From e26e00179a619464dabd52f23d6f5d7eabe8d23c Mon Sep 17 00:00:00 2001 From: admin Date: Wed, 27 Nov 2024 03:00:51 +0000 Subject: [PATCH] Jenkins update build 221. --- automated_tool_installation_log.tsv | 9 + staging.gvl.org.au/annotation.yml | 115 ++++--- staging.gvl.org.au/assembly.yml | 271 ++++++++-------- staging.gvl.org.au/bacterial_typing.yml | 10 +- staging.gvl.org.au/bb_tools.yml | 10 +- staging.gvl.org.au/bed.yml | 16 +- staging.gvl.org.au/blast.yml | 16 +- staging.gvl.org.au/chemicaltoolbox.yml | 52 ++-- staging.gvl.org.au/chip_seq.yml | 12 +- staging.gvl.org.au/collection_operations.yml | 10 +- staging.gvl.org.au/convert_formats.yml | 53 ++-- staging.gvl.org.au/deeptools.yml | 122 ++++---- staging.gvl.org.au/dna_metabarcoding.yml | 14 +- staging.gvl.org.au/emboss.yml | 2 +- staging.gvl.org.au/epigenetics.yml | 2 +- staging.gvl.org.au/fastafastq.yml | 134 ++++---- staging.gvl.org.au/fastq_quality_control.yml | 36 +-- staging.gvl.org.au/filter_and_sort.yml | 4 +- staging.gvl.org.au/gemini_tools.yml | 30 +- staging.gvl.org.au/genome_editing.yml | 4 +- staging.gvl.org.au/get_data.yml | 42 +-- staging.gvl.org.au/graphdisplay_data.yml | 84 ++--- staging.gvl.org.au/hca_single_cell.yml | 26 +- staging.gvl.org.au/hicexplorer.yml | 30 +- staging.gvl.org.au/imaging.yml | 62 ++-- staging.gvl.org.au/ivar.yml | 74 ++--- .../join_subtract_and_group.yml | 8 +- staging.gvl.org.au/machine_learning.yml | 46 +-- staging.gvl.org.au/mapping.yml | 56 ++-- staging.gvl.org.au/metabolomics.yml | 60 ++-- staging.gvl.org.au/metagenomic_analysis.yml | 170 ++++++----- staging.gvl.org.au/mothur.yml | 6 +- staging.gvl.org.au/multiple_alignments.yml | 66 ++-- staging.gvl.org.au/nanopore.yml | 57 ++-- staging.gvl.org.au/none.yml | 56 ++-- staging.gvl.org.au/phylogenetics.yml | 95 +++--- staging.gvl.org.au/picard.yml | 10 +- staging.gvl.org.au/proteomic_ai.yml | 16 +- staging.gvl.org.au/proteomics.yml | 226 +++++++------- staging.gvl.org.au/rad_seq.yml | 60 ++-- staging.gvl.org.au/rna_seq.yml | 182 +++++------ staging.gvl.org.au/rseqc.yml | 4 +- staging.gvl.org.au/sambam.yml | 76 ++--- staging.gvl.org.au/send_data.yml | 10 +- staging.gvl.org.au/single_cell.yml | 251 ++++++++------- staging.gvl.org.au/statistics.yml | 26 +- staging.gvl.org.au/text_manipulation.yml | 48 +-- staging.gvl.org.au/variant_calling.yml | 42 +-- staging.gvl.org.au/vcfbcf.yml | 288 +++++++++--------- usegalaxy.org.au/annotation.yml | 124 ++++---- usegalaxy.org.au/assembly.yml | 249 ++++++++------- usegalaxy.org.au/bacterial_typing.yml | 8 +- usegalaxy.org.au/bb_tools.yml | 8 +- usegalaxy.org.au/bed.yml | 16 +- usegalaxy.org.au/blast.yml | 12 +- usegalaxy.org.au/chemicaltoolbox.yml | 54 ++-- usegalaxy.org.au/chip_seq.yml | 12 +- usegalaxy.org.au/collection_operations.yml | 8 +- usegalaxy.org.au/convert_formats.yml | 36 +-- usegalaxy.org.au/deeptools.yml | 132 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 14 +- usegalaxy.org.au/emboss.yml | 2 +- usegalaxy.org.au/epigenetics.yml | 4 +- usegalaxy.org.au/fastafastq.yml | 114 +++---- usegalaxy.org.au/fastq_quality_control.yml | 40 +-- .../fetch_alignmentssequences.yml | 2 +- usegalaxy.org.au/filter_and_sort.yml | 6 +- usegalaxy.org.au/gemini_tools.yml | 28 +- usegalaxy.org.au/genome_editing.yml | 6 +- usegalaxy.org.au/get_data.yml | 46 +-- usegalaxy.org.au/graphdisplay_data.yml | 75 +++-- usegalaxy.org.au/hca_single_cell.yml | 26 +- usegalaxy.org.au/hicexplorer.yml | 32 +- usegalaxy.org.au/imaging.yml | 66 ++-- usegalaxy.org.au/ivar.yml | 74 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 6 +- usegalaxy.org.au/machine_learning.yml | 30 +- usegalaxy.org.au/mapping.yml | 56 ++-- usegalaxy.org.au/metabolomics.yml | 62 ++-- usegalaxy.org.au/metagenomic_analysis.yml | 190 ++++++------ usegalaxy.org.au/mothur.yml | 2 +- usegalaxy.org.au/multiple_alignments.yml | 56 ++-- usegalaxy.org.au/nