a46fe0 - - 9939786dd9c9 - b63363075c2e + - 9939786dd9c9 - f741330d4a71 - 5308ca68ef3d + - 7babd8a46fe0 + - 12d51d7be66f tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index ac265fe1c..0ec67decb 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,100 +2,100 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 699a5e9146b3 - - 0c777d708acc - - 81f0cbca04a7 - 3df9f0a4bf34 - - 8bccb36e055a - 7db4fc31dbee + - 8bccb36e055a + - 81f0cbca04a7 + - 0c777d708acc + - 699a5e9146b3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 2436a8807ad1 - - 0a53256b48c6 - 5bc8cdc17fd0 + - 0a53256b48c6 - 5791a7f65275 + - 2436a8807ad1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - e576b73a2e2f - - 9d47aabda459 - 6ad1d3cfdea1 + - 9d47aabda459 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - 70316d792fc9 - 77f7159d775a + - 70316d792fc9 - b1c2c210813c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - dba87c4b32d3 - d51310ab328a + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 - - b07f4839ca77 - - 10eed33aa9b2 - 85edbb7a436b + - f3360fbeda64 - fcadded98e61 + - 10eed33aa9b2 + - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 984358e43242 - 6e65fd971e13 + - 984358e43242 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - 664232d2a3f7 - - b58447a2eed2 - 5bf8eb50b280 + - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - 0e4dccaafef5 - eb6c08714244 + - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - bad171ed1e96 - e8f822eeb9fd + - bad171ed1e96 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - e7273daa5ae2 - 6070780813d9 + - e7273daa5ae2 - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - cdf8e3c57dae + - df3ad3ba5c6f - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -110,32 +110,32 @@ tools: - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - 11f177b1a59e - f2ed92b011a9 + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: + - d0178bdcd00e - f24c370e5ea4 - f8fa0f6718a3 - - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - ad271f78a87a - 3245681b2f6d + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - 993faa34333b + - b6eec6087271 - 87d4d92d7487 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -151,8 +151,8 @@ tools: owner: bgruening revisions: - 667a513e67e4 - - 3a05117669cf - b178453ea8d1 + - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity @@ -166,49 +166,49 @@ tools: - name: cp_measure_image_area_occupied owner: bgruening revisions: + - 20dbb1f7ec7b - a32c3f810ade - 91e03287f285 - - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 5499dc6f8ac1 - 8536b1ae0254 + - 5499dc6f8ac1 - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - 6f4715b8540a - d3890df07463 + - e972e07c7845 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - e52c75a28c4b - - 980aed9e8fd5 - 407925835dd9 + - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - 79e10d12d90a - - acf3aa487283 - d85f11570109 + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - - 80b200ae516b - b76841ee5560 + - 80b200ae516b + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -221,16 +221,16 @@ tools: owner: bgruening revisions: - 48102a685037 - - 3a3033222f61 - 8083a87d2fdf + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - 33f4fa1413fb - - 27edbb90ab2b - 4ecf93628f97 + - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -256,8 +256,8 @@ tools: - name: image_info owner: imgteam revisions: - - f8b4eada923c - 236ec78b2e53 + - f8b4eada923c - 7b6d9412c7f8 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index 60dd596fc..e222ec1fc 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - d6e72da3ec35 + - 3e4f434a69c6 - f362150bef41 + - 40737febe339 - a38934e303b9 - - 3e4f434a69c6 + - 1069f6db0a0e + - d6e72da3ec35 - e4ee04da1c19 - - e319b5b65879 - 78bbd17d0703 - 3a72fede57ce - - 1069f6db0a0e - - 40737febe339 + - e319b5b65879 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - c88553ec696e - - 72ddd32392cd + - 618297d23022 - 0135f1d487a0 + - 2b95d5c04908 + - 7fe36019c073 + - 72ddd32392cd + - 9537184d421f - fcbeda41d0ac + - c88553ec696e - 8f8df367470d - - 2b95d5c04908 - f91cfb73d369 - - 9537184d421f - - 618297d23022 - - 7fe36019c073 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - fafb3d685fa9 - ad0dc9f4c9e2 - - 2cf4a1cafc16 - d7e79eb3bcb3 + - fafb3d685fa9 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 6a1515bb0687 - - 8d36959b000d - - 5dc33613c288 - - 28a6f1908fcc - - 8c05afb547fa - - 7f1cfa4c0e32 - - 94df24c6bc00 + - bd2a7d1316b9 - 43aac8d29685 + - 94df24c6bc00 + - a1c2aecd7a0d + - 8d36959b000d + - 6a1515bb0687 + - 3d18f8c3c0f6 - ee2beb764a7b - - bd2a7d1316b9 - 9eaadf03e0df - - 3d18f8c3c0f6 - - a1c2aecd7a0d + - 8c05afb547fa + - 5dc33613c288 - ee29337f905c + - 28a6f1908fcc + - 7f1cfa4c0e32 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - e3bb03cf207a - - cb903c9dc33d - - d37ede8589b2 - - bcaa0d571ce2 - - c092052ed673 - - 86a20ae274fc - - 5d6ed46cc101 - - db536ad45f28 - - 364f4ffec275 - a250929be21b + - db536ad45f28 - 9f978da6528a + - 5d6ed46cc101 + - 364f4ffec275 + - e3bb03cf207a + - cb903c9dc33d - 8858fa037a15 + - d37ede8589b2 - 5671e1d3d5ee + - 86a20ae274fc + - c092052ed673 + - bcaa0d571ce2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 194e3ceee923 + - 230b05597996 + - f95f403841ad + - 12d66d0d05ac - 38b91a3190cd - - ed28dd32141c + - 194e3ceee923 - e1a015876aa9 - - 49236b03e4fd - - 12d66d0d05ac - 584beffa972b - - abbc8041e8ec - - 230b05597996 - - f95f403841ad - - 3b6a16d82c1b + - ed28dd32141c - c5c9f02b6167 + - 49236b03e4fd + - 3b6a16d82c1b + - abbc8041e8ec tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index 0514f178b..fd641bd5b 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 17e3b698dd52 - - f198773344e4 - b8a457820315 - 0f1724dd59d2 + - f198773344e4 + - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - a513e3fbb4c5 + - 374cb875d38a - ba0c40780ecf - ac092723240d - 22c2a1ac7ae3 - - 374cb875d38a + - a513e3fbb4c5 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index eb7bf9469..e0c11b2c9 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,9 +2,9 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - - 772e0e89fc68 - 522137aaa9c4 + - 772e0e89fc68 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config @@ -18,83 +18,83 @@ tools: - name: keras_train_and_eval owner: bgruening revisions: - - f1b9a42d6809 - e1317b5502fa - - 818f9b69d8a0 - b6ef6d0cb6b7 + - 818f9b69d8a0 - 2af1346e68c9 + - f1b9a42d6809 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 947c2eacccb8 - 1588f9076e32 - - 8334dc98c48e - - 05143043ca13 - c80db5d6fd8c + - 947c2eacccb8 + - 05143043ca13 + - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - - 25b46af53232 - - 83228baae3c5 - 9991c4ddde14 - 29e4122c90de + - 83228baae3c5 + - 1552b8cb4a94 + - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 53616c8b0865 - - 060ca94ac049 - 841a6cc5fc58 - - 1a53edc4b438 - - a07ab242b0b5 - f3dfa4bdf87e + - 53616c8b0865 + - a07ab242b0b5 + - 1a53edc4b438 + - 060ca94ac049 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 - - 91c4e3331208 - - dc4b5fd604a6 + - 927586a18553 - 40f4447733b2 + - 2fc89dcd41c8 - d4808d5b83da - - 927586a18553 + - dc4b5fd604a6 + - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 - - 7626ea9c2e1b + - 25ab6b4e376e - e5a5ad882f1f - - 36e8d6d5d01b - 301e07345c93 - - 25ab6b4e376e + - 7626ea9c2e1b + - 36e8d6d5d01b + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - f9639b488779 - - 02d2be90dedb + - 0630258dcf35 + - b7c3e9a3b954 - 80852884053f - 4ed102b922cb - - b7c3e9a3b954 - - 0630258dcf35 + - 02d2be90dedb + - f9639b488779 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - caeb57858702 - - 14180f9c831e - ec69cbe34b73 - 61634a87efc7 + - 14180f9c831e + - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 6e1b8b6f7..d8df6186f 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: + - 3ba8d4563129 + - 017aba02828d + - cd659e8cc5fa + - 749c918495f7 - 0d4acadabb04 - - 17062a0decb7 - d5ceb9f3c25b - 937aa69e715f - - f6877ad76b00 - - 03e9b2fbc005 - - 017aba02828d - - 749c918495f7 - - cd659e8cc5fa - a6d65b0c67af - - 3ba8d4563129 + - 03e9b2fbc005 + - 17062a0decb7 + - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: + - 2477830927ec - dfd8b7f78c37 - - 53646aaaafef - e188dc7a68e6 - - 64f11cf59c6e - - 2477830927ec + - 53646aaaafef - 3fe632431b68 + - 64f11cf59c6e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,45 +48,45 @@ tools: - name: lastz owner: devteam revisions: + - 60afcc2c1d05 - 3e1ea2facca6 + - 2ff111fac1d7 - e7f19d6a9af8 - 37b497aa133f - - 2ff111fac1d7 - - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 11a0d50a54e6 - - 09b53c1d4ab1 - - 53c0b7a1a0c3 + - b3eab4b67562 - 8c6cd2650d1f + - c0c2d0941de8 - 037c6e54df11 - - 5cc34c3f440d + - 11a0d50a54e6 + - 53c0b7a1a0c3 + - 3f4d6399997b - be1d967337e4 - - c0c2d0941de8 - - b3eab4b67562 - - f54f5baedfdd - 77b2770508f6 + - 09b53c1d4ab1 - 6b1e195506a3 - - 3f4d6399997b + - f54f5baedfdd + - 5cc34c3f440d tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: + - 13022c3d3076 - b8f5f6e87f5c + - 79b885ce78d7 - 1cd2511a396e - - 13022c3d3076 - - e403d27e8f24 - - 5ef7ec16b04f - - 00fbfac99d39 - ec9cbd6b9a49 - - 9ee34ba73ebf + - 5ef7ec16b04f - 45795f582ae9 - - 79b885ce78d7 + - e403d27e8f24 + - 00fbfac99d39 - 178bdbdb6d24 + - 9ee34ba73ebf - 42ce70172b72 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index 252b583ff..ee54516a1 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -63,8 +63,8 @@ tools: - name: isolib owner: recetox revisions: - - 6b0fef8a77c0 - 2b1118bce0b1 + - 6b0fef8a77c0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -89,11 +89,13 @@ tools: owner: recetox revisions: - 1d10d32fa3b3 + - a5d41764722d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_convert owner: recetox revisions: + - 9e83636da9d3 - c990df6afc24 - b9cc12600553 tool_panel_section_label: Metabolomics @@ -101,20 +103,23 @@ tools: - name: matchms_filtering owner: recetox revisions: - - 00e66c401366 + - 83c4b4359ac4 - a177ac3c752c + - 00e66c401366 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - - d7b517f2c5fe - 84af792d3a78 + - fd890f162ce6 + - d7b517f2c5fe tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: + - a5a5b147da70 - 9e3c83d2afc3 - 1b09315a3f87 tool_panel_section_label: Metabolomics @@ -122,27 +127,31 @@ tools: - name: matchms_metadata_export owner: recetox revisions: - - f04610d25411 - b576ed720711 + - 8832425b1ff6 + - f04610d25411 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: - - 03bc9b7f40f6 - 1d443ed476a1 + - 330b0dfae8da + - 03bc9b7f40f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge owner: recetox revisions: - 84ead993862c + - 1fd950c5586a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_networking owner: recetox revisions: - 1d74ae228df3 + - f04b378325e5 - 8147d93d372d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -150,11 +159,13 @@ tools: owner: recetox revisions: - 9d1b01d3fedd + - fbdb2ae524df tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_spectra owner: recetox revisions: + - d50ce2f51fc0 - fbe335d27d25 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -168,19 +179,22 @@ tools: owner: recetox revisions: - 9ff95a1a2705 + - 7ba589b01dbc - 7627b40601f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - - 0cf68b536cd1 - 500f473df7e4 + - 0cf68b536cd1 + - ea6c5636c0cf tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting owner: recetox revisions: + - 5bbd1a8404f5 - 6d2f2c565431 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -256,75 +270,75 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - 79ad928a0dae - ec196e27a61a - - 7b42ee54d757 - c53a97599181 + - 7b42ee54d757 + - 79ad928a0dae tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - f3a18e020cdd - 18ec7635bac6 - - 59c393d35e0e - 149b9cc7499b + - 59c393d35e0e + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - 50b9918aeff2 - - 481d769e2f7a - 134be5abb208 + - 50b9918aeff2 - dfebc82ba1f0 + - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 501a232f3cd5 - - 51332c2520c7 - a82db010c53e - - 30bf4e35da3e - 9064aecc78a7 - 02c772a49998 + - 51332c2520c7 + - 501a232f3cd5 + - 30bf4e35da3e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - e7305ba0dd38 - - 89178a72388a - b3413f335327 + - e7305ba0dd38 - b341cfd4baf8 + - 89178a72388a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - b7c8a44b9cc1 - dd7bbc2b99d1 - 17a48d0a80f4 - cf061712a184 - - b7c8a44b9cc1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - d7f5878a98c3 - - 24278c6b6d1c - f92b1b64da93 - 99d118321d5f + - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - ffbabefbd2e2 - - 7acd11ddc061 - - ea0758b41473 - d90187b0f247 + - ea0758b41473 + - 7acd11ddc061 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -386,8 +400,8 @@ tools: - name: use_theoretical_mz_annotations owner: recetox revisions: - - e0cac9994a72 - b3d41b1fcb18 + - e0cac9994a72 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: w4mclassfilter diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 81391117b..1de9b6ecf 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -9,8 +9,8 @@ tools: owner: iuc revisions: - 0094893f5001 - - 0e63d03c8790 - 18676df0cb3a + - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -22,8 +22,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -95,21 +95,21 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 5b5a7af9fbb4 - 76d3d2b10738 - - 63f86089423e - 65db807336bc - 7c2100246a2f + - 5b5a7af9fbb4 + - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 84fd33a60b35 - - 96336c6a2bb7 - 00f5005840fa - - 18a502a9d287 - 1c35dadbe76f + - 18a502a9d287 + - 84fd33a60b35 + - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim @@ -117,79 +117,79 @@ tools: revisions: - a9f4a217dcd6 - addaf9d22850 - - 34e55239e68b - - e8fba04706d3 - f732237754fc + - e8fba04706d3 + - 34e55239e68b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 0776d824d896 + - 04c15826a0b8 - 75403243703a - 5fe3edf19b9c - - 04c15826a0b8 - 8c202e741d68 - - 0776d824d896 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: + - e96bbb9e24ea + - 75c8945b0da2 - 8470de786d47 - 43c99742158b - 1c9b3bcd4261 - - 75c8945b0da2 - - e96bbb9e24ea tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 306a40d4bb8f + - 84743da21318 - 35176674168c + - 306a40d4bb8f - 1d75bd0595e2 - 5c865a382933 - - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a - 78faebd0879c + - ac72310b038a + - 555ccac8a4c5 - 8daf4564ccda - 32c9ea835770 - - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: + - f947b4bb5107 - 7b8cb2b02978 - - d60df8727f59 - cae017b76acb - a58e4a43f49c - - f947b4bb5107 + - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e - 073608a50ac3 - - 7f3b59dee073 + - 04144473e59e - 1bc3657cd694 - 7136e9ab70db + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af + - d943081510da - 0a1224c4b781 - - 9058d8943303 + - 19299bb1c6af - a7817705348e - - d943081510da + - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -202,13 +202,13 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - 5c7ba3d85a01 - - dbf1798c0dcc - - f8f56dd6449f - - 4d9445dff47b - - a68b985913ab - b907a3c0434f + - 4d9445dff47b - 65d52c693b8e + - dbf1798c0dcc + - a68b985913ab + - f8f56dd6449f + - 5c7ba3d85a01 - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -236,8 +236,8 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - bd7a9c6efb10 - e66ab198ec15 + - bd7a9c6efb10 - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -252,9 +252,9 @@ tools: - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - 7f208f1eb64f - 9704f1a3b32d + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -272,15 +272,15 @@ tools: - name: humann_barplot owner: iuc revisions: - - 5fea25ee6275 - 523ae8314ef5 + - 5fea25ee6275 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables owner: iuc revisions: - - 6bf703133209 - f01ca38fb6c5 + - 6bf703133209 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table @@ -293,33 +293,33 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 8237a0f225db + - c409a495841f - 79706f10d680 - 31c6d107e7a5 - e88b731dad59 - - c409a495841f + - 8237a0f225db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - 71ea608ddfa3 - - aabf8cfb8fef + - 172920f67a84 - 094ad9c068af - d24841f5c3d2 - 714d5a28cc5c - - 172920f67a84 + - aabf8cfb8fef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - - a293a742194f - a4d7148ccee4 - - 4137b492233e - - 12fb63b5f63f - 2bdd84912a2b + - a293a742194f + - d7e9a3c41657 + - 12fb63b5f63f + - 4137b492233e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -331,20 +331,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: + - 6fcb8ac37a3e - 75bedfb2078b + - e2c71b852aba - a92c06a3afa7 - - 64bc7acc22a9 - - 6fcb8ac37a3e - - cf87759761eb - 97f7bb0851e7 - - e2c71b852aba + - cf87759761eb + - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -356,11 +356,11 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 4e5e73d03f0d - 080ea153677c + - 4e5e73d03f0d - 5e5a999ffaa9 - - 4033827c76b8 - c82508e76ad1 + - 4033827c76b8 - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -368,8 +368,8 @@ tools: owner: iuc revisions: - 6b7622dda516 - - fc6c328c292f - c2803012bbb3 + - fc6c328c292f - 2cd76b089570 - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis @@ -389,8 +389,8 @@ tools: - name: jellyfish owner: iuc revisions: - - dcd30574a456 - 11658afb8c87 + - dcd30574a456 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single @@ -410,15 +410,15 @@ tools: - name: khmer_count_median owner: iuc revisions: - - b3d513c7093e - 570505540a7b + - b3d513c7093e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions owner: iuc revisions: - - 1061711538c6 - adb3dd5a899f + - 1061711538c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance @@ -431,15 +431,15 @@ tools: - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 19607c740d19 - 00f7064c564b + - 19607c740d19 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median owner: iuc revisions: - - b1fe2ef3d244 - 4d23ab83ea29 + - b1fe2ef3d244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -458,8 +458,8 @@ tools: - name: kraken2 owner: iuc revisions: - - 20e2f64aa1fe - 328c607150ff + - 20e2f64aa1fe - cdee7158adf3 - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis @@ -467,8 +467,8 @@ tools: - name: kraken2tax owner: devteam revisions: - - f03c7ba8d8bc - 50bd98b3ae5a + - f03c7ba8d8bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -526,8 +526,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 4960abe31b4d + - 073c867c5244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -576,22 +576,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 27250f92a01a - 4fd3b5d8706b - - 0270541aaf46 - - 3cc4a60615c0 + - 327d9f4cc95f - 2cff76cf35c6 + - 27250f92a01a - e073891b2afc + - 3cc4a60615c0 + - 0270541aaf46 - 7f5d7b0e9884 - - 327d9f4cc95f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - 76bc4efa1aeb - eb50e7eca3dc + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -657,33 +657,33 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: + - ff8f55893e7d + - 289b3807e80c + - ef65b083bd0c - fd69c607b43f - - 740fd2d16a28 - - b89b0765695d - 1a6cdf55390f + - a16313517e55 - 2131d7dca455 - 1a037928504c - - ff8f55893e7d - - ec368db926f4 - - 6dee4abadccb - - 289b3807e80c - a92a632c4d9b - - ef65b083bd0c - - a16313517e55 + - b89b0765695d + - 740fd2d16a28 + - 6dee4abadccb + - ec368db926f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - 2a8bc1d26d06 - e3a64a1d2a6e + - 2a8bc1d26d06 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -701,36 +701,36 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 6034c3f3ecf0 - 2f47a294ef49 + - 6034c3f3ecf0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: - - 6eafc1e01a8c - 3b133b8d578a + - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - 6077821e8ae7 - f53beb324696 + - 6077821e8ae7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - 540aedfc81c7 - d6bb2e3febda + - 540aedfc81c7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs @@ -743,8 +743,8 @@ tools: - name: picrust2_shuffle_predictions owner: iuc revisions: - - 881f2faa5fe7 - 677f3c8db525 + - 881f2faa5fe7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -795,6 +795,7 @@ tools: owner: iuc revisions: - f355085dd2aa + - 915637bd1d1a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: pynast @@ -812,20 +813,20 @@ tools: - name: recentrifuge owner: iuc revisions: - - 591175c0f051 - d4fbfd31696c + - 591175c0f051 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - be818ae858e4 - - aeaa20b96ef2 + - 4d83eccf5f81 - 4b9a8031ab74 - - 141afacabcfa - 3b22de20bd4b + - 141afacabcfa - 2fd4d4c9c5c2 - - 4d83eccf5f81 + - be818ae858e4 + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -855,8 +856,8 @@ tools: - name: vsearch owner: iuc revisions: - - 9495df9dd6ef - 576963db5f1b + - 9495df9dd6ef - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index df824d47f..dbd37638b 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - 12e856482d26 - bdb4a58a2025 + - 12e856482d26 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 007db25f4..6864160cc 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: + - cd07731e4434 + - 098506c54016 + - 8b67dd48fec1 + - 80f03df2e2ce + - 9eeb13a92d79 + - a74dbfee5a86 + - 9baa871cb1d1 + - 48c13389050d - 9422c5a87ee2 - bdfbaf0c10aa - - 48c13389050d - - 9baa871cb1d1 - - a74dbfee5a86 - - 80f03df2e2ce - - 8b67dd48fec1 - - 2263989660f5 - - 098506c54016 - - cd07731e4434 - 94b8c6013083 - 6ae5a7b5a0a2 - - 9eeb13a92d79 + - 2263989660f5 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - aaa0d6a8b808 + - '764845535798' + - 5abf2c2249aa + - be78f13134e2 + - 2e093badc689 + - d390fe1567dc + - f14193ec1f50 + - 4a60927aaca5 + - bc3831dd65c1 - f0af8936ed41 + - aaa0d6a8b808 + - 3ff17bad4006 - c18157c68134 - - bc3831dd65c1 - fc2e49f91e52 - - be78f13134e2 - c44f824c051a - - 3ff17bad4006 - d7ce0ec78e51 - - f14193ec1f50 - - '764845535798' - - 5abf2c2249aa - - 4a60927aaca5 - - d390fe1567dc - - 2e093badc689 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -53,75 +53,75 @@ tools: - name: clustalw owner: devteam revisions: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: - - 1de657a3198d - 5efbd15675ca + - 1de657a3198d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: + - a65296ffb4a0 + - 8e649f27aa0d - bf28a8cff401 - - 6f28e90db932 - c5908940967d - - 8e649f27aa0d + - 6f28e90db932 + - f1a5908ea2cb - 15974dd17515 - - a65296ffb4a0 - f0d493f8f84f - - f1a5908ea2cb tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - fbca557a4847 - - b3acbb3a6af0 - e8fdceffea4c + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - c9685bc0407c - - 60698466facd - 5561a1193611 + - 60698466facd + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - - 57f042937ba7 - bcd65de9725b + - 57f042937ba7 + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - fb43e8887350 + - 4fc0cb2ac8ae - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: + - e18267f90096 - 7cd7a55a678d - 636b049e6141 - - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - 959c1f8dae95 - - cf3c9489c088 - b4124df98b26 + - cf3c9489c088 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index 7b19cd6b0..572644aad 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,10 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 9aa9d92c3c51 - - 1145758d2f0b - 18a8d140ec6f - 28928576e1ea + - 1145758d2f0b + - 9aa9d92c3c51 - 7c47b3c9e493 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,9 +25,9 @@ tools: owner: galaxy-australia revisions: - 63d8ecfcfab1 + - 090ab4f31074 - fc5b6491cf78 - 6942f170cc43 - - 090ab4f31074 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -39,21 +39,21 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f + - 72b5e9dda577 - fc8804320156 - - a7228a7ea146 - 79e9a869f40e + - a7228a7ea146 + - cb34f00cc10f - 0e9e7fcdd543 - - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - 18505fe2bdb1 - - d6cddc06aeae - fa11aa8103b2 - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -65,22 +65,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - cc36773a3681 + - edf6d4003fad - 0f5f4a208660 + - 2bf63b38ee9b - ec699520444c - - eb746fa6f514 + - cc36773a3681 - 19f3b583a9b3 - - 222669c4afb6 - 43815fa60f3a - - 2bf63b38ee9b - - edf6d4003fad + - 222669c4afb6 + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - b833eff63b10 - c0fb573c1e8d + - b833eff63b10 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -92,28 +92,28 @@ tools: - name: nanoplot owner: iuc revisions: - - edbb6c5028f5 - a38bdcec9e4c - - a02b8b3f5a0c - - a3c4fe6f49ab - 0f1c34698076 - - 7b379e98b9a9 + - edbb6c5028f5 - 645159bcee2d + - a3c4fe6f49ab + - a02b8b3f5a0c + - 7b379e98b9a9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: + - d219b6d8158a - 3b6f94fc7e1d - 85a394edc247 - - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - a8d4be409446 + - 90a922f32523 - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -121,24 +121,24 @@ tools: owner: bgruening revisions: - 449e9aeded2d - - d376944466bf - 4857d5bcce52 + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: + - a3afc5f0a96c - de5b3d8f5b90 - bec636361cfd - - a3afc5f0a96c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 93d623d9979c - - 5f76b20953e5 - 543cbeef3949 + - 5f76b20953e5 + - 93d623d9979c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -151,8 +151,8 @@ tools: - name: poretools_extract owner: iuc revisions: - - 7e4f1ed70187 - 08064da7b7fb + - 7e4f1ed70187 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_hist @@ -172,31 +172,31 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 338d15b8d6fb - - 0433aad600e9 - 336791b5665f + - 0433aad600e9 + - 338d15b8d6fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist owner: iuc revisions: - - 72dfdbfab3cc - ae9060e764b5 + - 72dfdbfab3cc tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualpos owner: iuc revisions: - - 626b6c2be5c2 - 2e22ebec211a + - 626b6c2be5c2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - ce8af9373061 - - 34553d0caa5e - 26e6c9362b7b + - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -208,8 +208,8 @@ tools: - name: poretools_tabular owner: iuc revisions: - - 5f5f1da94d7f - 2cb2feb94f0e + - 5f5f1da94d7f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_times @@ -221,15 +221,15 @@ tools: - name: poretools_winner owner: iuc revisions: - - 6d93709247c7 - 79c1ac92f31b + - 6d93709247c7 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - c5c5a3e84989 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 64b67a5e4..c95485b63 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - a5921c09b7b7 - 592ef3959907 + - a5921c09b7b7 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: annotation_profiler @@ -21,15 +21,15 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 4e85a3a5dbd1 - 71186bb66ca2 + - 4e85a3a5dbd1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 96d2000977ab - 58341ad4fb42 + - 96d2000977ab tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -59,19 +59,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: + - baceff842902 - 3e73c97f025d + - 97b1b5ad1cda - adfd6bf710bd - d74850cf4e42 - - baceff842902 - - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - 83da94c0e4a6 - - 1586b111d2a3 - 9dd107db92c2 + - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -83,11 +83,12 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - 1e34d2e3d285 - 2f27f3b86827 + - ed1518ce2237 + - e9ee4d074d5d - e4b4837f06f5 - edacc4bcd3cb - - 1e34d2e3d285 - - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -113,23 +114,23 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 5711fc06a63e - 38ccd4589990 - 48a42ca61006 + - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -162,24 +163,24 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 - - b4b2b284230a - 5bcf0e24f42c + - b4b2b284230a - 172815da3d41 + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - df84aaed4769 - 10232d2b5062 + - df84aaed4769 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -199,8 +200,8 @@ tools: - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -225,12 +226,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 9c43baa60906 - - d8dc037e3c13 - - 2c61c30a57e7 - - 4ba60cb14cb0 - 0cb27ea69dc1 + - 2c61c30a57e7 + - 9c43baa60906 - 5fe20c915fa6 + - 4ba60cb14cb0 + - d8dc037e3c13 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -243,17 +244,17 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - - 0db22932bc39 - 9d09724f2bf1 + - 0db22932bc39 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - 6e24e79d3d69 - - ed7a967cb11b - 29c738066906 + - ed7a967cb11b - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -272,8 +273,8 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 3e4d45aca422 + - ad90c2da4f38 - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -293,16 +294,16 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - 64deddb6a8ec - c520a52b5174 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - 94a50db37d1a + - 625fd9476402 - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1053,15 +1054,15 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - d64562a4ebb3 - 544f6d2329ac + - d64562a4ebb3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbcavity owner: bgruening revisions: - - 7e5c2e4bc227 - 744a777e9f90 + - 7e5c2e4bc227 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbdock @@ -1082,10 +1083,10 @@ tools: owner: iuc revisions: - f77f7a7f3b83 - - 58a870ef434c + - ab5b7f6b7198 - ba7b0f11e470 - 9a22227bb6d0 - - ab5b7f6b7198 + - 58a870ef434c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_merge diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 4fb41a237..b142fda5b 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - d7c7ef3353fe - - f04a1264e2a2 - - '841557158611' - - c78f3d7dd1db - - d033ffc1c161 - - cce7b18495e4 - a6619171428e - 3b8b5bde0bd9 - - 5a7c56a5cc08 + - b89cac5156ec - 8834daeb9892 + - c78f3d7dd1db + - cce7b18495e4 + - 81e66674859e - 3f59ebfbfe3d - - b89cac5156ec + - '841557158611' + - f04a1264e2a2 + - d7c7ef3353fe + - 26de3a7b1cb9 + - 5a7c56a5cc08 - 107d3ba7024a - f73435dc282b - - 26de3a7b1cb9 - 6a457678efcb - - 81e66674859e + - d033ffc1c161 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 6a726db04d4b - - 02b8758214b0 + - 5fcd1ece3a6e - b0af57c1a968 - - 4755f52427c4 + - 6a726db04d4b + - e75442c7f4da + - 6283babe736e + - 3b96e92e8ec3 - 659517798cc4 - - 88c4aa435ded + - a185b079b095 + - 7a2092844346 + - 4755f52427c4 + - 02b8758214b0 - 6223845127ea - 5b777002c2de - df47d4845b62 - - 7a2092844346 - aa8cc71438cf - - a185b079b095 - - 6283babe736e - - 5fcd1ece3a6e - - e75442c7f4da - - 3b96e92e8ec3 + - 88c4aa435ded tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - 111bd54f6bc4 - - d1c340a5664b + - 0878b7fd5260 - b8476e82ac20 - - f97743d52b87 + - d1c340a5664b + - 24d024316465 - f87ac61981f0 - 524d31add34a - 70acec670c30 - - 24d024316465 - - 0878b7fd5260 + - f97743d52b87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - 9e10ba792be2 - - daddf188c13f - feb40665d7cd + - daddf188c13f - 4f6349228462 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,33 +111,33 @@ tools: - name: pangolin owner: iuc revisions: - - 81804a978fc0 - - 8ad84c5753ea - - ca0d8cf80567 - - 9d61d3fa046c - - abf6dbe8c9d7 - - b7e297c2ede6 + - a2099fb98cdb + - 437e28791761 - 2fa9d4f1b48f - - 42a174224817 + - abf6dbe8c9d7 + - 81804a978fc0 + - 7bb8726be37c + - 5f8727ff21e7 - ca337cce3888 - - 36912871ccdc - - a2099fb98cdb - - 03ed9524dcd1 + - 42a174224817 - 14ae456b8cc5 - - 5f8727ff21e7 - - 437e28791761 - 3a43c3982401 + - b6abccb1f25b - 83a69484cb87 + - b7e297c2ede6 + - 9d61d3fa046c + - ca0d8cf80567 + - 36912871ccdc + - 03ed9524dcd1 - 2f1019071464 - - b6abccb1f25b - - 7bb8726be37c + - 8ad84c5753ea tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -150,22 +150,22 @@ tools: owner: iuc revisions: - b1e68bbe4cef + - ba29b5e2a4be - a4b71be30c3c - 29ff6a849eac - - ba29b5e2a4be - - ea30d3089354 - 73a469f7dc96 + - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - dbe2b2204555 - - 809e42326fc2 + - e88a7de55d6e - 9b2b122d0415 - - 91887494eb97 - f1ccc8a6eb05 - - e88a7de55d6e + - 809e42326fc2 - 15ac71df11a0 + - 91887494eb97 + - dbe2b2204555 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index 84bfaf4fa..d6eef1fee 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - f6ced08779c4 - - b502c227b5e6 + - a1f0b3f4b781 - fc288950c3b7 - - 3f254c5ced1d - - 881d7645d1bf + - b502c227b5e6 - 7d34178f2812 - - f9242e01365a - - a1f0b3f4b781 - 1aac2a13842a + - 881d7645d1bf + - 3f254c5ced1d + - f6ced08779c4 + - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index d1f175af9..e87b34b61 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,18 +2,18 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - a58f7eb0df2c + - 7fbec959cf2b - 2f7702fd0a4c - 6ab1a261520a - - ca90d17ff51b - - e4a053d67e24 - 3f188450ca4f - 3bd420ec162d - - c0e71cb2bd1b + - 5b85006245f3 - d00e15139065 - - 7fbec959cf2b - - a58f7eb0df2c + - ca90d17ff51b + - c0e71cb2bd1b - eb085b3dbaf8 - e7f1b552a695 - - 5b85006245f3 + - e4a053d67e24 tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomics.yml b/staging.gvl.org.au/proteomics.yml index 05344cc14..e3d2b63c7 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,94 +2,94 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - b574b84afc4d - - f28ad96b76dc - b18329a8ac14 - - 4c177985028a + - 277dc652246e - 0a18ac48ac53 + - f28ad96b76dc + - 4c177985028a + - b574b84afc4d - ece627528a78 - - 277dc652246e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - 525f201b86c1 - - e215f71d7983 - e988563cc6e5 + - e215f71d7983 + - b41107d8fe89 - a9a28e46d54a + - 525f201b86c1 - bf06d196e23d - - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - - bb6397b94018 - 8da3511c9467 - 56da27be956a + - bb6397b94018 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - f23d67e28cc8 - - 890845926d4b - 528fb09022be - - b8c79e70516d + - 890845926d4b + - f23d67e28cc8 - a8157342d9a3 + - b8c79e70516d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a69865da6f80 + - 59e85306eae5 - 25b83cbd596a - a95a82eb4d50 - - 80600735685d - - 59e85306eae5 - ae304a72db7b + - 80600735685d + - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 798da6bdff3d + - 83aac7741200 + - 611d80c0e29d - e0669b1854b1 - - f1897eb07081 - ed9ed1e6cca2 - - 611d80c0e29d - - 83aac7741200 + - f1897eb07081 + - 798da6bdff3d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: + - 5a35e3a8d013 - 74b61bf5bc4b - - a7fb9b395ddf - d426a9107a6c - - 5a35e3a8d013 + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - 91f0f5922011 - df2187f9013b - 82f6c2f4332d - cc430977c8ff + - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: + - 043f9c91f686 - ba92b59cd529 - 10566783d718 - - 043f9c91f686 + - 1693b2126f30 - c5aa9fca18c6 - d2483487e077 - - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - 9fa3dbf06f17 + - ff8c9e0e8a7b - ae4dc0c041f9 - bf0728e000cd - - ff8c9e0e8a7b + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,9 +129,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: + - 1c5cbf8f79ce - 0fa397f4f40b - 4081e4faa4ab - - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -144,9 +144,9 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - d6a4dfdad269 - - ce1a157a41bd - 0d2e93e01e68 + - ce1a157a41bd + - d6a4dfdad269 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -158,38 +158,38 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - - 160538a890a6 - d286ff4600dd + - 160538a890a6 + - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - f522c08e900c - - 97a7f34fcb6a + - 1f39c833f65f - 837224ad1694 - - 2133b0be850a - - 9c52362ae7bb - 4d17fcdeb8ff + - 9c52362ae7bb + - 7f432d87c82c - e42225f8a659 + - 2133b0be850a - 37d669de2828 - - 1f39c833f65f - - 7f432d87c82c + - 97a7f34fcb6a + - f522c08e900c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,85 +201,85 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - 85b8866f06d7 - - e63db1aa82ee - a72ac2c7cc5b - 0ed07016d668 + - e63db1aa82ee + - 85b8866f06d7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 352b37c66d97 - 1974224d63c2 - 990b4560ead7 - 767c1d761aaf + - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - deaf035bbe9f - - 35cc7ca0bdc7 - 99450519d727 + - 4f359549383c + - 35cc7ca0bdc7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - e79958768a2c - 06f6826d380c - c1343e3389ca + - e79958768a2c - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 - - da986f83631b - b9d453dca8d3 + - da986f83631b + - d2eac53666f0 - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 8bd7734309f6 - - 1199751329b0 - 944b43462104 + - 1199751329b0 - 9bf325045235 + - 8bd7734309f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - 8295d959ca28 - e0104a9f20f0 + - 8295d959ca28 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert owner: galaxyp revisions: - - 6153e8ada1ee - ab6c14374bc0 + - 6153e8ada1ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats owner: galaxyp revisions: - - 593839e1f2c3 - - 28434abe6c5c - de7593c29499 + - 28434abe6c5c + - 593839e1f2c3 - 8212e342e482 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - a5e394b36d87 - bd1535813cfe + - a5e394b36d87 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid @@ -287,53 +287,53 @@ tools: revisions: - 01dbaf6a57e0 - f4be248c3d47 - - 8960fb791701 - 4e77b8f12cd3 + - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - 25529df60a81 + - 370141bc0da3 - 06cca574e337 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - c9eff69a7c62 - 518b1730cf2a - 6ccbf9a2072c - - 9cdf15d3cfc8 - f7fef900f5b2 + - c9eff69a7c62 + - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 - - 5e948629bc73 - dff6c756eee5 + - ca88bd28f116 - 9876bda3ec53 + - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 1595601708ec - - 890025d6e426 - 41859bbdc16e + - 890025d6e426 - 658494a2cb00 + - 1595601708ec tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - 9b7977080f6d - - 6634cad7d797 - 2a93a25f0599 + - 5ad0b5bf1deb + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter @@ -341,17 +341,17 @@ tools: revisions: - d6878d27f051 - 05d5e1ddc985 - - fe4e4587d265 - 0bb5056cb775 + - fe4e4587d265 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 4af67edd5aef + - 5ad830edc021 - 52ba9695e752 - febd569ad26f - - 5ad830edc021 + - 4af67edd5aef tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger @@ -359,64 +359,64 @@ tools: revisions: - b2fc8da99bcc - 27cba4c5fc42 - - 92352a475eed - 39e8fde08881 + - 92352a475eed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 0efbc235f314 - - d413dc49d650 - d3546bb9fd8e - 9e26f5c770f8 + - d413dc49d650 + - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: + - ca1740533b59 - 3720e349ba2a - 8a04ed1c1d1b - - ca1740533b59 - c28f13cab67a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c55dddc5844a - a5d785af0ad8 - - ca799a7246e7 - c427a8628cbe - 382cde407f81 + - c55dddc5844a + - ca799a7246e7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 39caaa778d2e - - adca857b4884 - - b5d0905419da - 8ddb7bab1138 + - b5d0905419da + - adca857b4884 + - 39caaa778d2e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 1c5f31b8d632 - - 34e7afee141d - f817513840a9 - 8d4db262964c + - 1c5f31b8d632 - 18f93351f8b6 + - 34e7afee141d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - c69f69d7867a + - 986e03d3201e - 5d9f175dff81 - 111c3a00136d - - 986e03d3201e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher @@ -424,8 +424,8 @@ tools: revisions: - be74a8cd7d66 - 0e52c85f3b15 - - 4204882495f2 - 476b5e296979 + - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -438,59 +438,59 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - c18d8efa4474 - 2b2a7551a857 - - a407b6790342 - f5ec766d80cf + - a407b6790342 + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - 4e66c4e73909 - - d0304fb829c0 - 021fdb80f204 + - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - 8098330f6d91 - - ee860980edc6 - 2735db4dd8d9 + - ee860980edc6 - bf32e0bcf554 + - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - 08488066d588 - 0ced5bc9f4dd + - 08488066d588 - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 2a9ff56cb279 - de7a553552a6 + - 2a9ff56cb279 - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - c1809c05ae8c - - e8f64a7dc470 - 1bf940c18d93 + - e8f64a7dc470 + - c1809c05ae8c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - f861ec9fbe59 - - 496cf619e311 - 9f505cd4428f + - 496cf619e311 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -504,9 +504,9 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 4bb198c0bd3e - 8b814eafce2c - 89254095cbf6 - - 4bb198c0bd3e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher @@ -521,35 +521,35 @@ tools: owner: galaxyp revisions: - 18826fb8e5db - - 6e8cc5ed2a9b - d31426ef20f6 + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - bc63b4d12779 - - 2aebe58de46e - 4a7b96835140 + - 2aebe58de46e + - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 6b01678ec2fc - - decc397c3b7e - - 5ae104d0da6e - 3d8d4ada5405 + - 5ae104d0da6e + - decc397c3b7e + - 6b01678ec2fc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - 5182338d5e7c + - d6aca689dd48 + - e039cc5c7aed - dd173849c3d8 - 539a3a4dcc9e - - e039cc5c7aed - - d6aca689dd48 - - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -563,41 +563,41 @@ tools: - name: openms_targetedfileconverter owner: galaxyp revisions: - - 9c70a651a53e - 43b9ed22e8ce + - 9c70a651a53e - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: - - d063e2fe4ba4 - 9020199dba0a - 1b03536aa3c9 + - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - - ad2ba3a95a02 - f036e8cf1a55 + - ad2ba3a95a02 + - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 5c2a97a234d6 - - 7f6a1f27553e - fb52e95a370c - c8b225c69a7f + - 5c2a97a234d6 + - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -609,21 +609,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: + - 3634c90301af - 7fdd9119cc4f - - da885ca16cb2 - - 1beff3ddce58 - - 943a34df6047 - - 3ec27b4cee7c - 07ff622ec007 - - 3634c90301af + - 3ec27b4cee7c - a72c48001f7c + - da885ca16cb2 + - 943a34df6047 + - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -683,10 +683,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - a371252a2cf6 - - 1a5690a5eedc - 265c35540faa - 12692567c7f9 + - 1a5690a5eedc + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/staging.gvl.org.au/qiime_2.yml b/staging.gvl.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/staging.gvl.org.au/qiime_2.yml +++ b/staging.gvl.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index d3a3812e3..de428bfcc 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -3,11 +3,11 @@ tools: owner: iuc revisions: - 289b7d6b69a4 - - 42201b90e3f4 - 110a346daf36 - 2f1d464ebfd2 - cd5f98911089 - e345aadf914f + - 42201b90e3f4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,11 +19,11 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 42d9087b4789 - - 0345dbaaa79b - - 8501601a118d - 0cd2df8af811 + - 8501601a118d - c207119ba5f6 + - 42d9087b4789 + - 0345dbaaa79b - fcce77c09289 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -37,11 +37,11 @@ tools: owner: iuc revisions: - 04db7fd6b238 - - 89eb29319bf4 - - 33486216eec0 - - ad5ab22ffe24 - 421c33b8bf17 - 405a212b32ab + - 33486216eec0 + - ad5ab22ffe24 + - 89eb29319bf4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - 7b72fde3d27e - - 1d839ead7ad3 - - fa51dc5e8386 - - eb784fa07f80 - f6e91108b7b1 - 7370bb65bad4 + - 1d839ead7ad3 + - eb784fa07f80 + - fa51dc5e8386 + - 7b72fde3d27e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - 8a55d29c8fcf - - 3d70c2996730 - a3e86cd9cac7 + - c9b77ced9a78 - d30e36c48c93 + - 3d70c2996730 - 1544278c272e - - c9b77ced9a78 + - 8a55d29c8fcf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - e2db212d64ad - - 887cf585cafc - - 7b881f5f5ad5 + - 564c33e5c3e3 - b242deb58952 - a5969aa9347e - - 564c33e5c3e3 + - 887cf585cafc + - e2db212d64ad + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,8 +104,8 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - 8cff84759bf6 + - e897c74a48bb - b4bab607eb05 - bd5ff77e2036 - 9a171f9a450b @@ -121,11 +121,11 @@ tools: owner: iuc revisions: - 6dafad990086 - - 5e10f396979e - 33f0793edf93 - 4f65e343ecdf - - 887e0991eb24 - adc7a7610d4f + - 5e10f396979e + - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,11 +137,11 @@ tools: - name: stacks2_shortreads owner: iuc revisions: + - c5d7050e4ad7 + - 17d39bf0a63a - 97575d01f06b - - c287418eb288 - 43e3eeb2e0ec - - 17d39bf0a63a - - c5d7050e4ad7 + - c287418eb288 - 4e280b27a831 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - 9586f08634c0 - - a819ec3b362d - 09b8edb56d80 - 0b8c84a7fdb5 - cd034465d4a4 - d9bf483266a1 + - 9586f08634c0 + - a819ec3b362d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - bf0e43ab0416 - - a4b4bd84f69e - - a9c34a289493 - 69842dd5aa48 - - 95351dd0fd3f + - a4b4bd84f69e - 2645575d1bf2 + - 95351dd0fd3f + - bf0e43ab0416 + - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: + - 8a35a3bc6752 - d033e1ccb386 - - cfb504394ae1 - 912f904a6e1e + - cfb504394ae1 - d1fda11e602f - bb0475c884ff - - 8a35a3bc6752 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - d504d945a655 - 95286af4139b + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 18fe09d56..22c3dace9 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,27 +2,27 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - - 7acb00fc980a - 31f8063eedea + - 7acb00fc980a + - cf01dd6c6b1f - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: + - 7a5a2d28c539 + - 703a2cb3fb38 - 125d20cb23d7 - 32e542c2a773 - - 703a2cb3fb38 - - 7a5a2d28c539 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: + - 3d61a698e5e1 - 01ccd366690d - 45c2ec061cf9 - - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -77,9 +77,9 @@ tools: - name: cuffcompare owner: devteam revisions: - - ad5d061fbdf2 - f648e5180e40 - e66b9b5b8580 + - ad5d061fbdf2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffcompare @@ -106,9 +106,9 @@ tools: owner: devteam revisions: - cf747d1bd79a - - 04adc9db1581 - - 22cf48ad7b16 - 6a6717a5f421 + - 22cf48ad7b16 + - 04adc9db1581 - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -121,9 +121,9 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 28b94cfbfdb9 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -161,8 +161,8 @@ tools: owner: iuc revisions: - 3b36efd62b3e - - e3b16fd7dd08 - 0693ccd171c4 + - e3b16fd7dd08 - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -175,13 +175,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 8fe98f7094de - - 24a09ca67621 - - 0696db066a5b - - cd9874cb9019 - - 9a882d108833 - 6a3a025714d3 + - cd9874cb9019 + - 24a09ca67621 + - 8fe98f7094de - d027d1f4984e + - 9a882d108833 + - 0696db066a5b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -209,18 +209,18 @@ tools: - name: edger owner: iuc revisions: + - 5bf899c13979 + - 334ce9b1bac5 - ae2aad0a6d50 - a8305cf0c951 - - df0c8d0a5992 - - 334ce9b1bac5 + - 070900306913 - 6e53e565fc6a + - 9bdff28ae1b1 + - 0cb907a2a810 - 3d89af8a44f0 - - 070900306913 - f2843df56434 + - df0c8d0a5992 - 555659de7321 - - 5bf899c13979 - - 0cb907a2a810 - - 9bdff28ae1b1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -232,8 +232,8 @@ tools: - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -252,17 +252,17 @@ tools: owner: iuc revisions: - ea04b737afa0 - - 1b851f87fbe0 - - a37612abf7f9 - - a56fbe2d6ba7 - - f3a5f075498f - 6f66ae7c5f7a - - 90d16db017d7 - - 38b6d12edc68 - - e6a2a912677a - af814359d244 + - f3a5f075498f + - a56fbe2d6ba7 - 7db9d3ea71c9 + - 1b851f87fbe0 + - a37612abf7f9 + - e6a2a912677a + - 90d16db017d7 - f9d49f5cb597 + - 38b6d12edc68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -292,9 +292,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 3c97c841a443 - 3c5e024a18cf - 0f710191a66d - - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -312,13 +312,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 6ab42baa56e9 - - f4af63aaf57a - 26371a1df031 - d4b55e2beb12 - - 3fb01a8c902d - 6c19daec423d + - f4af63aaf57a - a86e80d3c09c + - 6ab42baa56e9 + - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -356,9 +356,9 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 5ae5c312d718 - 01247aaf0a10 - 1c75aa5de15e + - 5ae5c312d718 - 87c11c05d238 - ce5d418183c5 tool_panel_section_label: RNA-seq @@ -372,9 +372,9 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 10c98fab6c5a - 4f9c4e6566e5 - c971db6f0fe5 + - 10c98fab6c5a - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -387,14 +387,14 @@ tools: - name: limma_voom owner: iuc revisions: - - 708348a17fa1 + - 0921444c832d + - 32511f586472 - d6f5fa4ee473 - - 97e06a4c7c75 - 119b069fc845 - - 0921444c832d - 58c35179ebf0 + - 97e06a4c7c75 + - 708348a17fa1 - e827f9aae031 - - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -463,20 +463,20 @@ tools: owner: iuc revisions: - 4014de1b6daf - - 79de45b5069b + - b0f2be869d6d - c7c55b694974 - - 7ed2edc1337f - - e132e7d02a3e - - 99b17b74a8cd + - 980d2a2e1180 - c772497b2c32 + - 4074fc1940e2 - 5ec75f5dae3c - 3ea5a2a63fa2 + - 79de45b5069b - b9e04854e2bb - - b0f2be869d6d - - 4df95e2d7f61 - - 4074fc1940e2 - - 980d2a2e1180 - 0a563fd2f22e + - 99b17b74a8cd + - 4df95e2d7f61 + - e132e7d02a3e + - 7ed2edc1337f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -500,13 +500,13 @@ tools: - name: salmon owner: bgruening revisions: - - 49121db48873 - - f4d5237a84f6 - - cc05793bb896 - - ebab418107f5 - 2c0ca397d302 - e3d32471da11 - 15cd64d7c58b + - 49121db48873 + - ebab418107f5 + - f4d5237a84f6 + - cc05793bb896 - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -519,23 +519,23 @@ tools: - name: seurat owner: iuc revisions: + - c0fd285eb553 - fab6ff46e019 - 56242ff81c84 - 8c28affc7c48 - - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 1ebd14235b92 + - 914cfcba0ec8 + - 258d696dbd7e - dd4df992d93d + - 76d290331481 - cbf488da3b2c - - 258d696dbd7e - cef79931dda5 - ae618321f34a - - 914cfcba0ec8 - - 76d290331481 + - 1ebd14235b92 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -571,10 +571,10 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - - ffd1300599a1 - d0d4cef4f967 - c6334cb383ff + - 0db979fead3a + - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -587,9 +587,9 @@ tools: owner: iuc revisions: - d6a479fd4281 - - bcc5f03f1900 - ba3720d7e68b - 74217fbfba4d + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -602,9 +602,9 @@ tools: owner: iuc revisions: - 478f36effca1 + - 2fb4ee002432 - c2b82a94493e - 56162e446004 - - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -616,9 +616,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - 3f4094b6a565 - fab23c3b5258 - 9ff3765e7172 + - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -630,9 +630,9 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 34a018cbee9c - 870ac06dff8e - 4687ecf0eb2d + - 34a018cbee9c - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -645,11 +645,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - c5fbddcac63a - - 33406f5a445c - - 05ab8d5e04a2 - 65e7dea767ea - 5192f657f305 + - 05ab8d5e04a2 + - 33406f5a445c + - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -662,9 +662,9 @@ tools: owner: iuc revisions: - 1fdb25a8384d - - e406ac71165d - a35cba31d904 - 6f0fb35b799c + - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -676,10 +676,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: + - c2c039e421af - 7c7fbf13aadd - - 37a1129c89d2 - 964b7efe2639 - - c2c039e421af + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -691,9 +691,9 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 24e94d84adc9 - - 1d689e4e1caf - 047c22569787 + - 1d689e4e1caf + - 24e94d84adc9 - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -706,8 +706,8 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 - 3a4ac03d1266 + - 04bb8bb7c198 - 9871104ea630 - 1812dbc5bb7b tool_panel_section_label: RNA-seq @@ -733,15 +733,15 @@ tools: - name: trinity owner: iuc revisions: - - cee61b3fcf78 + - d2bc35f3d1c5 + - 8f1c3df4dd49 - db1f362cca3e - - 9fa24d5aac68 + - d84caa5a98ad - 32b86cd8eb50 - 48636f857c4b - - 8f1c3df4dd49 - - d2bc35f3d1c5 - - d84caa5a98ad + - 9fa24d5aac68 - c9cfec002f71 + - cee61b3fcf78 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -753,10 +753,10 @@ tools: - name: trinotate owner: iuc revisions: - - 2b093007fab9 + - 6fd16fad465d - 4383070d29ed + - 2b093007fab9 - 9e61bc67866f - - 6fd16fad465d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index 855b567e3..a0868c72e 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -3,8 +3,8 @@ tools: owner: nilesh revisions: - 1a052c827e88 - - 27e16a30667a - 080fd5739bb4 - 473382134e56 + - 27e16a30667a tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index f710d3524..b013b0844 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 88eedb4abea0 - 10184eaa85fc - 3c661e57a88f + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,9 +16,9 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 108db6635177 - - 1dfd95ee241e - cb20f99fd45b + - 1dfd95ee241e + - 108db6635177 - 993b19f20c76 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 19ece8afbaab - - e7fd6754d093 - 5f8e69cc4c6e + - e7fd6754d093 - 30a201c9c310 + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -97,8 +97,8 @@ tools: - name: qualimap_multi_bamqc owner: iuc revisions: - - 17b35d23731f - e38af83df163 + - 17b35d23731f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -149,9 +149,9 @@ tools: - name: samtool_filter2 owner: devteam revisions: + - 56c31114ad4a - 649a225999a5 - dc6ff68ea5e8 - - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -163,9 +163,9 @@ tools: - name: samtools_bedcov owner: devteam revisions: + - 12749212f61b - 6856f8a01905 - 9149ad20699a - - 12749212f61b - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,8 +178,8 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 92ec40abcdcf - 33208952b99d + - 92ec40abcdcf - 26b4f9f98aca - 06dc50b7b711 tool_panel_section_label: SAM/BAM @@ -205,11 +205,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - b3d99709fe1a - - a8d69aee190e - 66e23b11feae - - b906586a6596 + - a8d69aee190e - 720217c23995 + - b3d99709fe1a + - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -228,11 +228,11 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - cc61ade70eb8 + - fe34990e5ce7 - fefd89ab563c - - 22970df7a40e + - cc61ade70eb8 - db17d5321bad - - fe34990e5ce7 + - 22970df7a40e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,11 +244,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - 811fc2d75ad4 - 88b8c2916784 - - 7def34e6cf4d - 7a6034296ae9 + - fa5d3e61e429 + - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -260,28 +260,28 @@ tools: - name: samtools_markdup owner: iuc revisions: - - a389f74c3630 - 40fa6c240105 + - a389f74c3630 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - b40e2d865d52 - 36677f429310 - 740ce0a18f0d - - cae2794d2deb + - b40e2d865d52 - 65a38e8c8e2a + - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - b61f5d6a7f25 - 583abf29fc8e - 9da0311ab1dd - - fa7ad9b89f4a - 329deb17a9f7 + - b61f5d6a7f25 + - fa7ad9b89f4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -293,8 +293,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -306,9 +306,9 @@ tools: - name: samtools_reheader owner: devteam revisions: - - db000c6007a0 - - 85e38b31e8b3 - 30388d878f81 + - 85e38b31e8b3 + - db000c6007a0 - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -327,9 +327,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - a4a10c7924d1 - b8beef827165 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: + - d54a4df48867 - cab3f8d35989 - e613c1ad4c4c - 6c2c1836728b - - d54a4df48867 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,12 +356,12 @@ tools: - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd - 818030fa6bbf + - 135c85f4cfaf + - bd850490c7f1 - 5d9ae78f34d3 + - b7f7826ef1cd - bcedabb53ddf - - bd850490c7f1 - - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: + - 541082d03bef + - 5a08c09b9311 - 1cc79f49b8d5 + - 24c5d43cb545 - 145f6d74ff5e - - 5a08c09b9311 - 3a0efe14891f - - 541082d03bef - - 24c5d43cb545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - 32dc5f781059 - - c370440f901e - - 350bbc5c2ffd - - 2dce91e11ca7 - - 6be888be75f9 + - b72793637686 - 0dbf49c414ae + - bf328cec6a42 + - 6be888be75f9 + - 350bbc5c2ffd - b01db2684fa5 - - b72793637686 + - 2dce91e11ca7 + - c370440f901e + - 32dc5f781059 - 5826298f6a73 - - bf328cec6a42 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.gvl.org.au/send_data.yml b/staging.gvl.org.au/send_data.yml index 5ba1aa53a..b4ce72ad6 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: - - ea5e944f447d - - 6f6537780379 - - d147d6455873 - - 59bb6d34fca6 - - 480d9e9d156b - 4aab5ae907b6 + - 6f6537780379 - a62c4a11a67d - 5cb6146337d8 + - 59bb6d34fca6 + - ea5e944f447d + - d147d6455873 + - 480d9e9d156b tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index 38e680d89..ae3c0c7c6 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,33 +8,33 @@ tools: - name: alevin owner: bgruening revisions: - - e4c01dcece8b - e32b215b7c04 - - f2000bc73102 - - c9944a2600f1 + - e4c01dcece8b - b0fe3e482cb7 - ecb9ea6269ee + - c9944a2600f1 + - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - e1c3c2f2a834 + - c0b037b12765 - 7a6655aa6eb2 - 707023fa62fe - - c0b037b12765 + - e1c3c2f2a834 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - cfc3f5a57dc6 - - 00712416fdaa - - 32e547223c9e + - 6f143dfe902a - 55e35e9203cf + - 32e547223c9e - 93dd15e13e6a + - 00712416fdaa + - cfc3f5a57dc6 - fb9e030ffae4 - - 6f143dfe902a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -46,13 +46,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 14c576ea6148 - - ee98d611afc6 + - 39e945f0b2c1 - 6f0d0c784f09 - - 038e32885fec - b9fac48532eb - 688357ad5e61 - - 39e945f0b2c1 + - ee98d611afc6 + - 038e32885fec + - 14c576ea6148 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -64,13 +64,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - ed4996a16f7f - - c4209ea387d4 + - d4af736e7b83 - 9bd945a03d7b + - c4209ea387d4 - b85871dd69f9 - 3d748954434b - 43cb7b5a6fe7 - - d4af736e7b83 + - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -82,45 +82,45 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: - - 2e8022f1923c - - fe75d2414dc0 - a4774b7b2e85 + - fe75d2414dc0 + - 2e8022f1923c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - 769d815e4b0d - - 0e70b2dfe4be - 02b1fe7aed76 - 4fff5a293013 + - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf - - a90f8efe08b4 - aa4a6f0916b4 + - c29e7bb492bf - 344c2af50552 + - a90f8efe08b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - b13d3e4c48e1 - - 5b7c81b35b89 - - 050cf43887d3 - c32347702e12 + - 050cf43887d3 + - 5b7c81b35b89 + - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - ae969fdb8442 - 1d77986f9ddc - 239193b96d72 - 02fc39c8610d + - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -156,11 +156,11 @@ tools: - name: dropletutils owner: iuc revisions: - - cfe1e6c28d95 - - 2c1200fba922 - - a9caad671439 - 8855361fcfc5 + - a9caad671439 + - 2c1200fba922 - cdf4443d5625 + - cfe1e6c28d95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -197,15 +197,15 @@ tools: owner: bgruening revisions: - 952abbc4b1de - - 01c37e54e86e - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - f1c35f3f310d - 9d42a6133690 + - f1c35f3f310d - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -213,24 +213,24 @@ tools: owner: bgruening revisions: - cab616fe7e64 - - 163fd744e235 - 23b8d6b8960c + - 163fd744e235 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - 013e53ccc7ac - b9ab56aecd18 - f47ac4a0b337 + - 013e53ccc7ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: + - 9ea228a9afc8 - b892fa1fcaec - a63e9713c39d - - 9ea228a9afc8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions @@ -244,65 +244,65 @@ tools: - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: + - f963c251ac77 - c354255ff705 - 9d02f1819e81 - - f963c251ac77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - c4ed35f4f77f - f881c94fb3b3 + - c4ed35f4f77f - 40fee49bc6c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - e06265d204f6 - - 782bdcb775fb - 2dccb6bb0add + - 782bdcb775fb + - e06265d204f6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: + - f0216498a666 - b05f662f9f35 - 63c8377c58b3 - - f0216498a666 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - c72fa6cb8817 - fe3aa71590d5 - 8a11d70b6cd8 + - c72fa6cb8817 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - e03780179ee5 - - 3ee5332bf57c - 4f9305d3bb34 + - 3ee5332bf57c + - e03780179ee5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - 4401ed529d2c - - a315574104c6 - 3a6a5381db36 + - a315574104c6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - c0737631eea1 - - a83732c79949 - 2ba6cee8e4db + - a83732c79949 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix @@ -316,9 +316,9 @@ tools: - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - cd40ca76865a - - 2786a931cad2 - 2b4d6a8dab36 + - 2786a931cad2 + - cd40ca76865a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops @@ -333,15 +333,15 @@ tools: owner: bgruening revisions: - 77d8e0fd162a - - 07dd436ea686 - 5dfba24d7bdd + - 07dd436ea686 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 972dcccb5bbc - f1b3902f8baf + - 972dcccb5bbc - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -356,9 +356,9 @@ tools: - name: hicexplorer_hicinfo owner: bgruening revisions: - - b0f33533181d - e4f8fceab96a - 51e40e9b6c3c + - b0f33533181d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad @@ -372,17 +372,17 @@ tools: - name: hicexplorer_hicmergedomains owner: bgruening revisions: + - 4b194e675916 - b376ef118807 - b6b8c8672756 - - 4b194e675916 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - 1511a8ebe906 - - 910c6a1c3a27 - ed900cd4a0a9 + - 910c6a1c3a27 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize @@ -397,23 +397,23 @@ tools: owner: bgruening revisions: - ea5d67ec94ab - - dd9988943f53 - 9b383d429659 + - dd9988943f53 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 6326cd29c1c3 - 11f39d7f6c64 + - 6326cd29c1c3 - 06ced663d24f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - 337705015ee8 - b4e780e93c91 + - 337705015ee8 - beb5b5917d2f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -428,17 +428,17 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - - 5cbd7a902a8d - ea8fb5e899e8 + - 5cbd7a902a8d + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 36dfa2825a59 - f81750434d70 - 1d6af10874d5 + - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -456,28 +456,28 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - f36828ebdc54 - 27fe5cd1729c - 1de2276f633f + - f36828ebdc54 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - cef9fb4ece1c - 1d201e8378b3 + - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: + - e98619de2776 + - 4b0adaa31c95 + - 7784821452ac - db575b4c8b22 - eeab712b0b99 - - 7784821452ac - 59be31ac9dc3 - - 4b0adaa31c95 - - e98619de2776 - 0f1aaff9b22d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -491,16 +491,16 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 2cfd0db49bbc - 7ffaa0968da3 + - 2cfd0db49bbc - 48f0fb3061b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 8cd2ecfa2e61 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -526,10 +526,10 @@ tools: owner: iuc revisions: - f911a64454fb - - 49776718ae90 + - 7e014059a88d - c4f39bf4a068 - a4b734cd253b - - 7e014059a88d + - 49776718ae90 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -541,10 +541,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - d45f092caf24 - - 43c146e25a43 - 8b917923f7d4 + - 43c146e25a43 - 7608d5faee41 + - d45f092caf24 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -556,9 +556,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - 2b0d3e2f402a - - c7ddb719554d - 37a47c4fd84d + - c7ddb719554d + - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -570,9 +570,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - - df8e4e54d367 - 6e90c8adf84f + - df8e4e54d367 + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -585,10 +585,10 @@ tools: owner: iuc revisions: - c92d0f9338c5 - - 2bfd55b87af3 - e93b008c637a - - 72979cac22b2 + - 2bfd55b87af3 - 44b935f2271b + - 72979cac22b2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -612,17 +612,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 6acb08931836 - - 77b91b9bdf52 + - 6f83f8fd381f + - b2df381a6004 + - aaa5da8e73a9 - 38db3fef7aad + - 4d8f983cd751 + - 77b91b9bdf52 - edec35114f72 - - aaa5da8e73a9 - - 6f83f8fd381f - - f9353ee6a0d4 - 8983e7a04ba7 - - 4d8f983cd751 - - b2df381a6004 + - 6acb08931836 - cb43c5d3acd3 + - f9353ee6a0d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -634,15 +634,15 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 64388be6d510 - 8cb783c81905 - - b409c2486353 - - a97abb8cd15b + - d636ce5cde16 - fc0321c000a3 - 72a6bebab2a5 - - d636ce5cde16 + - 64388be6d510 - 277313130da5 - a03ff8633507 + - b409c2486353 + - a97abb8cd15b - 3c86f71498bc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -655,17 +655,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: + - c0a80a16560f - 18262103fa61 - - 5c3ebe2adc77 - - 5e9171dc8244 - - c5d3684f7c4c - - cc0deb593fc8 - - d86cb2ce311b - f54f0f0598ad - - 3081ff5c84a3 - - c0a80a16560f + - 5e9171dc8244 - 6bd82ed14acd + - cc0deb593fc8 - 6c145a6868cc + - 5c3ebe2adc77 + - 3081ff5c84a3 + - c5d3684f7c4c + - d86cb2ce311b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -677,17 +677,17 @@ tools: - name: scanpy_normalize owner: iuc revisions: + - 9f354c7c8c92 + - 7b9fafe32c86 + - 146ae5d70b47 - 3bcd5445cd7a + - 94c19fb1281c + - 4bda4412b8c2 + - c9cb76cf8d6c + - 56c0d4acef02 - a407e7f8bdc1 - d844935c906c - - 56c0d4acef02 - - c9cb76cf8d6c - - 4bda4412b8c2 - - 9f354c7c8c92 - ab55fe8030b6 - - 94c19fb1281c - - 7b9fafe32c86 - - 146ae5d70b47 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -699,18 +699,18 @@ tools: - name: scanpy_plot owner: iuc revisions: - - 40812a65a78b - - 6f5349dd5c49 - - f7446fd8d5e7 - - 95777145cb92 - - 0185bd174ea0 + - dbbe1ea8ecb1 - 6adf98e782f3 - - 7647e5cd1b8b + - aa0c474463c2 + - 0185bd174ea0 + - f7446fd8d5e7 + - 9b0cdb8cf6be - 62acdd96d4a0 + - 6f5349dd5c49 + - 95777145cb92 - 1072ce66b426 - - 9b0cdb8cf6be - - dbbe1ea8ecb1 - - aa0c474463c2 + - 40812a65a78b + - 7647e5cd1b8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -722,17 +722,17 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - f2f6c703da06 + - a39040ae0a38 - 9fb627495ec2 - - c65fce500915 - - bf2017df9837 + - d18e7a6e5cd4 - fe8f16c594ec - - c5541bfb8feb - 73ab2ac53d06 - - 458e8f43a775 - - d18e7a6e5cd4 + - f2f6c703da06 + - c65fce500915 + - c5541bfb8feb - 215733a383f2 - - a39040ae0a38 + - bf2017df9837 + - 458e8f43a775 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -744,9 +744,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - - b834074a9aff - fd808de478b1 + - b834074a9aff + - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -778,8 +778,8 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - ef4c80837bc5 + - 2e41b35b5bdd - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -799,8 +799,8 @@ tools: owner: iuc revisions: - c99ba278dfa9 - - 46fc6751d746 - 9e5c0bb18d08 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -1049,16 +1049,16 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: + - 64fa083411f1 - 588c811fdd48 - 88192fe25375 - - 64fa083411f1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - 05bd4db20227 - fecf9664c885 + - 05bd4db20227 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 3a2cf45e0..d668d08cf 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -34,30 +34,30 @@ tools: revisions: - 746e8e4bf929 - 4c07ddedc198 - - 562f3c677828 - 2f3c6f2dcf39 + - 562f3c677828 - 419027d822d6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -70,8 +70,8 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - 6c29c7e347e8 - cb1c59d69557 + - 6c29c7e347e8 - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 4c4ec859c31a - 840f29aad145 + - 4c4ec859c31a - 7442b94d6a1e - - b1eda492f063 - aef56d0e7a61 - 9c3e1d3235c8 + - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 07843f917990 - - 30d21a6041f6 - 9fda0b82f419 - d0352e8b4c10 + - 07843f917990 - 375bbd555f4a + - 30d21a6041f6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 4cc980df6265 - 2c58b83c9bad - - 8b1b2b91f8d0 - - cd02bf168d23 - 7ae443e6217d + - cd02bf168d23 + - 8b1b2b91f8d0 + - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - e10e776f2109 - - 7dd3fb35904f - - 1dd433d2c92c - 4bbaf77573ef - - ad7e0b4291ee - bb9fc9d46ea4 + - 7dd3fb35904f + - e10e776f2109 + - ad7e0b4291ee + - 1dd433d2c92c tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index f4695e002..227445c45 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -27,22 +27,22 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: + - 464b9305180e + - 13b6f0007d9e + - be25c075ed54 - aff5135563c6 - 6595517c2dd8 - - 464b9305180e + - 9cd341095afd + - 02026300aa45 - 626658afe4cb - 6e8d94597139 - - 02026300aa45 - - be25c075ed54 - - 9cd341095afd - - 13b6f0007d9e tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -54,8 +54,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 6f54dc6b37da - 3a4694d4354f + - 6f54dc6b37da tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -79,9 +79,9 @@ tools: - name: filter_tabular owner: iuc revisions: - - 557ec8d7087d - - 34d29339abab - 37cde8134c6a + - 34d29339abab + - 557ec8d7087d - 90f657745fea - 9cc411a62277 tool_panel_section_label: Text Manipulation @@ -107,29 +107,29 @@ tools: - name: merge_cols owner: devteam revisions: + - ae7843d06f8f - f2aac0c5c60d - dd40b1e9eebe - - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 1ea4e668bf73 - - cf34c344508d - - 33d61c89fb8d + - 623f3eb7aa48 - 83069b38aa85 - 2e8f945f7285 - - 623f3eb7aa48 + - cf34c344508d - 3a6b78c39dca + - 33d61c89fb8d - cf4397560712 + - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 503bcd6ebe4b - 399da6b5ec21 + - 503bcd6ebe4b - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -142,31 +142,31 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - c4d18aa4ec4a - - bce29ec10b78 - b722161a845a - f768f6183386 + - bce29ec10b78 + - c4d18aa4ec4a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 60ff16842fcd - 3bf5661c0280 + - 60ff16842fcd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - 86755160afbf - - d698c222f354 - - 0a8c6b61f0f4 - - a6f147a050a2 - fbf99087e067 - - 12615d397df7 - - 9ff72e942410 - - f46f0e4f75c4 + - 0a8c6b61f0f4 + - d698c222f354 - ddf54b12c295 + - 9ff72e942410 - 74a8bef53a00 + - 86755160afbf + - f46f0e4f75c4 + - a6f147a050a2 + - 12615d397df7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index f42132e8c..7760d5d72 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -15,8 +15,8 @@ tools: owner: iuc revisions: - 0d18a3ba2d1c - - 85c57cc9b558 - 82fb5e3bb93e + - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -28,67 +28,67 @@ tools: - name: cutesv owner: iuc revisions: - - c0f8fe52948e - 23d7e75d850e - cb441f258c37 + - c0f8fe52948e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: - a5937157062f - - 57def2d7c093 - ef2c525bd8cd - - 04fa42777df9 - 156b60c1530f + - 57def2d7c093 - 3e954e7125bf + - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 09d6e4693887 - e61c9ac190ad - - 435b157bed6d - 791f73caa0c8 - - 09d6e4693887 + - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 3b4b2121842f - dfadc322b065 - - 03627f24605f - 4805fe3d8fda - 65432c3abf6c - - b11e8e9c23bf - 074d44697036 + - b11e8e9c23bf + - 3b4b2121842f - e1461b5c52a0 + - 03627f24605f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 9cb929f21cfa - 701d134358ad - 7dfca164d2e3 - - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 - - c27549b9aa1f - f4473557ffc7 + - 426d707dfc47 - 971e07ca4456 + - c27549b9aa1f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - dbd9f2db9ed8 - - cdaab621d454 - aa35ee7f3ab2 + - cdaab621d454 + - dbd9f2db9ed8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -100,18 +100,19 @@ tools: - name: sniffles owner: iuc revisions: - - 43fffeed243f - 93c4b04a0769 + - ceff2f6a5368 + - 43fffeed243f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: - - 5bbf9eada9c2 - - c9a8ef2aa380 - 9bccc8404a3c + - 5bbf9eada9c2 - fa016f1eea1a - d220115f882b + - c9a8ef2aa380 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -153,21 +154,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 32f14a2723ec + - 40f0591deda0 - e7aff4a85df5 - ee4a90760848 - - 40f0591deda0 - 3b1e7c170b10 + - 32f14a2723ec tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - adc0645b945c + - 42818629ec4c - 9793bc5d741b - - 02d81b994ef5 - 4934c0ac6197 - - 42818629ec4c - - adc0645b945c + - 02d81b994ef5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 1ea56721e..881130939 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,14 +2,14 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - e075b1be5abb - 6a88248893c4 - b7ea370b8f5d - - 265fe0f9ea64 + - 8a2e296c07ef + - 2c372041ed8c + - e075b1be5abb - ebe5fc018e72 - 95815a0bb307 - - 2c372041ed8c - - 8a2e296c07ef + - 265fe0f9ea64 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -22,12 +22,12 @@ tools: owner: iuc revisions: - 21687e35f066 - - b03984136ce4 - - 1001172b5089 + - c37b684e7f4e - 0fba2c15b40d - - 22637b1a55bf + - 1001172b5089 - 544cb432072b - - c37b684e7f4e + - b03984136ce4 + - 22637b1a55bf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,15 +39,15 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - ccb83bf54de0 - - 0238f68ad641 - - 8627b2b383b4 - - bf1f4994f104 - - 01d6b7d6365e - - 3a7084316a6e - 8408bffd5616 + - 3a7084316a6e + - 8627b2b383b4 - 8ca3647c90fd + - 01d6b7d6365e + - ccb83bf54de0 - 143796b504eb + - bf1f4994f104 + - 0238f68ad641 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,13 +59,13 @@ tools: - name: bcftools_concat owner: iuc revisions: - - 62ca6da715bf - - f430a1ec7ee4 - 6b6c992d3a14 + - 62ca6da715bf - 03e0645395d2 - - abd489215f73 - 81426b3cf18b + - f430a1ec7ee4 - d144af39073a + - abd489215f73 - 9b5abbf50d23 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - 1829900b5dcd - d3081540d175 - - e522022137f6 + - d37e313a41be + - 1829900b5dcd - 2363ef414c9b - - 95c6f3f4c77f - 1171446da5db + - 95c6f3f4c77f + - e522022137f6 - 8aa352093d73 - - d37e313a41be tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,13 +97,13 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 09f37afb3621 - - 1137ce8efc1e - - 012656fd329f - d58d2e8c7a57 - - 348cd212dbad + - 1137ce8efc1e - b14ff40958cb - 92c0aff8b53e + - 348cd212dbad + - 09f37afb3621 + - 012656fd329f - 9b29129fb491 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - 1f2183a23823 + - de68c11034f6 - cfd81f17580b - - 7291189e98b4 - - 55c0e906c14c - 367ba501b6eb - - de68c11034f6 + - 1f2183a23823 + - 55c0e906c14c - ecc9192912b8 + - 7291189e98b4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,13 +134,13 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 039ea3f1dea9 + - e6f4badbe6f3 - 7cbf3c66d4ad + - 039ea3f1dea9 - 6c790a091c7c - - d237eaef451f - ae68ceb4cca3 - 64a8f7dae3ad - - e6f4badbe6f3 + - d237eaef451f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -152,13 +152,13 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 33bd9301568c - - 963a3635b2e1 + - cdb7b4927742 + - 6ea7170a016d - 277719af4dd7 - 5d6653c989cb - - 6ea7170a016d + - 33bd9301568c - 46fcafba49ec - - cdb7b4927742 + - 963a3635b2e1 - e7452697afd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: + - 91c1e57d5c7f + - a29a2f40b665 + - a1213a0b7b66 + - 26d97cdd5410 - 501bfb078342 + - b7f0f59baa7e - 5a321fab1fe4 - - a1213a0b7b66 - 7b4454382d39 - - b7f0f59baa7e - - 26d97cdd5410 - - 91c1e57d5c7f - - a29a2f40b665 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 39bca000353d - - 5f27e814a119 - - d7d1663559e9 - c803c34361e0 - - 81e4014fa809 - - 768d04526638 - 15da1ddcfeff - - 97d19c008d15 + - 39bca000353d + - 5f27e814a119 - 709dd8291b83 + - 97d19c008d15 + - 768d04526638 + - 81e4014fa809 + - d7d1663559e9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -210,14 +210,14 @@ tools: - name: bcftools_merge owner: iuc revisions: + - b931e65638b8 + - b1eba148b35b + - 85ee7e6c4204 - 5b006286a458 - - 2215287d5cc9 - b84fda8ebef0 - 86296490704e - - 85ee7e6c4204 - - b1eba148b35b + - 2215287d5cc9 - 7ba36babba2d - - b931e65638b8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -229,16 +229,16 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 0a5dcc9a8ec2 - - 31ea13dfe5e6 - 4e1d23e5c691 - - 9c711df3258d + - 37757ffb4c5f + - 31ea13dfe5e6 - ce9396ddcb2b - - 56556e1267de - - 5660b21a0dbd - f506df85c652 - - 37757ffb4c5f - cf06b44624c7 + - 9c711df3258d + - 0a5dcc9a8ec2 + - 5660b21a0dbd + - 56556e1267de tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -250,13 +250,13 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 271965b55437 - - a404f786a94c - 021693fdadaa - - 6deb4d549bc9 - 1ca7418e46ee - - 19905c025d2a - 48291658fdf6 + - 6deb4d549bc9 + - a404f786a94c + - 19905c025d2a + - 271965b55437 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 69d8b7567281 + - 71c78e0eea52 + - 3f6fadf8b8ff + - f7879f1e77f9 + - c450406f722b - dadbd61dc4cf - 97e8145d7e30 - - f7879f1e77f9 - - 3f6fadf8b8ff - 5ad5d4243987 - - c450406f722b - - 71c78e0eea52 + - 69d8b7567281 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,14 +287,14 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 2514e684f8a3 - d31a2e310a52 - - 283911fe7e1a - - cc7f9a4e186b + - 0fe007201caf - 79f7a1acc2cd + - 2514e684f8a3 + - cc7f9a4e186b + - 283911fe7e1a - 6cf13a657cf6 - 52f9e4a660e3 - - 0fe007201caf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 6963a6841d22 - - a12844ca467a - - 0a62420cb9cd - - 80e6e399ccd0 - 75ddd081f608 - - 026a989b7cee - - 230e424bde67 - 1411bef27a75 + - 80e6e399ccd0 + - 230e424bde67 + - 0a62420cb9cd + - a12844ca467a + - 026a989b7cee + - 6963a6841d22 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - 450a265f92e8 - - 5808f77b2bb6 - - b10d1510fa84 - - 444e6a756c35 - 5acfca5a76af + - 450a265f92e8 - bca7ce81688f - - ba20340426fe + - b10d1510fa84 - e493702b19eb + - ba20340426fe + - 5808f77b2bb6 + - 444e6a756c35 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -344,14 +344,14 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - c43399f161f4 - d52b8947b269 + - dd72ff87cfd0 + - 157ffcdd3fa7 - f2482aa4862e + - 12152af85697 - 4d236c696844 - 68fec03a63b7 - - 157ffcdd3fa7 - - dd72ff87cfd0 - - 12152af85697 + - c43399f161f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -363,13 +363,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: + - 8dbce095986c + - 0e5d11004815 - 6f8e223f78f3 - - 29ba253e2e05 - 75becf493cd3 - - 8f2fc0ab30fb - - 8dbce095986c - cbe39e530cbf - - 0e5d11004815 + - 29ba253e2e05 + - 8f2fc0ab30fb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -381,14 +381,14 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 9708e3086f32 - - f544f71adb73 + - e0a856def0b0 + - 88bb477f45f7 - 3ff5654b4e7d - a367a15c6de5 - - e0a856def0b0 + - f544f71adb73 - 8f5962c43868 - a8630d4fbaf8 - - 88bb477f45f7 + - 9708e3086f32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -400,14 +400,14 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 4ed46189d6c6 - - 34dc0bbc7e93 - - 96d0145c041a + - 8b260d252ff4 + - 6ce175385dd9 - 03e30f06f15f - 5c9729d54721 + - 96d0145c041a + - 34dc0bbc7e93 + - 4ed46189d6c6 - 31c096c6b156 - - 8b260d252ff4 - - 6ce175385dd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -419,14 +419,14 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - a1aad8b559c6 - - 46eb13bc2c73 + - 11af7fce71cf - a730269af659 - - 09f5e45a8212 + - 681bdf1e22ff - 2c4941386820 - - 11af7fce71cf - 40daf124be88 - - 681bdf1e22ff + - 09f5e45a8212 + - a1aad8b559c6 + - 46eb13bc2c73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -439,13 +439,13 @@ tools: owner: iuc revisions: - 0594ea1417c8 + - 12038f59c0f4 + - 3897eaadfbff - f272b8ba0983 + - 8cb121b6a1d2 - 743cd1472aeb - 6cbb9c47795c - - 3897eaadfbff - - 12038f59c0f4 - b74b8cbfc1f1 - - 8cb121b6a1d2 - 882b2e649602 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -458,13 +458,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - 18cf9de1cf73 - adee7e8b746f - cced6715f926 - - dba06328556a - eccb508bb678 - - 238f78e38a8b + - 18cf9de1cf73 - a9826db86d9a + - 238f78e38a8b + - dba06328556a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -476,13 +476,13 @@ tools: - name: bcftools_query owner: iuc revisions: + - 9f36041495a3 + - e53501abf992 + - 3ce32adc55b2 - f64e7ca2efd2 - c9935c9e8a24 - - e53501abf992 - - 31a1b89eab9b - fdec14f69010 - - 3ce32adc55b2 - - 9f36041495a3 + - 31a1b89eab9b - e0ad88dec40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: + - d68c43202172 + - 4db0695a6fc7 + - 3b7b1fe7b937 + - fd3539749127 - d43eb39b989e + - 79489d5685dd - 2331ddcbd5aa - - 4db0695a6fc7 - b7be725976b6 - - d68c43202172 - - 79489d5685dd - - fd3539749127 - - 3b7b1fe7b937 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,13 +514,13 @@ tools: - name: bcftools_roh owner: iuc revisions: + - 78cd8b69da4c + - 58091e1be01b - 1a989b4110da - - 6a636d58dfc2 - 5296d26b0373 - - b0d39ef600a7 - 1ccf0e7fb4f6 - - 78cd8b69da4c - - 58091e1be01b + - b0d39ef600a7 + - 6a636d58dfc2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -533,13 +533,13 @@ tools: owner: iuc revisions: - 591cc8518033 - - b641062a2587 - b17394940c7a - '388983871932' - - baa8823f8073 + - 4d3ce9dc1525 + - b641062a2587 - bf8325a07ce7 - e8af591435d1 - - 4d3ce9dc1525 + - baa8823f8073 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: - - c2ab91a0d506 - - e6b5cbbf449b + - 3ca3de4e5291 + - 59fa8742285e - 3a233c8eb814 - 38d75661c235 - d1f8f55f564d - 1a2ef636f48e - - 3ca3de4e5291 - - 59fa8742285e + - c2ab91a0d506 + - e6b5cbbf449b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -584,15 +584,15 @@ tools: - name: vcfallelicprimitives owner: devteam revisions: - - 57a16b310fe8 - a8a4f94aa321 + - 57a16b310fe8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 01e0321aca98 - 6faa2c4c71d2 + - 01e0321aca98 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -605,8 +605,8 @@ tools: - name: vcfbedintersect owner: devteam revisions: - - 9edfe5145ba8 - aea8e90ad788 + - 9edfe5145ba8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -619,59 +619,59 @@ tools: - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine owner: devteam revisions: - - 53edb91ed051 - 1f0ba67cc85a + - 53edb91ed051 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples owner: devteam revisions: - - 254f285dbaaa - f1852ecef841 + - 254f285dbaaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - fa24bf0598f4 - eae7c08ebb6f - - 6b935ab36d7b - 4bdc111b2470 + - 6b935ab36d7b + - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten owner: devteam revisions: - - b24e368ae7b1 - f285aa6bdcfb + - b24e368ae7b1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes @@ -684,29 +684,29 @@ tools: - name: vcfhethom owner: devteam revisions: - - b07ef36cf7e6 - 8254e0fe7358 + - b07ef36cf7e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign owner: devteam revisions: - - d2406f98a782 - 29f9b782727e + - d2406f98a782 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers owner: devteam revisions: - - d226a7327946 - 17096387c0e6 + - d226a7327946 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample owner: devteam revisions: - - 12b570dd0bc5 - 6257ee3b50d3 + - 12b570dd0bc5 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples @@ -719,9 +719,9 @@ tools: - name: vcfsort owner: devteam revisions: - - f0580efedada - ee60203e68d9 - 5b7120c66efc + - f0580efedada tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate @@ -751,7 +751,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 166c4f50525f - 6f6bf10618d7 + - 166c4f50525f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/viral_tools.yml b/staging.gvl.org.au/viral_tools.yml index 06370d956..15250eab7 100644 --- a/staging.gvl.org.au/viral_tools.yml +++ b/staging.gvl.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 18aad692772a - 9def47f3c1e4 + - 18aad692772a tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 4f6fe131e..c5195c086 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -3,17 +3,17 @@ tools: owner: iuc revisions: - 78c75f134c16 - - 6e9aea89e388 - 3f3e247c053d - c2ef298da409 + - 6e9aea89e388 - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - 3f438bf5475d - c45c9dd066e2 + - 3f438bf5475d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval @@ -33,46 +33,46 @@ tools: - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - cd2480f35935 + - 3e1f6f6d557e + - 1aae04680c4b - f29602ae449e + - cd2480f35935 + - 44018dd6b447 - a79ee60b6926 - fe3ca740a485 - - 4f2967b27e67 - - 3e1f6f6d557e - b5d8e5475247 - - 44018dd6b447 + - 4f2967b27e67 - 133f36c29579 - - 1aae04680c4b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - - 6519ebe25019 - - f1e653756174 - 7be22100e5e1 - dc027fa56d55 + - f1e653756174 + - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 28433faa6e42 - bd0e53f3a891 + - 28433faa6e42 - ca6d970d931c - 09855551d713 tool_panel_section_label: Annotation @@ -81,9 +81,9 @@ tools: owner: iuc revisions: - da5f1924bb2e - - 92eee5f31117 - - 728dacaf08a9 - d77802fe76f7 + - 728dacaf08a9 + - 92eee5f31117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap @@ -116,9 +116,9 @@ tools: - name: cpat owner: bgruening revisions: - - 7ccc6234b54e - 1ac12c0cc7a0 - 8e9e228c54c4 + - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper @@ -156,60 +156,60 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 756376aeb1ae - 3bbe70fef6df + - 756376aeb1ae + - 582fd74dc2a1 + - 9c15ca7e764e - b6b5cd37f2a2 - 9f2455341fac - 14f588312c56 - - 9c15ca7e764e - - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 8e1ace8f77c6 + - 30fb23d4c31c - 73428a792541 + - a230ea445788 + - 8e1ace8f77c6 + - 989f7c061f35 - 1691af4a0d17 - 0ffe5be70caf - - 30fb23d4c31c - - 989f7c061f35 - - a230ea445788 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 563a19373357 + - 30f08d74024f - e94187d661df - - 494f0bb4a993 - 57c6718cbfcc - - 0418d28136de - 5a5ae61da69c - - 30f08d74024f + - 563a19373357 + - 494f0bb4a993 + - 0418d28136de tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: + - f77d7b685bb3 - f31125bb85ea - d6c7106b7b2e + - 4b96ced19f75 - 7abc5f6dd595 - - f77d7b685bb3 - 2bba2ff070d9 - 1bc5a03faf2e - - 4b96ced19f75 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - 52af33194019 - d3af38b9c7e1 + - b3cf4684e9c7 - d77fdcca400e - - 520e30695ec3 - - 52af33194019 - 54961e026fe4 - - b3cf4684e9c7 + - 520e30695ec3 - fed64e676186 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -236,10 +236,10 @@ tools: - name: goseq owner: iuc revisions: - - ef2ad746b589 - 8b3e3657034e - 602de62d995b - 43798b4caee0 + - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -271,8 +271,8 @@ tools: owner: bgruening revisions: - 74810db257cc - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -305,11 +305,11 @@ tools: - name: mitos2 owner: iuc revisions: - - 624606f7c996 - - c8ac28e8ac44 - - e95d52d295d7 - 033755194fe9 - b815ec682418 + - e95d52d295d7 + - 624606f7c996 + - c8ac28e8ac44 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -358,9 +358,9 @@ tools: owner: crs4 revisions: - 8a22554cdde2 + - bf68eb663bc3 - a17498c603ec - d643e3b03500 - - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -379,8 +379,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -404,30 +404,30 @@ tools: - name: snpeff owner: iuc revisions: - - 5b80f544c67f - - 68693743661e - cfcf33df7fc0 - - 5a29ab10dba6 - - 6322be79bd8e - - 268d162b9c49 - - ca2b512e8d7c - 8f92c2b26e6d + - 5a29ab10dba6 + - 68693743661e - 5c7b70713fb5 + - 268d162b9c49 + - 5b80f544c67f + - 6322be79bd8e + - c7275bd8b4d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: + - 2b3e65a4252f - 5fab4f81391d - 09d6806c609e - - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -439,24 +439,25 @@ tools: - name: tbprofiler owner: iuc revisions: - - e1a9d6fd258d - - ac8250086ac3 - - 200c378d85f3 - - 809dfc93d593 - - 037a11682176 - 51dd22484644 - ba6f87115e13 - - 37213cf56392 + - 200c378d85f3 - 4839e590cb26 + - 037a11682176 + - 809dfc93d593 + - ac8250086ac3 - 45083d070fb8 + - 37213cf56392 - d03af1c7002c + - e1a9d6fd258d + - 8cb134b8c1a5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index e1686d05f..1962c83ad 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,44 +2,44 @@ tools: - name: abyss owner: iuc revisions: - - 0124fce4654a - - 8f1b150a2487 - - 7547fcab5d19 - 890b794c997d + - d6d5ccc2c581 - fa5259cc561b + - 553bfe8bd0b5 + - 0124fce4654a + - 841084c5fc46 - a929ce596a34 + - 8f1b150a2487 + - 7547fcab5d19 - 0e93176640ac - - 841084c5fc46 - - 553bfe8bd0b5 - - d6d5ccc2c581 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b9e31c5c01c7 - b2860df42e16 + - ddddce450736 - 21e491ad532a - 067592b6b312 - - ddddce450736 - 94fe43e75ddc + - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 321347bd0494 - 25ca5d73aedf + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - 5258e18bbe23 - 3371c5bdc17a - 22286dab5aa1 - - faee8629b460 - a7f16f24e9a1 + - faee8629b460 + - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -47,36 +47,37 @@ tools: revisions: - 8c2167481e72 - 53dd00a4ab68 + - '392811378515' tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: + - 4048d82f0c88 - 41030a6c03b7 - - 2babe6d5c561 - - bb935709506a + - 5ecdeca79a0d - e4bd1e99bacf + - 1e62c28ba91d - ea8146ee148f - - 4048d82f0c88 - - 94170eee0ad8 - 2dd755c1c6ff - - 1440ae06552f - - 5ecdeca79a0d - - e5c372c91e46 - 46ae58b1d792 - - 1e62c28ba91d - - cf13a1e03e5b - 0d243f458b53 - 602fb8e63aa7 + - 2babe6d5c561 - e824f5d958d0 + - 1440ae06552f + - cf13a1e03e5b + - e5c372c91e46 + - bb935709506a + - 94170eee0ad8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a - 86f150c8019d - c5b7390290b1 + - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -88,15 +89,15 @@ tools: - name: flye owner: bgruening revisions: - - 1f0769f0b56b - 276f5d8712d5 - - e27815e82dd4 + - 1ce9b1d72ec3 - 8d4f03b5fe9d - - 3ee0ef312022 + - e27815e82dd4 + - 1f0769f0b56b + - 3e4f8642c77e - cb8dfd28c16f - 291923e6f276 - - 3e4f8642c77e - - 1ce9b1d72ec3 + - 3ee0ef312022 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope @@ -104,8 +105,8 @@ tools: revisions: - 01210c4e9144 - 460fad600dce - - b2f674562a18 - 3169a38c2656 + - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle @@ -120,12 +121,12 @@ tools: - name: gfastats owner: bgruening revisions: - - 5127a713de83 - - 3ef480892a9f - 3fba9c77550a + - 3ef480892a9f + - 5127a713de83 + - f4a3eff8ab85 - 6ec1b853c8fd - 690c2caa367e - - f4a3eff8ab85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -137,23 +138,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 41cea2aa2dce - - 366a11d316a7 - - 9ef6920c3089 - - f3c89da3af16 - - 284a1cb82b61 - 60024a528cbd - - 2061fb3b81b4 - - 0ee0c3089254 - - da9d8bf98802 - - 71740308d412 - - 5bec28269d95 - - 045c7c3d8e59 - - 3f7be05a1597 + - f3c89da3af16 - ec9e21e9c71b + - da9d8bf98802 + - 284a1cb82b61 - 5f625c63b8bc + - 3f7be05a1597 + - 045c7c3d8e59 + - 9ef6920c3089 + - 5bec28269d95 + - 41cea2aa2dce + - 2061fb3b81b4 - df25d4fb79b7 + - 366a11d316a7 + - 71740308d412 - 6505bd37670d + - 0ee0c3089254 - 5161f204ba63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -187,34 +188,34 @@ tools: - name: merqury owner: iuc revisions: - - d7edbc9c3a07 - - eb7b00ec347d - - 39edec572bae - - 09c589057ee8 - 9d79beb19ac3 + - eb7b00ec347d - f8113c25bc6b + - d7edbc9c3a07 + - 09c589057ee8 + - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 29dabd8db6f2 - - 51c2360aa807 - eadfd71dde37 + - 51c2360aa807 + - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - eb7a370f6588 - - 2ecf5a570907 + - 606b09cc9860 - f338e9942b27 + - 99ecfdafc64f + - f369ef5f210b - e731ea24e48d + - 2ecf5a570907 - 3ca2d2a9068c - - 606b09cc9860 + - eb7a370f6588 - fd128c111ab0 - - 99ecfdafc64f - - f369ef5f210b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -226,11 +227,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8b6d0d85252b - - 8dee0218ac7d - b799a615995d - 73a3846701e1 + - 8b6d0d85252b - a7b889b90140 + - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -249,8 +250,8 @@ tools: owner: iuc revisions: - 7c2f5268d01c - - 64a1c751d99b - 15200570e926 + - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -262,46 +263,47 @@ tools: - name: pretext_map owner: iuc revisions: - - bbe19ef04a74 - - dfb8a4497339 - - 02831bf9e95f - 2b16ba799da9 - - d256a51a656b + - dfb8a4497339 - 8fef980d48b5 - 79b48f02db49 + - c6cec5ab35c1 + - bbe19ef04a74 + - d256a51a656b + - 02831bf9e95f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - a315c25dc813 + - e9bd16ba5ebd - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 7594365c546b - - 72472698a2df - - 342a1d1fed7b - 875d0f36d66f - - 675488238c96 - - ebb0dcdb621a - 3061c8b029e5 - 59db8ea8c845 + - 342a1d1fed7b + - ebb0dcdb621a + - 675488238c96 + - 7594365c546b - 6fcbee531de6 + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - d865b62f501c - - a199cd7ac344 - cd06929b224b - - 39bed8de8017 + - a199cd7ac344 - 78c533842eeb - aa39b19ca11e + - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -313,31 +315,31 @@ tools: - name: raven owner: iuc revisions: - - 3edba9afc9bc - - f11b994b7eb2 - f8564b2d7f63 - - 33b7d8481a76 + - f11b994b7eb2 + - 3edba9afc9bc - 2b2a352488fa - 5c55448d0f33 + - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - f73ab5187eed - 8e66f695d859 + - f73ab5187eed tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - 53c2bc8c2ae3 - - 378e55aeeb25 + - 1d06c8b38e77 + - 28189050e437 - ef69617ecb42 - - e122f9101584 - 5fc94b3a4704 - - 28189050e437 - - 1d06c8b38e77 + - 53c2bc8c2ae3 + - e122f9101584 + - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -349,13 +351,13 @@ tools: - name: shovill owner: iuc revisions: - - d9f6a00b6db7 - - ad80238462c1 - ee17a294d3a3 + - ad80238462c1 - 83ead2be47b2 - - 865119fcb694 - - f698c7604b3b - 196a599ec43d + - f698c7604b3b + - d9f6a00b6db7 + - 865119fcb694 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot @@ -369,25 +371,25 @@ tools: - name: spades_biosyntheticspades owner: iuc revisions: + - 7490b213baa9 - 604782a8a53a + - c33a476f4001 + - 051fd2db8a27 - 1bb12736175c - - 7490b213baa9 - 1fc82fe7ebef - 904bf932cf78 - - 051fd2db8a27 - - c33a476f4001 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 655fa188c3cc - - d6e617c4e338 - 9678993ca5bd + - d6e617c4e338 - 808b3a0a6716 + - 655fa188c3cc - fee85957cebe - - 34305b013402 - ad8b536d1caa + - 34305b013402 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades @@ -395,10 +397,10 @@ tools: revisions: - 21da31ed41a1 - 037f9927c4ff + - b8002c3f7141 - 8d4b90bf9caf - - 6b5a5842531e - e5a3b75a271f - - b8002c3f7141 + - 6b5a5842531e - 7e27faaad80e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -406,134 +408,131 @@ tools: owner: iuc revisions: - 5b26685e5d3b - - 9de69775f512 - - f1532cb33c75 - - 7922870efcca - 328aa71f0f3c - 86f66ab58e14 + - 9de69775f512 + - 7922870efcca - 2a10645aeadd + - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 340bc17f49cf - - 8cc856b935ee - 6aad515a5270 - 1708851f8804 - - 85fb02c43042 + - 8cc856b935ee - e41dcb0e913b + - 85fb02c43042 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - d5fb354f745d - - de1260f8a300 - d159735a6a9f - b3490b036c5a + - de1260f8a300 + - d5fb354f745d - 6357b127161e - - 249f6a28c751 - b65a43f70b99 + - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - 7897763d14ec - - 33368fec3b70 - - a90db5dbaaf3 + - 9006e5836729 - dd7ad84f3943 - - d2d1df21dfb9 - - d5887ace0dd4 + - 33368fec3b70 - b7829778729f - - 9006e5836729 + - d5887ace0dd4 + - d2d1df21dfb9 + - a90db5dbaaf3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 189e837009c9 - - 8f631679571f - ced385aa976d - - 0368ac680e70 - 6f4c8ad6ea01 + - 0368ac680e70 - 505a9833ab5d + - 8f631679571f + - 189e837009c9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 356afed970b4 - 9ded6109434a - e59bee4565b3 + - 19bdfd1e6fe3 + - 356afed970b4 - a7ed21de23fe - d40ed4eb0c0e - - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 4688ae3b49b5 - - 6dd935e4984b + - 80a17897564d - ebd801e712bc - 7673a6c920b2 - - 80a17897564d + - 4688ae3b49b5 - b23249f81bc4 - - af40e971a8cc + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - cb1e3db43020 + - ed312479d9eb - 59bd28f6265d + - cb1e3db43020 + - b64696992ee9 - b5e35a2ca4f3 - - ed312479d9eb - - bb11fefb23a3 - 937ea677d437 - - b64696992ee9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - cb4768eeca3b - - 2628f6790eda + - 383bb5ad32e2 - 6015aa0303f2 - - 05bd7504fdb2 + - cb4768eeca3b - b9b0246a2be3 - - 383bb5ad32e2 - - 6bfab4a4a988 + - 05bd7504fdb2 + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 3e44ef016b45 - - 6e26c9afd301 - 8f9f06995f98 + - 3e44ef016b45 - 0a3a602cd1e3 - - e022dff952df - e92675014ac9 + - e022dff952df - 9e3e80cc4ad4 + - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - 8d09f8be269e - - 08256557922f - - 920677cd220f - 5da9a0e2fb2d + - 920677cd220f + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 82398ba86ba7 - 4a53b89fa703 + - 82398ba86ba7 - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index d4d80b666..9a6a526bc 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,26 +2,26 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - bfd290fe1588 - - 392f100eebcd - 4768f7f8e93f + - 1ae00120dd24 + - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - 1f5641a52664 - 31812e7a1315 + - 8e8dc9a1e3e5 - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - 24a7a95867b0 + - 5c8ff92e38a9 - 17fcac7ddf54 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 4b8fceb26..5d199212a 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -3,23 +3,26 @@ tools: owner: iuc revisions: - 0840ba83860c + - 159b04e36791 + - 204a131e47db + - a9c9d768b751 + - d58c27d2c5a7 - 1c427e24fb79 - d1f62024a08b - - a9c9d768b751 - 7beb76ffbc0f - - 159b04e36791 - - 204a131e47db tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge owner: iuc revisions: - cab19c0452c4 + - 1bb2b5b52030 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_tadpole owner: iuc revisions: - 0ddf147d1897 + - ce13b4678f18 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index b7394c4d8..cae2567e8 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - a68aa6c1204a - - a1a923cd89e8 - - ce3c7f062223 - - dde39ba9c031 - - 64e2edfe7a2c + - 589e7e57fd6d - a8eabd2838f6 - - 87ee588b3d45 + - e19bebe96cd2 - b28e0cfa7ba1 - - 0a5c785ac6db - - 589e7e57fd6d + - 87ee588b3d45 + - dde39ba9c031 + - 64e2edfe7a2c + - a1a923cd89e8 - 07e8b80f278c - - e19bebe96cd2 + - ce3c7f062223 + - a68aa6c1204a + - 0a5c785ac6db tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml index 130c44476..06ecde584 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,30 +8,30 @@ tools: - name: diamond owner: bgruening revisions: - - f921014aba5a - - e8ac2b53f262 - 54f751e413f4 + - f921014aba5a - 62c9df8382c2 + - e8ac2b53f262 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: + - 5edc472ec434 + - acf4e47b734c - cbf3f518b668 + - a52d2d93e595 + - 0e3cf9594bb7 - 2889433c7ae1 - e25d3acf6e68 - - a52d2d93e595 - - 5edc472ec434 - - acf4e47b734c - d999e774072a - - 0e3cf9594bb7 - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 9ea6e37cf..396353400 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 6ca543ec1bf8 - 095ad4d096d1 - - c8cdde00b105 + - 27ee142314a9 - da6bd1975a71 - 710301bc46fa - f4230f116196 - - 27ee142314a9 + - 6ca543ec1bf8 + - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -130,32 +130,32 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 79cfd9ead848 - - 88076940fa94 - - 3b8a9d5ced85 - 0fac8e2afc13 - bfb65cb551d8 + - 3b8a9d5ced85 + - 88076940fa94 + - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - eb6564a60136 - f5d979cb4b54 - 715cd0e87781 - - eb6564a60136 - - 55918daa5651 - - b46d4b4d995c - d532b7e5f64b + - b46d4b4d995c + - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 5579659312e6 - - fdf2cc80adb5 - dae135dfd519 - - f26afd1b7104 + - 5579659312e6 - d2f955aea23a + - f26afd1b7104 + - fdf2cc80adb5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files @@ -169,35 +169,35 @@ tools: - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - 4da9ee404eab + - ed736e6eee39 + - 070e3ecc3fda - 2c349b027a01 - cac1886249a2 - - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - c0c9a5024177 + - 525ca7c8065f + - 73008ef1f487 - d1f803b5943c - - da8753545526 - f197e34c33a9 - - 525ca7c8065f - - 2e219a2d9327 - - c0c9a5024177 - 807aa4c9293d - - 73008ef1f487 + - 2e219a2d9327 + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 7568ae18908a + - c4fbab8e03c5 - 1809414a9454 + - 7568ae18908a - 61094e01eff9 - - 27ea4e1a3f95 - - c4fbab8e03c5 - 2c8ed1b52bf7 + - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -210,10 +210,10 @@ tools: owner: chemteam revisions: - 730ef07b90ae - - ccfbd956a2d3 - - d7ec25187599 - 79e8ab8f1e81 - ba83f0923369 + - ccfbd956a2d3 + - d7ec25187599 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e2c36f62e22f - - b59c91adeac1 - e6011617c748 + - b59c91adeac1 - 4242b4d68e9c + - e2c36f62e22f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -351,10 +351,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - bf99565cec1f - - 9b48456a96fe - - 85fad59f8168 - d4c67ced6abc + - 85fad59f8168 + - 9b48456a96fe + - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index a19937ed7..7782bf53d 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,11 +2,11 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - fa56d93f7980 - - c97a786e8fb5 - - 2605cbdaa7d8 - f907216064f6 + - 2605cbdaa7d8 + - 163688bb8f73 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -18,31 +18,31 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - 86e2413cf3f8 - - 640d3af5d833 - 495a4173006f - 424aefbd7777 - f5d67c722d67 + - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator owner: pjbriggs revisions: - - b695071de766 - 087d9872fb0d + - b695071de766 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index cee4a1919..ae0baaae9 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: + - 830961c48e42 - 33151a38533a - - 25136a2b0cfe - 90981f86000f - - 830961c48e42 + - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - dfde09461b1e - 3ddd99c7efee + - dfde09461b1e tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - 6cbe2f30c2d7 - - baabc30154cd + - 0046692724f9 - 2dae863c8f42 + - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 43cfdbe09..c26d239e9 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,9 +2,9 @@ tools: - name: agat owner: bgruening revisions: - - abba05ead5d7 - - d6ede73082da - e7449b2c14bf + - d6ede73082da + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 6ef0b5664c69 + - 5e1240a87bcb + - 367b1ed91207 + - 3b6f97e7094c - a3b86937ead6 - - 0b3c3ad92827 - ab9350a8ab4d - - 3b6f97e7094c - - f3a19509108a + - 6ef0b5664c69 - e3cbd2287f63 - - 367b1ed91207 - - 5e1240a87bcb + - f3a19509108a + - 0b3c3ad92827 - 4a6ee918c13a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 54ccb7e1f49a - - d4d4e9febf5c + - 091bb5922a82 - e525f9ffb9ac + - d4d4e9febf5c + - 54ccb7e1f49a - 584008e574b2 - - 091bb5922a82 - - e177a8ea0bf1 - - 1b5fc03380d4 - bd46669113b9 + - 1b5fc03380d4 + - 72ed72122deb - 501c21cce614 - 33c99804a32f - - 72ed72122deb + - e177a8ea0bf1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,16 +59,16 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - 77b41c89d856 - - 8979c288aefb - 186b8d913e6c + - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -95,9 +95,9 @@ tools: - name: gffread owner: devteam revisions: - - 154d00cbbf2d - 4dea02886337 - 3e436657dcd0 + - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -115,8 +115,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - 705821bf30d2 - f5c632894818 + - 705821bf30d2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bam_to_cram @@ -135,18 +135,18 @@ tools: - name: tabular_to_fastq owner: devteam revisions: + - 78fb18899c99 - 68f57cc8fad0 - 2dcfbbf9071a - - 78fb18899c99 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - 26c6706bfb07 - - 92ac8e086317 - - b9b385097f13 - 63769c4217a7 + - b9b385097f13 + - 92ac8e086317 - 19e45916daf9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -160,15 +160,15 @@ tools: owner: iuc revisions: - 8067dfa00ed2 - - e9bbe2f71784 - 3c6f9e8a4c17 + - e9bbe2f71784 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - fa49730d1d4b - 98704d357ede + - fa49730d1d4b - a2f83a375bf2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 4737b076c..784fdcd82 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,205 +2,205 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - de72ba3ed6f2 + - 29451af70c52 - e821645ef8fc + - de72ba3ed6f2 + - c929a006727f - 5f6d123679f4 - - 268e91e540ee - a1ca9bccc7f2 - - 29451af70c52 - - c929a006727f + - 268e91e540ee tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 2d2cf5c1ea8a - - 0e143b4c3987 + - 0e49b109abc2 + - bb1e4f63e0e6 - 12af64f93288 - 5d11599b8a7d - - 0e49b109abc2 + - 0e143b4c3987 - 7a7fd0f5f15d - - bb1e4f63e0e6 + - 2d2cf5c1ea8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - c06951d10364 - - 1d848bc4585f - - 81b1e3e1fc6c - 7c1beb6d6eca - - 195e98217334 + - 81b1e3e1fc6c - dc059492a995 + - 1d848bc4585f + - 195e98217334 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 3d211717a775 + - a67ac707496a - 07418a30ed01 - - 93eb012d9eed - - 26e7304d6737 - 71aa86af6762 - - a67ac707496a + - 93eb012d9eed - bfff7454b59a + - 3d211717a775 + - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 2bc10a9ca58b - dd0b7398bb96 - - 26983857c91a - 56d5b797ce84 + - 5be24eba848d + - 26983857c91a - b8858746dc1f - 29fcfd36e90a - - 2bc10a9ca58b - - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 9384cd033f30 - - 72bfafe3330b - 7e6bcd2e5128 - - ee3a1b0f45f1 - - e6d0bff01239 + - 72bfafe3330b + - 9384cd033f30 - 7ef978dc1b8a + - e6d0bff01239 + - ee3a1b0f45f1 - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fb9cf9c97ec4 - - fd1275e01605 + - 9470f29702f8 - d9a637e83828 - 167788df3b46 + - b73e213add0c + - fd1275e01605 - 514fa53b5efb - a60c359ec43c - - b73e213add0c - - 9470f29702f8 + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: + - ca0616bb2cdf - c34d11ea4ba6 - 2c37ce318bc3 - 5bffaa8354a1 - - 86febdcc4283 - a02cfa31e9cb - - ca0616bb2cdf - e479c7ca5570 + - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 004aea905d4d - - 78f405266706 - - 1fcb7adc39b8 + - 2d466b530754 + - 01fb6a7654e6 - 69a8621ca2f0 + - 78f405266706 - 192ef85c0b0b - - 01fb6a7654e6 - - 2d466b530754 + - 004aea905d4d + - 1fcb7adc39b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - d9ce4897dbb2 + - 2f9e4843f480 + - db940c262830 - 9ecba5e225a6 + - 3c9f0c486cca + - 137c4beed34b - d580d6acd1df - 459cfa861f0b - - db940c262830 - - d9ce4897dbb2 - - 137c4beed34b - - 3c9f0c486cca - - 2f9e4843f480 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fd408d755394 - - bd7db9e2f2cb - - 32e451def88c - fbe773640707 - 2c66e43f1c86 + - 32e451def88c - f264afa9fa6f + - bd7db9e2f2cb - bad3ca889618 + - fd408d755394 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 9368fbc49c8b - 7fda5607e777 - - 4e12ea27f788 + - 231994413f89 - 3b9d990a0a0e - - 7e361d147872 - 56bce3c82278 - - 231994413f89 + - 7e361d147872 + - 9368fbc49c8b + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - ce4ce3316f74 - - 94ca68515826 - - c03c3384cd81 - 4431f39ede55 - - b1779366c8e9 - - e65d16fb2724 + - c03c3384cd81 - d9114ef1c8a5 + - e65d16fb2724 + - b1779366c8e9 + - ce4ce3316f74 + - 94ca68515826 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - f8fc4e5aff9d + - d57251071381 - 793665fff0f8 - 23f7c5f1fdaf - - 2da482e408b8 - - d57251071381 - - b88ebb3672a1 - 4ed32329e0ed + - b88ebb3672a1 + - f8fc4e5aff9d + - 2da482e408b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - e4c7985d4585 - - 010e58e9d822 - - 25d830337d31 - - ba6efa77fb79 - a7849312d328 - a4dfb122e52b - - 512155688d98 - c60570fa602f + - 25d830337d31 + - 010e58e9d822 + - e4c7985d4585 + - ba6efa77fb79 + - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - c899e0ccff8c + - 4d678170d29b - 69264da0ce77 - - aa200e4f3939 - 38e3f226248b - - 443d9a9d6d11 - - 4d678170d29b - 00d869ea03a1 + - 443d9a9d6d11 + - aa200e4f3939 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - aac8444d6681 + - a2d70c4fd406 - d806504e96d9 - 10301d137111 - - 6662b1a8d326 - c361b12d207a - - a2d70c4fd406 + - 6662b1a8d326 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index a76b69d05..c8e193153 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 7d16de45c021 - 08d873cdd5f6 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -37,29 +37,29 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 91a1ed0b486f - 76e69de726b2 + - 91a1ed0b486f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort owner: iuc revisions: - - 12b9e285ca1c - b6d9ea2fb41b + - 12b9e285ca1c tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 5f4544915893 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 4cf47c504672 - 3299c7d5268f + - 4cf47c504672 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index e1f7bb3ff..e9a6db869 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - ce385837c160 + - dba489bfcd62 - 63dd26468588 - 832c20329690 - - dba489bfcd62 - - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 64123eae0..d52d1276e 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - d82648ad25a3 - - 62f5fab76dfb + - cf1322aeb137 - 6da3972210ee + - 62f5fab76dfb + - d82648ad25a3 - 29bdbc353f20 - - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index ccbde1720..a243c0d38 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 5eb7e84243f2 - - b1c926deaa2d - - 49370cb85f0f - - 44e2cc14f75b - - 48f587c13075 - - e4691e1589d3 - - 288f97432497 + - fe74900d6dc7 - 5915ea1ec9b1 - - 093678460093 - - 8c0175e03cee - - 64172f1c1202 - 660cffd8d92a - - 135b80fb1ac2 - - 8665bcc8b847 - de6cebe3c043 - - fe74900d6dc7 - - c4b82dce8335 + - e4691e1589d3 + - 8c0175e03cee + - 44e2cc14f75b + - 49370cb85f0f + - 5eb7e84243f2 - c5e2e5902201 - - c053d4cad713 + - c4b82dce8335 + - 8665bcc8b847 + - 64172f1c1202 + - 093678460093 + - 288f97432497 + - 48f587c13075 + - b1c926deaa2d + - 135b80fb1ac2 - 4e5056fefd88 + - c053d4cad713 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -41,8 +41,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - 5cbde03c1103 - 7d37cfda8e00 + - 5cbde03c1103 - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -61,9 +61,9 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - 9457a20156db - 516b97a23d7e + - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -76,8 +76,8 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - ec0b5076173a + - f773e98b26cf - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -94,68 +94,69 @@ tools: owner: iuc revisions: - ecb9f4854617 - - dbfc505896e9 - - 65b93b623c77 + - a626e8c0e1ba - c59d48774d03 - d60c3f704da0 - - dbf9c561ef29 + - dbfc505896e9 - 1d8fe9bc4cb0 + - 65b93b623c77 + - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - 9115b978ce10 - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 + - 9115b978ce10 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: + - 10b75444feae - 81a9090d6df3 - '144275714590' - - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - - 8611b80a14d6 - - 47e5dbc3e790 - e9f8633db0a2 + - 47e5dbc3e790 + - 8611b80a14d6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - - e30352e889fe - - 5b87038565bb - 7861f3b10c68 + - 5b87038565bb + - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 4e1d64e6385f - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed + - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb - 523c2aff0376 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - - 2ccb8dcabddc - 3e396e702cea - b41c2c1bcfbf + - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -169,66 +170,66 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 249c8393f2d4 - 35e38452bb3f - e39cc71d3ed6 - 397dc333436b + - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - 045f0e1043f7 - - 74db4cffab1f - 54053ea6c77e + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - f86c27295151 + - f0e7deab6518 - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - f0b18efb97f1 - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 + - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: - - 297962e79f39 - ac3fed111eb6 + - 297962e79f39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 - - 567d5b3c52b1 - - d5e9e83cd3d8 - 09070cacefd8 + - d5e9e83cd3d8 + - 567d5b3c52b1 + - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - 4bedca26c133 - - 0b7ec11b3c7c - 8abdedf55101 + - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - 736b8f6ee456 - - 90858c306551 - cb1e251cac37 + - 90858c306551 - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -243,26 +244,26 @@ tools: - name: fastx_renamer owner: devteam revisions: + - 02f8a17a4ebd - b29d37ca9e41 - f984bb114520 - 3599f5451ee2 - - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - 6027ef51ef91 - - e246088b6e34 - 0c2907307ba4 - 177f0621c266 + - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 61b4cedc8934 - 377ac2829eac + - 61b4cedc8934 - 73194cdd4f57 - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ @@ -276,10 +277,10 @@ tools: - name: pear owner: iuc revisions: + - 037f0acc7830 - f69501361cec - - b4c6f054210a - 2f804526f5fd - - 037f0acc7830 + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -293,24 +294,24 @@ tools: owner: iuc revisions: - 61eb4cfc7313 - - fdc21382376d - 29ef2c5ec205 + - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - - 812705bcf39c - 795cd16de38f + - 812705bcf39c - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - a019807f4e67 - 3da72230c066 - 4b494533146a + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic @@ -331,12 +332,12 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 71ad4a56c40c + - e654095ab143 - a535cf1e5da4 + - 71ad4a56c40c + - 24013bf85a6f - b557acca0b56 - 8250ea3a1501 - - 24013bf85a6f - - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -349,14 +350,14 @@ tools: - name: umi_tools_extract owner: iuc revisions: + - 27ac32a22ad2 - 9fa7803d1c51 + - 015cf18f4a15 + - 828dba98cdb4 + - 7a7e33d28f62 - f3759eec3018 - 6a675c3aa610 - - 828dba98cdb4 - - 015cf18f4a15 - 7accf7407811 - - 7a7e33d28f62 - - 27ac32a22ad2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group @@ -369,8 +370,8 @@ tools: - name: umi_tools_whitelist owner: iuc revisions: - - 953b4821b183 - - e4e12f0b3af1 - 4c8a1c7d3608 + - e4e12f0b3af1 + - 953b4821b183 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index 108c1efe8..400eb94a8 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,54 +2,54 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - ce9cd02d5b88 - e41385662e5e - - 7b4468117008 - 64e9a6afdd0c + - ce9cd02d5b88 + - 7b4468117008 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: + - 5ec9f6bceaee - ff9530579d1f - - 2c64fded1286 - 2b0c9d9fc6ca - - e7b2202befea - - f2e8552cf1d0 - - 5ec9f6bceaee - - 3d0c7bdf12f5 - 9da02be9c6cc + - 3d0c7bdf12f5 + - f2e8552cf1d0 + - 2c64fded1286 + - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - c1a33f603da2 - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - ad116ae3f4d9 - b6b54ba71bd8 - 18a51655db17 + - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - 59003d0543cd - - cc0fd298cc17 - 7306ec78632a + - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong @@ -63,23 +63,23 @@ tools: - name: multiqc owner: iuc revisions: - - 75c93c70d094 - - 3d93dd18d9f8 - - 1c2db0054039 - 9a913cdee30e - - bf675f34b056 + - 1c2db0054039 - f7e2f1eb3a16 - b2f1f75d49c4 - - abfd8a6544d7 - - c1a4b5f3b432 + - 75c93c70d094 + - bf675f34b056 - 5e33b465d8d5 + - c1a4b5f3b432 + - abfd8a6544d7 + - 3d93dd18d9f8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - 949f01671246 + - cd7e644cae1d - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fetch_alignmentssequences.yml b/usegalaxy.org.au/fetch_alignmentssequences.yml index 0dfc5355c..c01999d90 100644 --- a/usegalaxy.org.au/fetch_alignmentssequences.yml +++ b/usegalaxy.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 19f42b3ea391 - 9e776e7fab4f + - 19f42b3ea391 tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 3abd34b99..2d183e1d1 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,22 +2,22 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs owner: peterjc revisions: - - bdaefd241921 - 7c40a1fbc82e + - bdaefd241921 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_filter_by_id owner: peterjc revisions: - - 141612f8c3e3 - - 85ef5f5a0562 - 83a19df00eab + - 85ef5f5a0562 + - 141612f8c3e3 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 18849db1d..1dd47cff5 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -17,22 +17,22 @@ tools: owner: iuc revisions: - 0c8f7322f8fc - - 8f53b238a360 - f2f3bc622a16 + - 8f53b238a360 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - df57188562f0 - 1a4c5adcd587 + - df57188562f0 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -52,15 +52,15 @@ tools: - name: gemini_dump owner: iuc revisions: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -79,8 +79,8 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load @@ -94,15 +94,15 @@ tools: - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -122,23 +122,23 @@ tools: - name: gemini_query owner: iuc revisions: - - 666f60a9331a - 840fb4850be3 - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 86f3aac4418d - 05124dc72dba + - 86f3aac4418d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -151,15 +151,15 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - e4e2128460e3 - ef9991a4a9a7 + - e4e2128460e3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 659e8a5eb..9844ff03b 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,35 +2,35 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index a66c78d5c..4ebeec7e0 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - c1b437242fee + - b39347891609 - e9df53a75f3c - 983bf725dfc2 - - b39347891609 + - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -25,28 +25,28 @@ tools: - name: sra_tools owner: iuc revisions: + - aad3885b3216 - ba931a59dd59 - - c441583adae5 - 6591f049cf7e - 4317d3cb6cba - - 653e89d73fc4 - - 4df8de2d0e48 + - 7068f48d0ef9 - 69ebb7f46e45 - - 8848455c0270 - - 6ea73833cf67 - - aad3885b3216 - 9a776b080193 + - 8848455c0270 + - 5e6237d58b0c + - e08a7ad4378b + - c441583adae5 - 83c7d564b128 - 734abc7ac21d - - f8054ea1c365 - 1ec814014652 + - e407b9da183a + - 6ea73833cf67 - 516a54ddf218 - - e08a7ad4378b - - 5e6237d58b0c - f5ea3ce9b9b0 - - e407b9da183a - - 7068f48d0ef9 - 1790dcf3c32d + - 653e89d73fc4 + - f8054ea1c365 + - 4df8de2d0e48 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept @@ -61,10 +61,10 @@ tools: - name: uniprot_rest_interface owner: bgruening revisions: - - 054483e27a35 - - af5eccf83605 - 468c71dac78a - 95fb5712344f - bfdc6a7ffd3a + - 054483e27a35 + - af5eccf83605 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 5731bf8ac..764add73f 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: + - 290a11559985 - df7356989ac1 - - c4bde687c846 + - 4b519282a05b - 740057a5126d - - fd59d783248a - - a64dc31ab7f2 - - ae9994cf526f - 7f13dc906cb9 - - 290a11559985 - - 4b519282a05b + - ae9994cf526f + - a64dc31ab7f2 + - fd59d783248a + - c4bde687c846 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -42,24 +42,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - - 3b37b1b1c3a7 - - '566197475670' - 51c6ccaace7e - 48b42ee61bc5 - - ca7cb0eaad62 + - 53460afd5115 - 374e9062d874 + - 3b37b1b1c3a7 + - ca7cb0eaad62 + - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - d3a9e32672ec + - 10515715c940 - 391a4cc45fea - - 3d059e9c2fba - 1a72f938213e + - 3d059e9c2fba - da4c086cff5b - - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -79,12 +79,12 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 - - e3a675da7fd0 - 299307abd804 - 5298e06f14f9 - - d0fc8b746d57 - 5fe1dc76176e + - e3a675da7fd0 + - 1acf88921176 + - d0fc8b746d57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -110,8 +110,8 @@ tools: - name: graphlan owner: iuc revisions: - - 8f62f666dcb6 - 6e8eb0c0d91f + - 8f62f666dcb6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -129,17 +129,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 6cd09d7b5f37 - - ca2def38369c - - 836d1aa3e89a - 112eb40ba6cf - - fd5dbf0f732e - - 4542035c1075 - - 2bb2e07a7a21 - a6e57ff585c0 - 1cfc579079a6 - - 667e17248bfe + - 2bb2e07a7a21 + - ca2def38369c - 17359b808b01 + - 667e17248bfe + - 836d1aa3e89a + - 4542035c1075 + - 6cd09d7b5f37 + - fd5dbf0f732e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -157,8 +157,8 @@ tools: - name: pathview owner: iuc revisions: - - fe154a7af404 - f1691de443a7 + - fe154a7af404 - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -172,24 +172,24 @@ tools: - name: plot_ragtag_paf owner: galaxy-australia revisions: - - 501dcf66c0ce - c1bed78b9ed5 + - 501dcf66c0ce tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: + - 1c5dcef5ce0f - 62e3a4e8c54c - f234e2e59d76 - - 1c5dcef5ce0f - 85da91bbdbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -201,10 +201,11 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 + - 26f2fe7e53a1 - 7c9417381ad5 - - 6c571966cfb9 - 326098bc19cc + - 44c66e8d21e6 + - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -216,23 +217,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - a1abfa420d9d + - 326a3db8d9d1 - 7dd841a32245 + - 36b848d5f3ec - 14e7c35f3d00 + - 2824d77cd8f8 - 4ac4e7083b7e + - a1abfa420d9d - 360df4999907 - - 2824d77cd8f8 - - 326a3db8d9d1 - - 36b848d5f3ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 83c573f2e73c - - 2f557f6abbfb - 73b8cb5bddcd - 44608d0193ed + - 2f557f6abbfb + - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 4c4e211be..169e09a7a 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -35,8 +35,8 @@ tools: - name: scanpy_filter_cells owner: ebi-gxa revisions: - - 361608369dda - bf1e0bdec1db + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes @@ -63,29 +63,29 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - 9d76c3d6dff6 - c9da9192eee5 + - 9d76c3d6dff6 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 3c47bc560688 - 352cdf3b2f75 + - 3c47bc560688 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - c354af93f567 - 6903bc865d63 + - c354af93f567 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn @@ -106,8 +106,8 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 3027cb62adbd - 28b1546857b0 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -127,22 +127,22 @@ tools: - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 6f5509cf3176 - 4a74b45c1ce4 + - 6f5509cf3176 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - cb1992d1804b - d3df472a21dc + - cb1992d1804b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x owner: ebi-gxa revisions: - - 078aa23c9374 - 287503c35cb4 + - 078aa23c9374 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable @@ -176,15 +176,15 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - b2768cae00a1 - 6d4f88995e40 + - b2768cae00a1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: - - 4428dba93375 - 0cf90e01d9f8 + - 4428dba93375 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne @@ -197,15 +197,15 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - ea91cfd0444e - 767a675b5254 - 0f98603d0116 + - ea91cfd0444e tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 5738c0ec3..efcda67d6 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,32 +2,32 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 0f611e7d7858 - - a4c13ddcc8ee - 9edf8894a22d - - 921a2da49a0c - - ed2cca6b5de4 - 29f66c353bcb + - ed2cca6b5de4 + - 921a2da49a0c + - a4c13ddcc8ee + - 0f611e7d7858 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 78fb5e286609 - - 755df866ad0c + - 11de0d28ab30 - d404277cc87a - ec4b948dc6f0 + - 78fb5e286609 - 5746d61f0a91 - - 11de0d28ab30 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 03dd3c16ae4e + - 11fa44ee0603 - 977dc15add20 + - 03dd3c16ae4e - 9e357a8b2ec3 - - 11fa44ee0603 - 4d511437b1e5 - f72063d9426b tool_panel_section_label: HiCExplorer @@ -35,20 +35,20 @@ tools: - name: hicexplorer_hicpca owner: bgruening revisions: - - c3e5e2cf12b7 + - 77919cc3618e + - 0ba4f56a3613 - 1da5f169b491 - 3b5b54ed6392 - - 0ba4f56a3613 - 41dbf4d162a2 - - 77919cc3618e + - c3e5e2cf12b7 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - f741330d4a71 - - 12d51d7be66f - 9939786dd9c9 + - 12d51d7be66f + - f741330d4a71 - b63363075c2e - 7babd8a46fe0 - 5308ca68ef3d diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index 9034f2446..598e74c9f 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -3,18 +3,18 @@ tools: owner: imgteam revisions: - 7db4fc31dbee - - 0c777d708acc - - 3df9f0a4bf34 - 81f0cbca04a7 - 699a5e9146b3 + - 3df9f0a4bf34 + - 0c777d708acc - 8bccb36e055a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5bc8cdc17fd0 - 5791a7f65275 + - 5bc8cdc17fd0 - 2436a8807ad1 - 0a53256b48c6 tool_panel_section_label: Imaging @@ -22,17 +22,17 @@ tools: - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 6ad1d3cfdea1 - 9d47aabda459 - e576b73a2e2f + - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - 77f7159d775a - - b1c2c210813c - 70316d792fc9 + - b1c2c210813c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter @@ -52,10 +52,10 @@ tools: - name: bfconvert owner: imgteam revisions: - - b07f4839ca77 - - 85edbb7a436b - 10eed33aa9b2 + - 85edbb7a436b - f3360fbeda64 + - b07f4839ca77 - fcadded98e61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,15 +78,15 @@ tools: owner: bgruening revisions: - 0e4dccaafef5 - - e917a2424690 - eb6c08714244 + - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common @@ -101,15 +101,15 @@ tools: owner: bgruening revisions: - ef4aed1d34c4 - - df3ad3ba5c6f - cdf8e3c57dae + - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - 6a7da2e5f696 + - 5d28ac336861 - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -117,8 +117,8 @@ tools: owner: bgruening revisions: - f2ed92b011a9 - - 11f177b1a59e - bace5a93a97c + - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet @@ -133,24 +133,24 @@ tools: owner: bgruening revisions: - 3245681b2f6d - - ad271f78a87a - 31d195bedf6d + - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 87d4d92d7487 - b6eec6087271 + - 87d4d92d7487 - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: + - 6100a22bf4f2 - ff1a86a87364 - c09dcda1143f - - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -180,64 +180,64 @@ tools: - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - 5499dc6f8ac1 - 8536b1ae0254 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: + - d3890df07463 - e972e07c7845 - 6f4715b8540a - - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: + - 407925835dd9 - e52c75a28c4b - 980aed9e8fd5 - - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - acf3aa487283 - - 79e10d12d90a - d85f11570109 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - 80b200ae516b - - 035a58c7f54a - b76841ee5560 + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines owner: bgruening revisions: - - b44b081bcf37 - 91560258e972 + - b44b081bcf37 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - 48102a685037 - 8083a87d2fdf + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 4ecf93628f97 - 33f4fa1413fb - 27edbb90ab2b + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -249,23 +249,23 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids owner: iuc revisions: - - f92941d1a85e - 4b794652dcdc + - f92941d1a85e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - - f8b4eada923c - 7b6d9412c7f8 + - f8b4eada923c + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index bdbea88e5..1cac3c429 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,59 +2,59 @@ tools: - name: ivar_consensus owner: iuc revisions: + - 1069f6db0a0e - 3a72fede57ce + - 78bbd17d0703 + - 40737febe339 - f362150bef41 - - e4ee04da1c19 - - a38934e303b9 - - 1069f6db0a0e - e319b5b65879 - - d6e72da3ec35 + - e4ee04da1c19 - 3e4f434a69c6 - - 78bbd17d0703 - - 40737febe339 + - d6e72da3ec35 + - a38934e303b9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 618297d23022 - - fcbeda41d0ac + - 9537184d421f - 7fe36019c073 - - 2b95d5c04908 - - c88553ec696e - 8f8df367470d - 0135f1d487a0 - - f91cfb73d369 - 72ddd32392cd - - 9537184d421f + - 618297d23022 + - f91cfb73d369 + - c88553ec696e + - fcbeda41d0ac + - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - d7e79eb3bcb3 - - 2cf4a1cafc16 - ad0dc9f4c9e2 - fafb3d685fa9 + - d7e79eb3bcb3 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 8c05afb547fa - 7f1cfa4c0e32 - a1c2aecd7a0d - - 8d36959b000d + - bd2a7d1316b9 + - 9eaadf03e0df + - 6a1515bb0687 - ee29337f905c - - 28a6f1908fcc - - 3d18f8c3c0f6 - - 94df24c6bc00 - ee2beb764a7b - - bd2a7d1316b9 + - 8d36959b000d - 43aac8d29685 - - 9eaadf03e0df - 5dc33613c288 - - 6a1515bb0687 + - 94df24c6bc00 + - 3d18f8c3c0f6 + - 8c05afb547fa + - 28a6f1908fcc tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim @@ -62,33 +62,33 @@ tools: revisions: - a250929be21b - bcaa0d571ce2 + - 5671e1d3d5ee + - e3bb03cf207a + - 86a20ae274fc + - 9f978da6528a + - 8858fa037a15 + - cb903c9dc33d - c092052ed673 - - d37ede8589b2 - 5d6ed46cc101 - - cb903c9dc33d - 364f4ffec275 - - 9f978da6528a - - 5671e1d3d5ee - - 86a20ae274fc - - e3bb03cf207a - db536ad45f28 - - 8858fa037a15 + - d37ede8589b2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - f95f403841ad - - 49236b03e4fd - - ed28dd32141c - - 3b6a16d82c1b - - 230b05597996 - e1a015876aa9 + - 38b91a3190cd - c5c9f02b6167 - 12d66d0d05ac - - 38b91a3190cd - - abbc8041e8ec + - 49236b03e4fd - 194e3ceee923 + - abbc8041e8ec + - 3b6a16d82c1b + - ed28dd32141c - 584beffa972b + - 230b05597996 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/join_subtract_and_group.yml b/usegalaxy.org.au/join_subtract_and_group.yml index f4e1afb1b..09ead8e2c 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: + - 17e3b698dd52 - 0f1724dd59d2 - b8a457820315 - - 17e3b698dd52 - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - a513e3fbb4c5 - - 374cb875d38a - - ba0c40780ecf - - 22c2a1ac7ae3 - ac092723240d + - 22c2a1ac7ae3 + - ba0c40780ecf + - 374cb875d38a + - a513e3fbb4c5 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index b261528b3..737bbc5e2 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,27 +2,27 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 772e0e89fc68 - - 522137aaa9c4 - 66d7efc06000 + - 522137aaa9c4 + - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 8a794e6d3388 - f22a9297440f + - 8a794e6d3388 - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: + - f1b9a42d6809 - 818f9b69d8a0 - b6ef6d0cb6b7 - - 2af1346e68c9 - - f1b9a42d6809 - e1317b5502fa + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex @@ -30,8 +30,8 @@ tools: revisions: - c80db5d6fd8c - 947c2eacccb8 - - 1588f9076e32 - 8334dc98c48e + - 1588f9076e32 - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -41,60 +41,60 @@ tools: - 83228baae3c5 - 1552b8cb4a94 - 9991c4ddde14 - - 25b46af53232 - 29e4122c90de + - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - a07ab242b0b5 - 1a53edc4b438 - - f3dfa4bdf87e - - 53616c8b0865 - 060ca94ac049 + - a07ab242b0b5 + - 53616c8b0865 + - f3dfa4bdf87e - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: + - 91c4e3331208 + - 2fc89dcd41c8 + - 40f4447733b2 - d4808d5b83da - 927586a18553 - - 40f4447733b2 - - 91c4e3331208 - dc4b5fd604a6 - - 2fc89dcd41c8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 301e07345c93 - - e5a5ad882f1f - - 25ab6b4e376e - - c6ae57f774c6 - 7626ea9c2e1b - 36e8d6d5d01b + - c6ae57f774c6 + - e5a5ad882f1f + - 301e07345c93 + - 25ab6b4e376e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - b7c3e9a3b954 + - f9639b488779 - 80852884053f - - 4ed102b922cb - 0630258dcf35 + - 4ed102b922cb - 02d2be90dedb - - f9639b488779 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: + - 61634a87efc7 - 14180f9c831e - caeb57858702 - ec69cbe34b73 - - 61634a87efc7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index e5935b34d..1940d40d3 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - 3ba8d4563129 + - cd659e8cc5fa + - 03e9b2fbc005 + - d5ceb9f3c25b - 937aa69e715f - 749c918495f7 - 0d4acadabb04 - - 03e9b2fbc005 - - 017aba02828d - - a6d65b0c67af - - cd659e8cc5fa - - d5ceb9f3c25b - f6877ad76b00 + - 017aba02828d - 17062a0decb7 + - a6d65b0c67af + - 3ba8d4563129 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,11 +31,11 @@ tools: - name: bwa owner: devteam revisions: - - 53646aaaafef - - 64f11cf59c6e - dfd8b7f78c37 - e188dc7a68e6 - 2477830927ec + - 64f11cf59c6e + - 53646aaaafef - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: + - e7f19d6a9af8 - 60afcc2c1d05 - 3e1ea2facca6 - - 2ff111fac1d7 - 37b497aa133f - - e7f19d6a9af8 + - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - be1d967337e4 - 53c0b7a1a0c3 - - 77b2770508f6 - - 3f4d6399997b - - 8c6cd2650d1f - b3eab4b67562 + - 5cc34c3f440d + - 3f4d6399997b + - be1d967337e4 - 11a0d50a54e6 - 037c6e54df11 - - 6b1e195506a3 - - 5cc34c3f440d - 09b53c1d4ab1 + - 6b1e195506a3 - c0c2d0941de8 - f54f5baedfdd + - 77b2770508f6 + - 8c6cd2650d1f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 79b885ce78d7 - 00fbfac99d39 + - 79b885ce78d7 - 1cd2511a396e - - 5ef7ec16b04f - - b8f5f6e87f5c - - 45795f582ae9 - - 42ce70172b72 - 178bdbdb6d24 + - 42ce70172b72 + - e403d27e8f24 - ec9cbd6b9a49 + - 5ef7ec16b04f - 9ee34ba73ebf - - e403d27e8f24 + - b8f5f6e87f5c - 13022c3d3076 + - 45795f582ae9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metabolomics.yml b/usegalaxy.org.au/metabolomics.yml index 48e51c5e0..74813531a 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -57,8 +57,8 @@ tools: - name: isolib owner: recetox revisions: - - 2b1118bce0b1 - 6b0fef8a77c0 + - 2b1118bce0b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -70,14 +70,16 @@ tools: - name: matchms_add_key owner: recetox revisions: + - a5d41764722d - 1d10d32fa3b3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_convert owner: recetox revisions: - - b9cc12600553 + - 9e83636da9d3 - c990df6afc24 + - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering @@ -85,11 +87,13 @@ tools: revisions: - 00e66c401366 - a177ac3c752c + - 83c4b4359ac4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: + - fd890f162ce6 - 84af792d3a78 - d7b517f2c5fe tool_panel_section_label: Metabolomics @@ -98,12 +102,14 @@ tools: owner: recetox revisions: - 9e3c83d2afc3 + - a5a5b147da70 - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export owner: recetox revisions: + - 8832425b1ff6 - f04610d25411 - b576ed720711 tool_panel_section_label: Metabolomics @@ -112,6 +118,7 @@ tools: owner: recetox revisions: - 1d443ed476a1 + - 330b0dfae8da - 03bc9b7f40f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -119,24 +126,28 @@ tools: owner: recetox revisions: - 84ead993862c + - 1fd950c5586a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_networking owner: recetox revisions: - - 1d74ae228df3 + - f04b378325e5 - 8147d93d372d + - 1d74ae228df3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key owner: recetox revisions: - 9d1b01d3fedd + - fbdb2ae524df tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_spectra owner: recetox revisions: + - d50ce2f51fc0 - fbe335d27d25 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -151,6 +162,7 @@ tools: revisions: - 9ff95a1a2705 - 7627b40601f6 + - 7ba589b01dbc tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -158,19 +170,21 @@ tools: revisions: - 500f473df7e4 - 0cf68b536cd1 + - ea6c5636c0cf tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting owner: recetox revisions: - 6d2f2c565431 + - 5bbd1a8404f5 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msmetaenhancer owner: recetox revisions: - - 90745ecc5e9f - b5467dead5b1 + - 90745ecc5e9f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -232,17 +246,17 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: + - ec196e27a61a + - c53a97599181 - 79ad928a0dae - 7b42ee54d757 - - c53a97599181 - - ec196e27a61a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - 59c393d35e0e - 18ec7635bac6 + - 59c393d35e0e - f3a18e020cdd - 149b9cc7499b tool_panel_section_label: Metabolomics @@ -250,48 +264,48 @@ tools: - name: recetox_aplcms_compute_template owner: recetox revisions: - - 134be5abb208 - - 481d769e2f7a - 50b9918aeff2 + - 481d769e2f7a + - 134be5abb208 - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: + - a82db010c53e - 9064aecc78a7 + - 501a232f3cd5 - 02c772a49998 - 30bf4e35da3e - - 501a232f3cd5 - - a82db010c53e - 51332c2520c7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: + - e7305ba0dd38 - b3413f335327 - 89178a72388a - - e7305ba0dd38 - b341cfd4baf8 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - b7c8a44b9cc1 - - dd7bbc2b99d1 - cf061712a184 + - dd7bbc2b99d1 + - b7c8a44b9cc1 - 17a48d0a80f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - f92b1b64da93 - d7f5878a98c3 - - 24278c6b6d1c - 99d118321d5f + - f92b1b64da93 + - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise @@ -331,8 +345,8 @@ tools: - name: rmassbank owner: recetox revisions: - - 5a6bb93ec656 - 0b28816c1c2c + - 5a6bb93ec656 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index f641fef94..a45e0a520 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -9,16 +9,16 @@ tools: - name: cat_bins owner: iuc revisions: + - 0094893f5001 - 18676df0cb3a - 0e63d03c8790 - - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise owner: iuc revisions: - - 7f1aaa1932d8 - a8216def322b + - 7f1aaa1932d8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -90,19 +90,19 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 65db807336bc - 7c2100246a2f - - 63f86089423e - - 5b5a7af9fbb4 + - 65db807336bc - 76d3d2b10738 + - 5b5a7af9fbb4 + - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 96336c6a2bb7 - 1c35dadbe76f - 18a502a9d287 + - 96336c6a2bb7 - 84fd33a60b35 - 00f5005840fa tool_panel_section_label: Metagenomic Analysis @@ -111,114 +111,114 @@ tools: owner: iuc revisions: - 34e55239e68b - - e8fba04706d3 - - f732237754fc - a9f4a217dcd6 + - e8fba04706d3 - addaf9d22850 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 5fe3edf19b9c - - 8c202e741d68 - 0776d824d896 - - 75403243703a + - 5fe3edf19b9c - 04c15826a0b8 + - 75403243703a + - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 8470de786d47 + - 43c99742158b - 75c8945b0da2 - - 1c9b3bcd4261 - e96bbb9e24ea - - 43c99742158b + - 8470de786d47 + - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - 306a40d4bb8f - - 84743da21318 - - 1d75bd0595e2 - 5c865a382933 - 35176674168c + - 1d75bd0595e2 + - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 32c9ea835770 + - ac72310b038a - 555ccac8a4c5 - 78faebd0879c - - ac72310b038a + - 32c9ea835770 - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - - cae017b76acb - 7b8cb2b02978 - a58e4a43f49c + - f947b4bb5107 - d60df8727f59 + - cae017b76acb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - 7f3b59dee073 - - 1bc3657cd694 + - 7136e9ab70db - 04144473e59e - 073608a50ac3 - - 7136e9ab70db + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af - - 0a1224c4b781 - a7817705348e - - d943081510da + - 0a1224c4b781 - 9058d8943303 + - 19299bb1c6af + - d943081510da tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - e005e659ae21 - c7e73acfa3eb + - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: + - b907a3c0434f - f8f56dd6449f - a68b985913ab - - b907a3c0434f - - dbf1798c0dcc - - 65d52c693b8e - 5c7ba3d85a01 - - c4db8c4de66f + - 65d52c693b8e - 4d9445dff47b + - c4db8c4de66f + - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 213df31ba341 - 15dbb444df71 + - 213df31ba341 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6d364c65c946 - 6c84982ee6f7 + - 6d364c65c946 - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -231,25 +231,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - 6aad8ca3918b - e66ab198ec15 - bd7a9c6efb10 - - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - c6676a890f50 - - d77397f09da1 - b084117133af + - d77397f09da1 + - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: + - cad93abecac9 - 9704f1a3b32d - 7f208f1eb64f - - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -281,40 +281,40 @@ tools: - name: humann_reduce_table owner: iuc revisions: - - 6552df6efe6b - 60749924ad62 + - 6552df6efe6b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - e88b731dad59 - - 79706f10d680 - - 31c6d107e7a5 - c409a495841f + - 79706f10d680 - 8237a0f225db + - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 094ad9c068af - - 172920f67a84 - aabf8cfb8fef - - 714d5a28cc5c - d24841f5c3d2 - 71ea608ddfa3 + - 094ad9c068af + - 172920f67a84 + - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - - 12fb63b5f63f - - 2bdd84912a2b - a4d7148ccee4 + - 12fb63b5f63f - 4137b492233e + - d7e9a3c41657 - a293a742194f + - 2bdd84912a2b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -326,13 +326,13 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - a92c06a3afa7 + - 75bedfb2078b - cf87759761eb - - 64bc7acc22a9 + - 97f7bb0851e7 - e2c71b852aba + - a92c06a3afa7 - 6fcb8ac37a3e - - 75bedfb2078b - - 97f7bb0851e7 + - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -351,22 +351,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c - 5e5a999ffaa9 - - 4033827c76b8 - - c82508e76ad1 + - 080ea153677c - 4e5e73d03f0d + - c82508e76ad1 - 2d35528d2141 + - 4033827c76b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - c2803012bbb3 - - 2cd76b089570 - - 95bf7479d53c - 6b7622dda516 - fc6c328c292f + - c2803012bbb3 + - 95bf7479d53c + - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: itsx @@ -378,22 +378,22 @@ tools: - name: jellyfish owner: iuc revisions: - - 11658afb8c87 - dcd30574a456 + - 11658afb8c87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single owner: iuc revisions: - - 65b382bf9b7c - 385a965c6f87 + - 65b382bf9b7c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution owner: iuc revisions: - - 7624945cacd3 - e699e2747356 + - 7624945cacd3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median @@ -427,15 +427,15 @@ tools: - name: khmer_normalize_by_median owner: iuc revisions: - - b1fe2ef3d244 - 4d23ab83ea29 + - b1fe2ef3d244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition owner: iuc revisions: - - 5a0fa29951ae - 8388fe31d604 + - 5a0fa29951ae tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kmc @@ -447,10 +447,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 + - 20e2f64aa1fe - cdee7158adf3 - 328c607150ff - - 20e2f64aa1fe + - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -483,8 +483,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - bfae8da6082c - 27d65c78863c + - bfae8da6082c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -515,8 +515,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 4960abe31b4d - 073c867c5244 + - 4960abe31b4d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -565,22 +565,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 4fd3b5d8706b + - e073891b2afc + - 0270541aaf46 + - 27250f92a01a - 7f5d7b0e9884 - 327d9f4cc95f - - 27250f92a01a - - 3cc4a60615c0 + - 4fd3b5d8706b - 2cff76cf35c6 - - 0270541aaf46 - - e073891b2afc + - 3cc4a60615c0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - eb50e7eca3dc - 708abf08a626 - 76bc4efa1aeb - - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -646,33 +646,33 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 1a6cdf55390f - - ec368db926f4 - - 6dee4abadccb - 1a037928504c - - a92a632c4d9b - - ef65b083bd0c + - ec368db926f4 + - ff8f55893e7d + - 2131d7dca455 + - fd69c607b43f - b89b0765695d + - ef65b083bd0c - 289b3807e80c + - 1a6cdf55390f + - 6dee4abadccb - a16313517e55 - 740fd2d16a28 - - fd69c607b43f - - 2131d7dca455 - - ff8f55893e7d + - a92a632c4d9b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - e3a64a1d2a6e - 2a8bc1d26d06 + - e3a64a1d2a6e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -696,22 +696,22 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 6034c3f3ecf0 - 2f47a294ef49 + - 6034c3f3ecf0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: - - 6eafc1e01a8c - 3b133b8d578a + - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline @@ -724,8 +724,8 @@ tools: - name: picrust2_pipeline owner: iuc revisions: - - 540aedfc81c7 - d6bb2e3febda + - 540aedfc81c7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs @@ -738,8 +738,8 @@ tools: - name: picrust2_shuffle_predictions owner: iuc revisions: - - 881f2faa5fe7 - 677f3c8db525 + - 881f2faa5fe7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -770,8 +770,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 65e5f9caefcc - 2e62e32d4f33 + - 65e5f9caefcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -790,25 +790,26 @@ tools: owner: iuc revisions: - f355085dd2aa + - 915637bd1d1a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: recentrifuge owner: iuc revisions: - - d4fbfd31696c - 591175c0f051 + - d4fbfd31696c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 - - 3b22de20bd4b - 4b9a8031ab74 - - 4d83eccf5f81 + - 2fd4d4c9c5c2 + - 141afacabcfa - be818ae858e4 + - 4d83eccf5f81 + - 3b22de20bd4b - aeaa20b96ef2 - - 141afacabcfa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index d28bbc559..f3b33a02e 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - 12e856482d26 - bdb4a58a2025 + - 12e856482d26 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - ab12df91b47f - 7238968f58f7 + - ab12df91b47f tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 7b187c0e1..14940925c 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 098506c54016 - - a74dbfee5a86 - - 94b8c6013083 - 6ae5a7b5a0a2 - - 9baa871cb1d1 - - 8b67dd48fec1 + - a74dbfee5a86 - 48c13389050d - - bdfbaf0c10aa - - 9eeb13a92d79 - - 2263989660f5 - 80f03df2e2ce - - cd07731e4434 + - 94b8c6013083 + - 2263989660f5 - 9422c5a87ee2 + - 098506c54016 + - 9eeb13a92d79 + - cd07731e4434 + - 8b67dd48fec1 + - 9baa871cb1d1 + - bdfbaf0c10aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 5abf2c2249aa - - d7ce0ec78e51 - - d390fe1567dc + - 4a60927aaca5 - c18157c68134 - - aaa0d6a8b808 + - 2e093badc689 + - d390fe1567dc - 3ff17bad4006 - - c44f824c051a - - be78f13134e2 - - fc2e49f91e52 - - f14193ec1f50 - '764845535798' - - f0af8936ed41 - - 2e093badc689 + - f14193ec1f50 + - be78f13134e2 - bc3831dd65c1 - - 4a60927aaca5 + - f0af8936ed41 + - d7ce0ec78e51 + - 5abf2c2249aa + - aaa0d6a8b808 + - c44f824c051a + - fc2e49f91e52 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -68,60 +68,60 @@ tools: owner: rnateam revisions: - bf28a8cff401 - - c5908940967d - - 8e649f27aa0d - - 15974dd17515 - - f0d493f8f84f - a65296ffb4a0 + - 15974dd17515 - 6f28e90db932 + - 8e649f27aa0d + - f0d493f8f84f + - c5908940967d - f1a5908ea2cb tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 - e8fdceffea4c + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - c9685bc0407c - 60698466facd - 5561a1193611 + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - - 57f042937ba7 - 48823c9635a4 + - 57f042937ba7 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - fb43e8887350 + - 4fc0cb2ac8ae - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 7cd7a55a678d - e18267f90096 - 636b049e6141 + - 7cd7a55a678d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - b4124df98b26 - - cf3c9489c088 - 959c1f8dae95 + - cf3c9489c088 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index ef60aa6b8..c28def525 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -8,11 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: + - 9aa9d92c3c51 + - 28928576e1ea - 7c47b3c9e493 - 18a8d140ec6f - - 28928576e1ea - - 9aa9d92c3c51 - - 3479b06460a4 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -25,20 +24,19 @@ tools: owner: galaxy-australia revisions: - 6942f170cc43 - - 63d8ecfcfab1 - - 090ab4f31074 - fc5b6491cf78 - 99c9427219d3 + - 63d8ecfcfab1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - a7228a7ea146 + - cb34f00cc10f - 79e9a869f40e - - fc8804320156 - 72b5e9dda577 - - cb34f00cc10f + - a7228a7ea146 + - fc8804320156 - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -46,8 +44,8 @@ tools: owner: iuc revisions: - d6cddc06aeae - - fa11aa8103b2 - 18505fe2bdb1 + - fa11aa8103b2 - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -60,15 +58,15 @@ tools: - name: medaka_variant owner: iuc revisions: - - edf6d4003fad - - 2bf63b38ee9b - - 43815fa60f3a + - cc36773a3681 + - ec699520444c + - 222669c4afb6 - 0f5f4a208660 - eb746fa6f514 + - 2bf63b38ee9b + - edf6d4003fad + - 43815fa60f3a - 19f3b583a9b3 - - ec699520444c - - cc36773a3681 - - 222669c4afb6 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -87,28 +85,28 @@ tools: - name: nanoplot owner: iuc revisions: - - a02b8b3f5a0c + - 645159bcee2d + - edbb6c5028f5 - a38bdcec9e4c + - 0f1c34698076 - a3c4fe6f49ab - - edbb6c5028f5 - 7b379e98b9a9 - - 645159bcee2d - - 0f1c34698076 + - a02b8b3f5a0c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - - 3b6f94fc7e1d - d219b6d8158a + - 3b6f94fc7e1d + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - be95355fef8d + - a8d4be409446 - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -123,17 +121,17 @@ tools: - name: nanopolish_variants owner: bgruening revisions: - - a3afc5f0a96c - bec636361cfd + - a3afc5f0a96c - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - - 93d623d9979c - 5f76b20953e5 + - 93d623d9979c + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -152,8 +150,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - d1805f9c4c82 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -165,8 +163,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 0433aad600e9 + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -216,8 +214,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - c5c5a3e84989 - 64a83664b814 + - c5c5a3e84989 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index da51a434a..cb135e3df 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - 592ef3959907 - a5921c09b7b7 + - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -28,9 +28,9 @@ tools: owner: iuc revisions: - d74850cf4e42 - - baceff842902 - - 97b1b5ad1cda - 3e73c97f025d + - 97b1b5ad1cda + - baceff842902 - adfd6bf710bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -38,8 +38,8 @@ tools: owner: devteam revisions: - 83da94c0e4a6 - - 9dd107db92c2 - 1586b111d2a3 + - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -51,19 +51,20 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - e9ee4d074d5d + - 19b6a2f0dbe2 + - ed1518ce2237 + - 2f27f3b86827 - 1e34d2e3d285 - 13851aefa67a - e4b4837f06f5 - - ed1518ce2237 - - 2f27f3b86827 - - 19b6a2f0dbe2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -82,9 +83,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - - 48a42ca61006 - 5711fc06a63e + - 48a42ca61006 + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -97,8 +98,8 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -131,10 +132,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 + - 52b6a4d98009 - 172815da3d41 - b4b2b284230a - - 52b6a4d98009 + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -167,8 +168,8 @@ tools: - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -193,36 +194,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 0cb27ea69dc1 - 5fe20c915fa6 - - 9c43baa60906 - - 4ba60cb14cb0 - d8dc037e3c13 + - 4ba60cb14cb0 - 2c61c30a57e7 + - 0cb27ea69dc1 + - 9c43baa60906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - 14785f8a3725 - d9339bb8127e + - 14785f8a3725 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 9d09724f2bf1 - 0db22932bc39 - aec831b54a5b + - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - 29c738066906 - - df30a2f1db55 - 6e24e79d3d69 - ed7a967cb11b + - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -261,17 +262,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: + - 64deddb6a8ec - d63c1442407f - c520a52b5174 - - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - 9946bc39c834 - 94a50db37d1a + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -782,8 +783,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - 544f6d2329ac - d64562a4ebb3 + - 544f6d2329ac tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -797,9 +798,9 @@ tools: revisions: - 9a22227bb6d0 - ab5b7f6b7198 - - 58a870ef434c - - f77f7a7f3b83 - ba7b0f11e470 + - f77f7a7f3b83 + - 58a870ef434c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index f2c573b5a..09e37cbee 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,64 +33,64 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - cce7b18495e4 - - f73435dc282b - - '841557158611' - - 5a7c56a5cc08 - 8834daeb9892 - - 6a457678efcb - - d033ffc1c161 + - 107d3ba7024a + - c78f3d7dd1db + - 3f59ebfbfe3d - 3b8b5bde0bd9 + - 6a457678efcb + - 81e66674859e + - 5a7c56a5cc08 + - cce7b18495e4 + - d7c7ef3353fe - a6619171428e - f04a1264e2a2 - - 3f59ebfbfe3d + - f73435dc282b - 26de3a7b1cb9 - b89cac5156ec - - d7c7ef3353fe - - 81e66674859e - - 107d3ba7024a - - c78f3d7dd1db + - '841557158611' + - d033ffc1c161 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - e75442c7f4da + - 6223845127ea + - 5b777002c2de + - df47d4845b62 - b0af57c1a968 - - 7a2092844346 - - aa8cc71438cf - - 6a726db04d4b - 4755f52427c4 - - 659517798cc4 - - 5fcd1ece3a6e - - 6223845127ea - - 6283babe736e - - 3b96e92e8ec3 - - a185b079b095 + - 7a2092844346 - 88c4aa435ded + - e75442c7f4da - 02b8758214b0 - - df47d4845b62 - - 5b777002c2de + - 659517798cc4 + - a185b079b095 + - 3b96e92e8ec3 + - 6a726db04d4b + - 6283babe736e + - aa8cc71438cf + - 5fcd1ece3a6e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - b8476e82ac20 - - d1c340a5664b + - 70acec670c30 - 111bd54f6bc4 - - f97743d52b87 - - 24d024316465 - c1d53e95327f - f87ac61981f0 - - 70acec670c30 + - b8476e82ac20 + - d1c340a5664b + - 24d024316465 + - f97743d52b87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 4f6349228462 - 9e10ba792be2 + - 4f6349228462 - feb40665d7cd - daddf188c13f tool_panel_section_label: Phylogenetics @@ -104,33 +104,33 @@ tools: - name: pangolin owner: iuc revisions: - - 2f1019071464 - - abf6dbe8c9d7 - b6abccb1f25b - - 14ae456b8cc5 + - 42a174224817 + - a2099fb98cdb + - 81804a978fc0 - 9d61d3fa046c - 437e28791761 + - 2fa9d4f1b48f + - 5f8727ff21e7 - 36912871ccdc - - 8ad84c5753ea + - 03ed9524dcd1 + - abf6dbe8c9d7 - 3a43c3982401 + - b7e297c2ede6 + - 2f1019071464 - ca0d8cf80567 - - 2fa9d4f1b48f - - 5f8727ff21e7 - - 7bb8726be37c - - a2099fb98cdb - - 42a174224817 - - 81804a978fc0 - ca337cce3888 - - b7e297c2ede6 - - 03ed9524dcd1 + - 14ae456b8cc5 + - 8ad84c5753ea - 83a69484cb87 + - 7bb8726be37c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - a4b71be30c3c + - b1e68bbe4cef - ea30d3089354 - - 29ff6a849eac - - 73a469f7dc96 - ba29b5e2a4be - - b1e68bbe4cef + - 73a469f7dc96 + - a4b71be30c3c + - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - e88a7de55d6e - - 9b2b122d0415 - - 91887494eb97 - - 809e42326fc2 - - 15ac71df11a0 - dbe2b2204555 + - 809e42326fc2 + - 91887494eb97 + - e88a7de55d6e - f1ccc8a6eb05 + - 15ac71df11a0 + - 9b2b122d0415 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index dc96116bd..f65c5a041 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - 1aac2a13842a - - b502c227b5e6 - fc288950c3b7 + - 7d34178f2812 - f6ced08779c4 - - f9242e01365a + - 3f254c5ced1d + - b502c227b5e6 - 881d7645d1bf - a1f0b3f4b781 - - 7d34178f2812 - - 3f254c5ced1d + - 1aac2a13842a + - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index bdf7209c7..09f26f36b 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -3,17 +3,17 @@ tools: owner: galaxy-australia revisions: - 5b85006245f3 - - c0e71cb2bd1b + - d00e15139065 - 3f188450ca4f - - ca90d17ff51b - - eb085b3dbaf8 - - e7f1b552a695 - 2f7702fd0a4c - - 3bd420ec162d - - e4a053d67e24 - 7fbec959cf2b + - c0e71cb2bd1b + - e4a053d67e24 + - ca90d17ff51b - 6ab1a261520a - a58f7eb0df2c - - d00e15139065 + - e7f1b552a695 + - eb085b3dbaf8 + - 3bd420ec162d tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomics.yml b/usegalaxy.org.au/proteomics.yml index fc9157b5d..219438464 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,94 +2,94 @@ tools: - name: cardinal_classification owner: galaxyp revisions: + - ece627528a78 + - b574b84afc4d - f28ad96b76dc - 277dc652246e - - b18329a8ac14 - - 4c177985028a - - ece627528a78 - 0a18ac48ac53 - - b574b84afc4d + - 4c177985028a + - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - bf06d196e23d - 525f201b86c1 - b41107d8fe89 - - e215f71d7983 - - e988563cc6e5 + - bf06d196e23d - a9a28e46d54a + - e988563cc6e5 + - e215f71d7983 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd + - 8da3511c9467 - 56da27be956a - bb6397b94018 - - 8da3511c9467 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 890845926d4b - - a8157342d9a3 - b8c79e70516d - - f23d67e28cc8 + - a8157342d9a3 + - 890845926d4b - 528fb09022be + - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - ae304a72db7b + - a69865da6f80 - 80600735685d - 25b83cbd596a - - 59e85306eae5 + - ae304a72db7b - a95a82eb4d50 - - a69865da6f80 + - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - 798da6bdff3d - - f1897eb07081 - 83aac7741200 + - ed9ed1e6cca2 + - f1897eb07081 - e0669b1854b1 - 611d80c0e29d - - ed9ed1e6cca2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 74b61bf5bc4b - - 5a35e3a8d013 - d426a9107a6c - a7fb9b395ddf + - 74b61bf5bc4b + - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - 91f0f5922011 - df2187f9013b - - 82f6c2f4332d - cc430977c8ff + - 82f6c2f4332d + - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - ba92b59cd529 + - 1693b2126f30 - c5aa9fca18c6 - - d2483487e077 - 043f9c91f686 + - ba92b59cd529 + - d2483487e077 - 10566783d718 - - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - 9fa3dbf06f17 - - ff8c9e0e8a7b - bf0728e000cd - ae4dc0c041f9 + - 9fa3dbf06f17 + - ff8c9e0e8a7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,17 +122,17 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: + - eac99effe86f - d0ea7589e95f - d263296cd73e - - eac99effe86f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: + - 0fa397f4f40b - 1c5cbf8f79ce - 4081e4faa4ab - - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -145,9 +145,9 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: + - ce1a157a41bd - d6a4dfdad269 - 0d2e93e01e68 - - ce1a157a41bd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -159,16 +159,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: + - d286ff4600dd - e66f552a3c47 - 160538a890a6 - - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -181,16 +181,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - 37d669de2828 - - 7f432d87c82c - - 1f39c833f65f - - 97a7f34fcb6a - - f522c08e900c - - e42225f8a659 - - 4d17fcdeb8ff - - 837224ad1694 - 9c52362ae7bb + - 837224ad1694 + - 4d17fcdeb8ff - 2133b0be850a + - 97a7f34fcb6a + - 1f39c833f65f + - 7f432d87c82c + - 37d669de2828 + - e42225f8a659 + - f522c08e900c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,44 +202,44 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - e63db1aa82ee - - 0ed07016d668 - 85b8866f06d7 - a72ac2c7cc5b + - e63db1aa82ee + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 990b4560ead7 + - 352b37c66d97 - 767c1d761aaf - 1974224d63c2 - - 352b37c66d97 + - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - - 4f359549383c - - 99450519d727 - 35cc7ca0bdc7 + - 99450519d727 + - 4f359549383c + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - e79958768a2c - 06f6826d380c - c7745841de24 + - e79958768a2c - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d46d64e7964d - d2eac53666f0 + - d46d64e7964d - da986f83631b - b9d453dca8d3 tool_panel_section_label: Proteomics @@ -247,10 +247,10 @@ tools: - name: metaquantome_viz owner: galaxyp revisions: - - 9bf325045235 - 1199751329b0 - - 8bd7734309f6 + - 9bf325045235 - 944b43462104 + - 8bd7734309f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -263,16 +263,16 @@ tools: - name: msconvert owner: galaxyp revisions: - - 6153e8ada1ee - ab6c14374bc0 + - 6153e8ada1ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - - de7593c29499 - 593839e1f2c3 + - de7593c29499 + - 28434abe6c5c - 8212e342e482 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -286,8 +286,8 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 8960fb791701 - 01dbaf6a57e0 + - 8960fb791701 - 4e77b8f12cd3 - f4be248c3d47 tool_panel_section_label: Proteomics @@ -295,8 +295,8 @@ tools: - name: openms_decoydatabase owner: galaxyp revisions: - - 25529df60a81 - 06cca574e337 + - 25529df60a81 - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -304,99 +304,99 @@ tools: owner: galaxyp revisions: - 6ccbf9a2072c - - 9cdf15d3cfc8 - - 518b1730cf2a - c9eff69a7c62 + - 9cdf15d3cfc8 - f7fef900f5b2 + - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - ca88bd28f116 - - 5e948629bc73 - 9876bda3ec53 + - dff6c756eee5 + - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e + - 658494a2cb00 - 890025d6e426 + - 41859bbdc16e - 1595601708ec - - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: + - 6634cad7d797 - 5ad0b5bf1deb - - 9b7977080f6d - 2a93a25f0599 - - 6634cad7d797 + - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: + - 0bb5056cb775 - d6878d27f051 - - 05d5e1ddc985 - fe4e4587d265 - - 0bb5056cb775 + - 05d5e1ddc985 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - febd569ad26f - - 5ad830edc021 - - 52ba9695e752 - 4af67edd5aef + - 52ba9695e752 + - 5ad830edc021 + - febd569ad26f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 27cba4c5fc42 + - 92352a475eed - b2fc8da99bcc - 39e8fde08881 - - 92352a475eed + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - d413dc49d650 + - 0efbc235f314 - d3546bb9fd8e - 9e26f5c770f8 - - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - ca1740533b59 - 3720e349ba2a - c28f13cab67a - 8a04ed1c1d1b + - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - 382cde407f81 + - a5d785af0ad8 - ca799a7246e7 - c427a8628cbe - - a5d785af0ad8 - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - adca857b4884 - 39caaa778d2e + - adca857b4884 - b5d0905419da - 8ddb7bab1138 tool_panel_section_label: Proteomics @@ -404,45 +404,45 @@ tools: - name: openms_idmerger owner: galaxyp revisions: - - 18f93351f8b6 - - 8d4db262964c + - f817513840a9 - 1c5f31b8d632 - 34e7afee141d - - f817513840a9 + - 18f93351f8b6 + - 8d4db262964c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - c69f69d7867a - - 986e03d3201e - - 111c3a00136d - 5d9f175dff81 + - 111c3a00136d + - 986e03d3201e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - 4204882495f2 + - be74a8cd7d66 - 0e52c85f3b15 - 476b5e296979 - - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - f5ec766d80cf - - c18d8efa4474 - a407b6790342 - 2b2a7551a857 + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - d0304fb829c0 - 4e66c4e73909 + - d0304fb829c0 - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -450,40 +450,40 @@ tools: owner: galaxyp revisions: - ee860980edc6 + - bf32e0bcf554 - 2735db4dd8d9 - 8098330f6d91 - - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - a2a6e9551046 - - 08488066d588 - 0ced5bc9f4dd + - 08488066d588 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - 2a9ff56cb279 - - de7a553552a6 - 8c01da82292c + - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - e8f64a7dc470 - - c1809c05ae8c - 1bf940c18d93 + - c1809c05ae8c + - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - f861ec9fbe59 - 9f505cd4428f + - f861ec9fbe59 - 496cf619e311 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -498,93 +498,93 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 4bb198c0bd3e - - 8b814eafce2c - 89254095cbf6 + - 8b814eafce2c + - 4bb198c0bd3e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f82b320ceb90 - - f9ed7e074900 - 05ec9fb05ed1 + - f9ed7e074900 + - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - d31426ef20f6 + - 6e8cc5ed2a9b - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 2aebe58de46e - 4a7b96835140 + - 2aebe58de46e - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - - 5ae104d0da6e - 3d8d4ada5405 + - decc397c3b7e - 6b01678ec2fc + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - 539a3a4dcc9e - - 5182338d5e7c - - dd173849c3d8 + - e039cc5c7aed - d6aca689dd48 + - dd173849c3d8 + - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - 16026cdb1330 - - d426affe977c - 8a45fd5a608a + - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: + - 9c70a651a53e - 43b9ed22e8ce - dd71e020e2aa - - 9c70a651a53e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: - 1b03536aa3c9 - - 9020199dba0a - d063e2fe4ba4 + - 9020199dba0a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: + - ad2ba3a95a02 - f036e8cf1a55 - 78c080d36945 - - ad2ba3a95a02 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - - 7f6a1f27553e - c8b225c69a7f - 5c2a97a234d6 + - 7f6a1f27553e + - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -603,8 +603,8 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker @@ -612,12 +612,12 @@ tools: revisions: - 3634c90301af - 1beff3ddce58 + - a72c48001f7c - da885ca16cb2 - 943a34df6047 - - 3ec27b4cee7c - 7fdd9119cc4f - - a72c48001f7c - 07ff622ec007 + - 3ec27b4cee7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -677,10 +677,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 12692567c7f9 - 1a5690a5eedc - - 265c35540faa + - 12692567c7f9 - a371252a2cf6 + - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 6b8dbdd0c..ba1413ffa 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,132 +2,132 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 110a346daf36 + - 2f1d464ebfd2 - cd5f98911089 - 42201b90e3f4 - 289b7d6b69a4 - - 110a346daf36 - e345aadf914f - - 2f1d464ebfd2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - fcce77c09289 - - 0cd2df8af811 - - 8501601a118d + - 0345dbaaa79b - 42d9087b4789 + - 8501601a118d + - 0cd2df8af811 + - fcce77c09289 - c207119ba5f6 - - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 405a212b32ab - - 04db7fd6b238 - 89eb29319bf4 - 421c33b8bf17 - - 33486216eec0 - ad5ab22ffe24 + - 405a212b32ab + - 33486216eec0 + - 04db7fd6b238 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - eb784fa07f80 - - 7370bb65bad4 + - 1d839ead7ad3 - fa51dc5e8386 - 7b72fde3d27e - - 1d839ead7ad3 + - 7370bb65bad4 - f6e91108b7b1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - 1544278c272e - - 3d70c2996730 - - d30e36c48c93 - c9b77ced9a78 + - 1544278c272e - 8a55d29c8fcf - a3e86cd9cac7 + - 3d70c2996730 + - d30e36c48c93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - 7b881f5f5ad5 + - a5969aa9347e - e2db212d64ad + - 7b881f5f5ad5 + - 887cf585cafc - b242deb58952 - 564c33e5c3e3 - - 887cf585cafc - - a5969aa9347e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - b4bab607eb05 - - 9a171f9a450b - - 8cff84759bf6 - bd5ff77e2036 + - b4bab607eb05 - e897c74a48bb + - 8cff84759bf6 + - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - 6dafad990086 + - 887e0991eb24 + - 33f0793edf93 - 5e10f396979e - 4f65e343ecdf - - 887e0991eb24 - adc7a7610d4f - - 33f0793edf93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 17d39bf0a63a - - 43e3eeb2e0ec - - 4e280b27a831 - - 97575d01f06b - c287418eb288 - c5d7050e4ad7 + - 4e280b27a831 + - 17d39bf0a63a + - 97575d01f06b + - 43e3eeb2e0ec tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: + - a819ec3b362d + - d9bf483266a1 + - 0b8c84a7fdb5 - cd034465d4a4 - 9586f08634c0 - - 0b8c84a7fdb5 - 09b8edb56d80 - - a819ec3b362d - - d9bf483266a1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: + - 95351dd0fd3f - bf0e43ab0416 + - 2645575d1bf2 - 69842dd5aa48 - a4b4bd84f69e - a9c34a289493 - - 95351dd0fd3f - - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - 8a35a3bc6752 + - d033e1ccb386 - cfb504394ae1 - - bb0475c884ff - 912f904a6e1e - - d033e1ccb386 - d1fda11e602f + - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - d504d945a655 - 95286af4139b + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 574e44fe2..dcbaea176 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,18 +2,18 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f + - 31f8063eedea - 7acb00fc980a + - cf01dd6c6b1f - 2d4e3aff9dc7 - - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - 703a2cb3fb38 - - 125d20cb23d7 - 7a5a2d28c539 + - 125d20cb23d7 - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -90,34 +90,34 @@ tools: owner: devteam revisions: - ad5d061fbdf2 - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - - 6926716bbfb5 - d080005cffe1 + - 6926716bbfb5 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - 86285ddd4512 - - cf747d1bd79a - - 22cf48ad7b16 - 6a6717a5f421 - 04adc9db1581 + - 86285ddd4512 + - 22cf48ad7b16 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 9a854107dbb2 - 28b94cfbfdb9 - 6cbfede05833 + - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -142,20 +142,20 @@ tools: - name: describe_samples owner: iuc revisions: - - 8f0181aacb7a - 3b36efd62b3e - - e3b16fd7dd08 - 0693ccd171c4 + - 8f0181aacb7a + - e3b16fd7dd08 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: + - d027d1f4984e - cd9874cb9019 + - 8fe98f7094de - 6a3a025714d3 - - d027d1f4984e - 0696db066a5b - - 8fe98f7094de - 24a09ca67621 - 9a882d108833 tool_panel_section_label: RNA-seq @@ -163,28 +163,28 @@ tools: - name: dexseq owner: iuc revisions: + - 9a7c5b6d8f1e - 2872c633f07e - df929f257179 - - b47c006d90c5 - - 9a7c5b6d8f1e - 62adf13b86ea + - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 0cb907a2a810 - 9bdff28ae1b1 - - 334ce9b1bac5 - - 6e53e565fc6a - - f2843df56434 - 3d89af8a44f0 - - df0c8d0a5992 - - ae2aad0a6d50 - - 5bf899c13979 - - 555659de7321 + - 0cb907a2a810 - a8305cf0c951 + - f2843df56434 + - 5bf899c13979 + - 334ce9b1bac5 + - df0c8d0a5992 - 070900306913 + - 555659de7321 + - ae2aad0a6d50 + - 6e53e565fc6a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -203,18 +203,18 @@ tools: - name: featurecounts owner: iuc revisions: - - 1b851f87fbe0 - - e6a2a912677a - - 7db9d3ea71c9 - - 38b6d12edc68 - - ea04b737afa0 - af814359d244 - - f3a5f075498f + - 90d16db017d7 - 6f66ae7c5f7a - a56fbe2d6ba7 + - 1b851f87fbe0 + - 7db9d3ea71c9 - f9d49f5cb597 + - f3a5f075498f + - 38b6d12edc68 + - ea04b737afa0 + - e6a2a912677a - a37612abf7f9 - - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -238,9 +238,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c5e024a18cf - - 3c97c841a443 - 0f710191a66d + - 3c97c841a443 + - 3c5e024a18cf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -252,21 +252,21 @@ tools: - name: hisat2 owner: iuc revisions: - - 26371a1df031 - - a86e80d3c09c + - f4af63aaf57a - 6ab42baa56e9 + - a86e80d3c09c - d4b55e2beb12 - - f4af63aaf57a - 3fb01a8c902d - 6c19daec423d + - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - 916cb26bd9d3 - 4418229c501e + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -279,32 +279,32 @@ tools: owner: iuc revisions: - 1c75aa5de15e - - ce5d418183c5 - - 5ae5c312d718 - 87c11c05d238 + - 5ae5c312d718 - 01247aaf0a10 + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 - 10c98fab6c5a - - 4f9c4e6566e5 + - 40985510cd98 - c971db6f0fe5 + - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 119b069fc845 - - 58c35179ebf0 + - 0921444c832d - 97e06a4c7c75 - - 708348a17fa1 - 32511f586472 + - 119b069fc845 + - 58c35179ebf0 - d6f5fa4ee473 - e827f9aae031 - - 0921444c832d + - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -316,8 +316,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -341,8 +341,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -360,21 +360,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 4074fc1940e2 - - 7ed2edc1337f - - 99b17b74a8cd - - 79de45b5069b + - b0f2be869d6d + - 4df95e2d7f61 - c7c55b694974 - - b9e04854e2bb - - 980d2a2e1180 - - c772497b2c32 + - 4014de1b6daf - e132e7d02a3e - 3ea5a2a63fa2 - - b0f2be869d6d - - 4df95e2d7f61 + - 79de45b5069b - 5ec75f5dae3c - - 4014de1b6daf + - 4074fc1940e2 + - c772497b2c32 + - b9e04854e2bb - 0a563fd2f22e + - 980d2a2e1180 + - 7ed2edc1337f + - 99b17b74a8cd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -386,36 +386,36 @@ tools: - name: salmon owner: bgruening revisions: - - 53e9709776a0 - cc05793bb896 - - e3d32471da11 - - f4d5237a84f6 - - ebab418107f5 - - 2c0ca397d302 - 49121db48873 + - 2c0ca397d302 - 15cd64d7c58b + - 53e9709776a0 + - ebab418107f5 + - e3d32471da11 + - f4d5237a84f6 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - 8c28affc7c48 - - c0fd285eb553 - - fab6ff46e019 - 56242ff81c84 + - fab6ff46e019 + - c0fd285eb553 + - 8c28affc7c48 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cef79931dda5 - - ae618321f34a - - 914cfcba0ec8 - cbf488da3b2c - - dd4df992d93d - 258d696dbd7e - 76d290331481 + - ae618321f34a + - cef79931dda5 - 1ebd14235b92 + - 914cfcba0ec8 + - dd4df992d93d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -445,35 +445,35 @@ tools: - name: transdecoder owner: iuc revisions: - - c6334cb383ff - d0d4cef4f967 - - 0db979fead3a + - c6334cb383ff - ffd1300599a1 + - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - ba3720d7e68b - d6a479fd4281 - 74217fbfba4d + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - c2b82a94493e - - 2fb4ee002432 - 478f36effca1 - 56162e446004 + - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - 9ff3765e7172 + - fab23c3b5258 - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -490,37 +490,37 @@ tools: owner: iuc revisions: - 5192f657f305 - - 65e7dea767ea - - 05ab8d5e04a2 - - 33406f5a445c - c5fbddcac63a + - 33406f5a445c + - 05ab8d5e04a2 + - 65e7dea767ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - e406ac71165d - - 1fdb25a8384d - - a35cba31d904 - 6f0fb35b799c + - a35cba31d904 + - 1fdb25a8384d + - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 - - 7c7fbf13aadd - 37a1129c89d2 - c2c039e421af + - 964b7efe2639 + - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - 24e94d84adc9 - 047c22569787 - - 1d689e4e1caf + - 24e94d84adc9 - eafea3083352 + - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -547,15 +547,15 @@ tools: - name: trinity owner: iuc revisions: + - d2bc35f3d1c5 - c9cfec002f71 - - 32b86cd8eb50 - - d84caa5a98ad - 9fa24d5aac68 - - 48636f857c4b - 8f1c3df4dd49 - cee61b3fcf78 + - d84caa5a98ad + - 48636f857c4b - db1f362cca3e - - d2bc35f3d1c5 + - 32b86cd8eb50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index 5c8b52871..6715dd810 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 + - 27e16a30667a - 1a052c827e88 - 080fd5739bb4 - - 27e16a30667a + - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index 3b6509c74..e4fe1406f 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -11,8 +11,8 @@ tools: owner: devteam revisions: - 1dfd95ee241e - - 993b19f20c76 - 108db6635177 + - 993b19f20c76 - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -32,8 +32,8 @@ tools: - name: bamtools_split_tag owner: iuc revisions: - - e30af4e78cd3 - e9b9c489aacc + - e30af4e78cd3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools @@ -75,17 +75,17 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 19ece8afbaab - - e7fd6754d093 - 30a201c9c310 + - e7fd6754d093 - 5f8e69cc4c6e + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam2interval @@ -103,15 +103,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - 0e60e2dd20af - cf1ffd88f895 + - 0e60e2dd20af tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -123,17 +123,17 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 649a225999a5 - 56c31114ad4a + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - - 9149ad20699a - - 6856f8a01905 - 46c6639921f1 + - 6856f8a01905 + - 9149ad20699a + - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -160,81 +160,81 @@ tools: - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - 66e23b11feae + - b906586a6596 - 720217c23995 - b3d99709fe1a - - b906586a6596 + - a8d69aee190e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate owner: iuc revisions: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - fe34990e5ce7 + - 22970df7a40e - cc61ade70eb8 - db17d5321bad - - 22970df7a40e - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - - 7def34e6cf4d - 811fc2d75ad4 - - 7a6034296ae9 - 88b8c2916784 + - 7a6034296ae9 + - fa5d3e61e429 + - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup owner: iuc revisions: - - a389f74c3630 - 40fa6c240105 + - a389f74c3630 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 36677f429310 - - cae2794d2deb - 65a38e8c8e2a + - cae2794d2deb - 740ce0a18f0d + - 36677f429310 - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - - 583abf29fc8e - - b61f5d6a7f25 - 9da0311ab1dd - 8da515fbc1bf + - 329deb17a9f7 + - b61f5d6a7f25 + - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - - 85e38b31e8b3 - db000c6007a0 - - 30388d878f81 - bb8cfc6f6e0c + - 30388d878f81 + - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -246,54 +246,54 @@ tools: - name: samtools_slice_bam owner: devteam revisions: + - b8beef827165 - a4a10c7924d1 - 344fc91e1bfd - - b8beef827165 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: + - cab3f8d35989 + - d54a4df48867 - e613c1ad4c4c - 6c2c1836728b - - d54a4df48867 - - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - bcedabb53ddf - - 135c85f4cfaf - b7f7826ef1cd + - 5d9ae78f34d3 + - 135c85f4cfaf + - bcedabb53ddf - bd850490c7f1 - 818030fa6bbf - - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 145f6d74ff5e + - 5a08c09b9311 - 1cc79f49b8d5 - 24c5d43cb545 - - 5a08c09b9311 - 3a0efe14891f + - 145f6d74ff5e - 541082d03bef tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: + - 5826298f6a73 + - b01db2684fa5 - c370440f901e - - 350bbc5c2ffd - - 32dc5f781059 - 0dbf49c414ae - - 5826298f6a73 + - 32dc5f781059 + - bf328cec6a42 - b72793637686 - - 2dce91e11ca7 - 6be888be75f9 - - b01db2684fa5 - - bf328cec6a42 + - 2dce91e11ca7 + - 350bbc5c2ffd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/send_data.yml b/usegalaxy.org.au/send_data.yml index d4b542c3a..ffca37932 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -9,12 +9,12 @@ tools: owner: iuc revisions: - 5cb6146337d8 - - d147d6455873 - - 59bb6d34fca6 - 4aab5ae907b6 - - ea5e944f447d - 6f6537780379 - a62c4a11a67d + - d147d6455873 + - ea5e944f447d - 480d9e9d156b + - 59bb6d34fca6 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index 49a3cc31f..55ec55afe 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -9,99 +9,99 @@ tools: owner: bgruening revisions: - e4c01dcece8b - - ecb9ea6269ee - - f2000bc73102 - e32b215b7c04 + - ecb9ea6269ee - b0fe3e482cb7 + - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - e1c3c2f2a834 - c0b037b12765 - 707023fa62fe + - e1c3c2f2a834 - 7a6655aa6eb2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: + - cfc3f5a57dc6 - 93dd15e13e6a - fb9e030ffae4 - - 00712416fdaa - 6f143dfe902a - - 55e35e9203cf - - cfc3f5a57dc6 - 32e547223c9e + - 00712416fdaa + - 55e35e9203cf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 038e32885fec - - 39e945f0b2c1 - - 688357ad5e61 - - 14c576ea6148 + - b9fac48532eb - ee98d611afc6 + - 14c576ea6148 - 6f0d0c784f09 - - b9fac48532eb + - 39e945f0b2c1 + - 038e32885fec + - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: + - 9bd945a03d7b - 3d748954434b - - d4af736e7b83 - - ed4996a16f7f - b85871dd69f9 + - ed4996a16f7f - 43cb7b5a6fe7 + - d4af736e7b83 - c4209ea387d4 - - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - a4774b7b2e85 - - 2e8022f1923c - fe75d2414dc0 + - 2e8022f1923c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: + - 769d815e4b0d + - 4fff5a293013 - 0e70b2dfe4be - 02b1fe7aed76 - - 4fff5a293013 - - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - aa4a6f0916b4 - a90f8efe08b4 - 344c2af50552 + - aa4a6f0916b4 - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 050cf43887d3 - - 5b7c81b35b89 - c32347702e12 + - 5b7c81b35b89 + - 050cf43887d3 - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 239193b96d72 + - 02fc39c8610d - 1d77986f9ddc + - 239193b96d72 - ae969fdb8442 - - 02fc39c8610d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -137,11 +137,11 @@ tools: - name: dropletutils owner: iuc revisions: - - 2c1200fba922 - - a9caad671439 - - 8855361fcfc5 - cfe1e6c28d95 + - 8855361fcfc5 - cdf4443d5625 + - a9caad671439 + - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -171,16 +171,16 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e - 952abbc4b1de - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 9d42a6133690 - 57aeaf6b237d + - 9d42a6133690 - f1c35f3f310d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -188,8 +188,8 @@ tools: owner: bgruening revisions: - 163fd744e235 - - 23b8d6b8960c - cab616fe7e64 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint @@ -203,72 +203,72 @@ tools: - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: + - a63e9713c39d - b892fa1fcaec - 9ea228a9afc8 - - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - f8320df1866b - - 640e0e45518a - 45a386d18509 + - 640e0e45518a + - f8320df1866b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - f963c251ac77 - - 9d02f1819e81 - c354255ff705 + - 9d02f1819e81 + - f963c251ac77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - c4ed35f4f77f - - 40fee49bc6c3 - f881c94fb3b3 + - 40fee49bc6c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: + - e06265d204f6 - 2dccb6bb0add - 782bdcb775fb - - e06265d204f6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - 63c8377c58b3 - - b05f662f9f35 - f0216498a666 + - b05f662f9f35 + - 63c8377c58b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - 8a11d70b6cd8 - - c72fa6cb8817 - fe3aa71590d5 + - c72fa6cb8817 + - 8a11d70b6cd8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - - 4f9305d3bb34 - e03780179ee5 + - 4f9305d3bb34 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 3a6a5381db36 - 4401ed529d2c + - 3a6a5381db36 - a315574104c6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -299,17 +299,17 @@ tools: - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - ffc33339cd3e - 0410b6aada45 - bf9379529c3e + - ffc33339cd3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - 5dfba24d7bdd - - 77d8e0fd162a - 07dd436ea686 + - 77d8e0fd162a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites @@ -323,73 +323,73 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 7f7c6ead2d0d - bb8849fca57c - 409396ea5cf0 + - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - 51e40e9b6c3c - e4f8fceab96a + - 51e40e9b6c3c - b0f33533181d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 55b013e59018 - - 32173084d53f - c261b6b05ee3 + - 32173084d53f + - 55b013e59018 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - 4b194e675916 - - b376ef118807 - b6b8c8672756 + - b376ef118807 + - 4b194e675916 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1511a8ebe906 - - ed900cd4a0a9 - 910c6a1c3a27 + - ed900cd4a0a9 + - 1511a8ebe906 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 2aa5b6b65197 - f34ab9882252 + - 2aa5b6b65197 - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: + - dd9988943f53 - ea5d67ec94ab - 9b383d429659 - - dd9988943f53 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 11f39d7f6c64 - - 6326cd29c1c3 - 06ced663d24f + - 6326cd29c1c3 + - 11f39d7f6c64 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: + - beb5b5917d2f - b4e780e93c91 - 337705015ee8 - - beb5b5917d2f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint @@ -403,17 +403,17 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 5cbd7a902a8d - - ea8fb5e899e8 - 21d859ad4502 + - ea8fb5e899e8 + - 5cbd7a902a8d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 1d6af10874d5 - f81750434d70 - 36dfa2825a59 + - 1d6af10874d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -439,19 +439,19 @@ tools: - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - 1d201e8378b3 - cef9fb4ece1c + - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - e98619de2776 - - 7784821452ac - db575b4c8b22 - - 4b0adaa31c95 + - e98619de2776 - eeab712b0b99 + - 4b0adaa31c95 + - 7784821452ac - 59be31ac9dc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -464,8 +464,8 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 2cfd0db49bbc - 7ffaa0968da3 + - 2cfd0db49bbc - 48f0fb3061b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -479,8 +479,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - fde4c972e7c5 - 8c64a2da3869 + - fde4c972e7c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -498,20 +498,20 @@ tools: - name: raceid_clustering owner: iuc revisions: - - f911a64454fb - - c4f39bf4a068 + - a4b734cd253b - 49776718ae90 + - c4f39bf4a068 - 7e014059a88d - - a4b734cd253b + - f911a64454fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - 43c146e25a43 - - 8b917923f7d4 - 7608d5faee41 - d45f092caf24 + - 8b917923f7d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -525,18 +525,18 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - - df8e4e54d367 - 6e90c8adf84f + - df8e4e54d367 + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - e93b008c637a - - 2bfd55b87af3 - c92d0f9338c5 - 44b935f2271b + - e93b008c637a + - 2bfd55b87af3 - 72979cac22b2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -556,102 +556,102 @@ tools: owner: iuc revisions: - 77b91b9bdf52 - - 6f83f8fd381f - - b2df381a6004 + - 4d8f983cd751 - aaa5da8e73a9 + - 8983e7a04ba7 + - 6f83f8fd381f - 6acb08931836 - - f9353ee6a0d4 - cb43c5d3acd3 + - b2df381a6004 - 38db3fef7aad - - 4d8f983cd751 - - 8983e7a04ba7 + - f9353ee6a0d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 277313130da5 - - 8cb783c81905 + - d636ce5cde16 - 64388be6d510 - - a97abb8cd15b - - a03ff8633507 - 72a6bebab2a5 - - fc0321c000a3 - b409c2486353 - - d636ce5cde16 + - 8cb783c81905 + - a97abb8cd15b + - a03ff8633507 - 3c86f71498bc + - 277313130da5 + - fc0321c000a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - d86cb2ce311b - - 3081ff5c84a3 - - 6c145a6868cc - - 6bd82ed14acd - f54f0f0598ad - - c0a80a16560f - - c5d3684f7c4c + - 6c145a6868cc - 18262103fa61 + - c5d3684f7c4c + - 3081ff5c84a3 - 5e9171dc8244 + - 6bd82ed14acd + - c0a80a16560f - 5c3ebe2adc77 + - d86cb2ce311b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 94c19fb1281c - - c9cb76cf8d6c - - 3bcd5445cd7a + - 56c0d4acef02 + - d844935c906c + - ab55fe8030b6 - 7b9fafe32c86 + - a407e7f8bdc1 - 146ae5d70b47 + - 94c19fb1281c + - 3bcd5445cd7a + - c9cb76cf8d6c - 4bda4412b8c2 - - 56c0d4acef02 - - a407e7f8bdc1 - 9f354c7c8c92 - - ab55fe8030b6 - - d844935c906c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - f7446fd8d5e7 + - 0185bd174ea0 - 1072ce66b426 - - 6f5349dd5c49 + - 9b0cdb8cf6be + - 62acdd96d4a0 + - 40812a65a78b + - 95777145cb92 + - 6adf98e782f3 - 7647e5cd1b8b + - f7446fd8d5e7 - dbbe1ea8ecb1 - - 6adf98e782f3 - - 0185bd174ea0 - - 95777145cb92 - - 9b0cdb8cf6be + - 6f5349dd5c49 - aa0c474463c2 - - 40812a65a78b - - 62acdd96d4a0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - a39040ae0a38 + - c5541bfb8feb + - 9fb627495ec2 - bf2017df9837 - 215733a383f2 - - fe8f16c594ec - - 73ab2ac53d06 - - 9fb627495ec2 - - c65fce500915 - - 458e8f43a775 - f2f6c703da06 - - c5541bfb8feb + - c65fce500915 + - fe8f16c594ec - d18e7a6e5cd4 + - 458e8f43a775 + - a39040ae0a38 + - 73ab2ac53d06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - - b834074a9aff - fd808de478b1 + - b834074a9aff + - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -671,9 +671,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - - 81e5bdff4853 - ef4c80837bc5 + - 81e5bdff4853 + - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_exprs_freq @@ -685,9 +685,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 9e5c0bb18d08 - - c99ba278dfa9 - 46fc6751d746 + - c99ba278dfa9 + - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -909,8 +909,8 @@ tools: - name: sinto_barcode owner: iuc revisions: - - fb61eb03e313 - d1b34ac42b8f + - fb61eb03e313 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: sinto_fragments @@ -950,8 +950,8 @@ tools: - name: snapatac2_preprocessing owner: iuc revisions: - - c5c94e01a1b5 - cec3e76eaf05 + - c5c94e01a1b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 1e8317b1f..feeadf51d 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 746e8e4bf929 - 2f3c6f2dcf39 - - 4c07ddedc198 + - 746e8e4bf929 - 419027d822d6 + - 4c07ddedc198 - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -56,23 +56,23 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 7a15159140d1 - cb1c59d69557 - 6c29c7e347e8 + - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - aef56d0e7a61 - - 840f29aad145 - - 7442b94d6a1e - 9c3e1d3235c8 + - 840f29aad145 + - aef56d0e7a61 - 4c4ec859c31a + - 7442b94d6a1e - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 9fda0b82f419 + - 375bbd555f4a - 30d21a6041f6 - - d0352e8b4c10 - 07843f917990 - - 375bbd555f4a + - 9fda0b82f419 + - d0352e8b4c10 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - 7ae443e6217d - 4cc980df6265 + - 8b1b2b91f8d0 - 2c58b83c9bad - - 7ae443e6217d - cd02bf168d23 - - 8b1b2b91f8d0 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - e10e776f2109 - 4bbaf77573ef - ad7e0b4291ee - 7dd3fb35904f - 1dd433d2c92c - bb9fc9d46ea4 + - e10e776f2109 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 9aa2c8c20..1a3aaf4b2 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -27,21 +27,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 464b9305180e - - 9cd341095afd - 6595517c2dd8 + - 02026300aa45 + - 9cd341095afd - aff5135563c6 + - 6e8d94597139 - be25c075ed54 - - 02026300aa45 - 13b6f0007d9e - - 6e8d94597139 + - 464b9305180e tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -53,8 +53,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -79,10 +79,10 @@ tools: owner: iuc revisions: - 9cc411a62277 - - 90f657745fea + - 37cde8134c6a - 34d29339abab + - 90f657745fea - 557ec8d7087d - - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -113,22 +113,22 @@ tools: - name: query_tabular owner: iuc revisions: + - 83069b38aa85 - cf4397560712 - - 623f3eb7aa48 - - 1ea4e668bf73 - - 33d61c89fb8d - 2e8f945f7285 - 3a6b78c39dca - - 83069b38aa85 + - 1ea4e668bf73 + - 33d61c89fb8d - cf34c344508d + - 623f3eb7aa48 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - ae8c4b2488e7 - 399da6b5ec21 - 503bcd6ebe4b - - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -140,10 +140,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - c4d18aa4ec4a - f768f6183386 - - b722161a845a - bce29ec10b78 + - c4d18aa4ec4a + - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -156,14 +156,14 @@ tools: - name: text_processing owner: bgruening revisions: + - 9ff72e942410 + - 86755160afbf + - fbf99087e067 - 12615d397df7 - ddf54b12c295 - - 74a8bef53a00 - f46f0e4f75c4 - - d698c222f354 - - 86755160afbf + - 74a8bef53a00 - a6f147a050a2 - - fbf99087e067 - - 9ff72e942410 + - d698c222f354 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml index 3b524f235..403f24a31 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -14,8 +14,8 @@ tools: - name: breseq owner: iuc revisions: - - 0d18a3ba2d1c - 85c57cc9b558 + - 0d18a3ba2d1c - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -28,8 +28,8 @@ tools: - name: cutesv owner: iuc revisions: - - 23d7e75d850e - c0f8fe52948e + - 23d7e75d850e - cb441f258c37 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -37,32 +37,32 @@ tools: owner: devteam revisions: - 04fa42777df9 - - a5937157062f - - 57def2d7c093 - ef2c525bd8cd + - 57def2d7c093 - 3e954e7125bf + - a5937157062f - 156b60c1530f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 09d6e4693887 + - 791f73caa0c8 - 435b157bed6d - e61c9ac190ad - - 791f73caa0c8 + - 09d6e4693887 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - 03627f24605f - - e1461b5c52a0 - - 65432c3abf6c - - 074d44697036 - dfadc322b065 - - 3b4b2121842f - 4805fe3d8fda + - 3b4b2121842f + - 65432c3abf6c + - 074d44697036 + - e1461b5c52a0 - b11e8e9c23bf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -77,10 +77,10 @@ tools: - name: lofreq_indelqual owner: iuc revisions: + - f4473557ffc7 + - 971e07ca4456 - 426d707dfc47 - c27549b9aa1f - - 971e07ca4456 - - f4473557ffc7 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi @@ -100,15 +100,16 @@ tools: - name: sniffles owner: iuc revisions: - - 93c4b04a0769 - 43fffeed243f + - ceff2f6a5368 + - 93c4b04a0769 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: - - 5bbf9eada9c2 - fa016f1eea1a + - 5bbf9eada9c2 - d220115f882b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -145,21 +146,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 32f14a2723ec - 40f0591deda0 - - e7aff4a85df5 - 3b1e7c170b10 + - 32f14a2723ec + - e7aff4a85df5 - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 9793bc5d741b - - 42818629ec4c - adc0645b945c - 02d81b994ef5 - 4934c0ac6197 + - 42818629ec4c + - 9793bc5d741b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/usegalaxy.org.au/vcfbcf.yml b/usegalaxy.org.au/vcfbcf.yml index 1d8a4fbf1..b48b84001 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ b/usegalaxy.org.au/vcfbcf.yml @@ -2,127 +2,127 @@ tools: - name: bcftools_annotate owner: iuc revisions: + - 265fe0f9ea64 - 2c372041ed8c + - 95815a0bb307 - ebe5fc018e72 + - b7ea370b8f5d - 6a88248893c4 - - 265fe0f9ea64 - - e075b1be5abb - 8a2e296c07ef - - b7ea370b8f5d - - 95815a0bb307 + - e075b1be5abb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call owner: iuc revisions: - - c37b684e7f4e - - b03984136ce4 - - 544cb432072b - 22637b1a55bf - - 1001172b5089 - - 21687e35f066 - - 07396b423218 + - 544cb432072b - 0fba2c15b40d + - b03984136ce4 + - 07396b423218 + - c37b684e7f4e + - 21687e35f066 + - 1001172b5089 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv owner: iuc revisions: + - 3a7084316a6e - ccb83bf54de0 - - bf1f4994f104 + - 8408bffd5616 - 01d6b7d6365e - - 143796b504eb - 8627b2b383b4 - - 8ca3647c90fd - - 3a7084316a6e + - bf1f4994f104 - 0238f68ad641 - - 8408bffd5616 + - 8ca3647c90fd + - 143796b504eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat owner: iuc revisions: - 05f317e50e61 - - abd489215f73 - - 03e0645395d2 - f430a1ec7ee4 - - 6b6c992d3a14 - - 9b5abbf50d23 - d144af39073a - 81426b3cf18b + - abd489215f73 + - 9b5abbf50d23 + - 6b6c992d3a14 + - 03e0645395d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus owner: iuc revisions: - - 95c6f3f4c77f + - 8aa352093d73 + - 1171446da5db + - d3081540d175 - 1829900b5dcd - - d37e313a41be + - 95c6f3f4c77f - e522022137f6 - - d3081540d175 - - 1171446da5db + - d37e313a41be - 2363ef414c9b - - 8aa352093d73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf owner: iuc revisions: - - d58d2e8c7a57 - - 09f37afb3621 - - 348cd212dbad - 9b29129fb491 + - d58d2e8c7a57 - b14ff40958cb - - 1137ce8efc1e - 92c0aff8b53e + - 348cd212dbad + - 1137ce8efc1e - 012656fd329f + - 09f37afb3621 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf owner: iuc revisions: - - 1f2183a23823 - - 55c0e906c14c - de68c11034f6 - ecc9192912b8 + - 1f2183a23823 - 7291189e98b4 - - cfd81f17580b + - 55c0e906c14c - 367ba501b6eb + - cfd81f17580b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq owner: iuc revisions: - 64a8f7dae3ad + - d237eaef451f - e6f4badbe6f3 + - 6c790a091c7c - 039ea3f1dea9 - ae68ceb4cca3 - 7cbf3c66d4ad - - 6c790a091c7c - - d237eaef451f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter owner: iuc revisions: - - 277719af4dd7 - - 963a3635b2e1 - - 46fcafba49ec - 6ea7170a016d + - 33bd9301568c - e7452697afd9 - - 5d6653c989cb + - 46fcafba49ec + - 963a3635b2e1 + - 277719af4dd7 - cdb7b4927742 - - 33bd9301568c + - 5d6653c989cb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck owner: iuc revisions: - - 91c1e57d5c7f - b7f0f59baa7e - - a1213a0b7b66 - - 5a321fab1fe4 - a29a2f40b665 + - 91c1e57d5c7f + - 5a321fab1fe4 + - a1213a0b7b66 - 501bfb078342 - 7b4454382d39 - 26d97cdd5410 @@ -131,104 +131,104 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 39bca000353d - - 81e4014fa809 + - c803c34361e0 - 768d04526638 - 5f27e814a119 - - d7d1663559e9 - - 15da1ddcfeff - 97d19c008d15 - - c803c34361e0 - 709dd8291b83 + - 39bca000353d + - 81e4014fa809 + - d7d1663559e9 + - 15da1ddcfeff tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge owner: iuc revisions: - 86296490704e - - 2215287d5cc9 - - b1eba148b35b - b931e65638b8 - b84fda8ebef0 - - 85ee7e6c4204 - 7ba36babba2d - 5b006286a458 + - 2215287d5cc9 + - 85ee7e6c4204 + - b1eba148b35b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup owner: iuc revisions: - - 31ea13dfe5e6 - - 5660b21a0dbd - - ce9396ddcb2b - 37757ffb4c5f + - f506df85c652 - 9c711df3258d - - 56556e1267de - cf06b44624c7 - - f506df85c652 - 0a5dcc9a8ec2 + - ce9396ddcb2b + - 31ea13dfe5e6 + - 56556e1267de + - 5660b21a0dbd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm owner: iuc revisions: - - 021693fdadaa - 1ca7418e46ee - - 48291658fdf6 - - 19905c025d2a + - 271965b55437 - 6deb4d549bc9 + - 19905c025d2a + - 021693fdadaa + - 48291658fdf6 - a404f786a94c - - 271965b55437 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts owner: iuc revisions: - - dadbd61dc4cf - - 71c78e0eea52 - 97e8145d7e30 - - c450406f722b + - 71c78e0eea52 + - 5ad5d4243987 - f7879f1e77f9 + - c450406f722b + - dadbd61dc4cf - 69d8b7567281 - - 5ad5d4243987 - 3f6fadf8b8ff tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage owner: iuc revisions: - - 6cf13a657cf6 - 52f9e4a660e3 - - 0fe007201caf - - 79f7a1acc2cd - - cc7f9a4e186b - - 283911fe7e1a - d31a2e310a52 + - 79f7a1acc2cd + - 0fe007201caf - 2514e684f8a3 + - 6cf13a657cf6 + - 283911fe7e1a + - cc7f9a4e186b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 1411bef27a75 - - 0a62420cb9cd - - 230e424bde67 - - 75ddd081f608 - - 6963a6841d22 + - 026a989b7cee - 80e6e399ccd0 - a12844ca467a - - 026a989b7cee + - 230e424bde67 + - 6963a6841d22 + - 75ddd081f608 + - 0a62420cb9cd + - 1411bef27a75 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags owner: iuc revisions: - - e493702b19eb + - 444e6a756c35 - bca7ce81688f - b10d1510fa84 - - 5acfca5a76af - - 444e6a756c35 - 5808f77b2bb6 + - 5acfca5a76af + - e493702b19eb - ba20340426fe - 450a265f92e8 tool_panel_section_label: VCF/BCF @@ -236,158 +236,158 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - f2482aa4862e - - dd72ff87cfd0 - - 68fec03a63b7 - - d52b8947b269 + - 12152af85697 - 157ffcdd3fa7 + - 68fec03a63b7 + - dd72ff87cfd0 - 4d236c696844 - - 12152af85697 - c43399f161f4 + - f2482aa4862e + - d52b8947b269 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info owner: iuc revisions: - - 8f2fc0ab30fb - bc5332d47b1c - - cbe39e530cbf - 0e5d11004815 + - 75becf493cd3 + - 8f2fc0ab30fb - 6f8e223f78f3 + - cbe39e530cbf - 8dbce095986c - - 75becf493cd3 - 29ba253e2e05 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian owner: iuc revisions: - - 3ff5654b4e7d - - 8f5962c43868 - - e0a856def0b0 - - a8630d4fbaf8 - a367a15c6de5 + - 8f5962c43868 + - f544f71adb73 - 9708e3086f32 - 88bb477f45f7 - - f544f71adb73 + - 3ff5654b4e7d + - e0a856def0b0 + - a8630d4fbaf8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref owner: iuc revisions: - 6ce175385dd9 - - 34dc0bbc7e93 - - 4ed46189d6c6 - - 5c9729d54721 - 03e30f06f15f - - 8b260d252ff4 + - 5c9729d54721 + - 34dc0bbc7e93 - 31c096c6b156 - 96d0145c041a + - 8b260d252ff4 + - 4ed46189d6c6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt owner: iuc revisions: - - 40daf124be88 - - 2c4941386820 - a730269af659 - - 46eb13bc2c73 - 681bdf1e22ff - - a1aad8b559c6 + - 40daf124be88 - 11af7fce71cf + - 46eb13bc2c73 + - a1aad8b559c6 + - 2c4941386820 - 09f5e45a8212 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 8cb121b6a1d2 - - 6cbb9c47795c + - 0594ea1417c8 - 882b2e649602 + - 8cb121b6a1d2 + - f272b8ba0983 - 12038f59c0f4 - b74b8cbfc1f1 - 743cd1472aeb - - 0594ea1417c8 - - f272b8ba0983 + - 6cbb9c47795c - 3897eaadfbff tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples owner: iuc revisions: - - dba06328556a - a9826db86d9a - - 238f78e38a8b - - adee7e8b746f - cced6715f926 - - eccb508bb678 - - 2c80b0d6bde0 - 18cf9de1cf73 + - adee7e8b746f + - 2c80b0d6bde0 + - 238f78e38a8b + - dba06328556a + - eccb508bb678 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query owner: iuc revisions: - - f64e7ca2efd2 + - e53501abf992 - c9935c9e8a24 + - e0ad88dec40d + - fdec14f69010 - 3ce32adc55b2 - - 9f36041495a3 + - f64e7ca2efd2 - 31a1b89eab9b - - fdec14f69010 - - e53501abf992 - - e0ad88dec40d + - 9f36041495a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader owner: iuc revisions: - - 3b7b1fe7b937 - - b7be725976b6 + - 79489d5685dd - fd3539749127 - - 2331ddcbd5aa - - 4db0695a6fc7 - d68c43202172 - - 79489d5685dd + - b7be725976b6 + - 3b7b1fe7b937 - d43eb39b989e + - 4db0695a6fc7 + - 2331ddcbd5aa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh owner: iuc revisions: - - 1ccf0e7fb4f6 - - 6a636d58dfc2 - 58091e1be01b - - b0d39ef600a7 + - 1ccf0e7fb4f6 - 78cd8b69da4c - - 5296d26b0373 - - fa65af07ce7d - 1a989b4110da + - fa65af07ce7d + - 5296d26b0373 + - 6a636d58dfc2 + - b0d39ef600a7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats owner: iuc revisions: - - 4d3ce9dc1525 + - bf8325a07ce7 - e8af591435d1 - - baa8823f8073 - - b17394940c7a - '388983871932' - - bf8325a07ce7 - - b641062a2587 - 591cc8518033 + - b641062a2587 + - 4d3ce9dc1525 + - baa8823f8073 + - b17394940c7a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view owner: iuc revisions: - - 3ca3de4e5291 - - c2ab91a0d506 - - 38d75661c235 - - d1f8f55f564d - - e6b5cbbf449b - 59fa8742285e - 3a233c8eb814 - 1a2ef636f48e + - d1f8f55f564d + - 38d75661c235 + - 3ca3de4e5291 + - c2ab91a0d506 + - e6b5cbbf449b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2tsv @@ -400,8 +400,8 @@ tools: - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives @@ -414,15 +414,15 @@ tools: - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes owner: devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -492,8 +492,8 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes @@ -506,8 +506,8 @@ tools: - name: vcfhethom owner: devteam revisions: - - 8254e0fe7358 - b07ef36cf7e6 + - 8254e0fe7358 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign @@ -520,15 +520,15 @@ tools: - name: vcfprimers owner: devteam revisions: - - 17096387c0e6 - d226a7327946 + - 17096387c0e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample owner: devteam revisions: - - 12b570dd0bc5 - 6257ee3b50d3 + - 12b570dd0bc5 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples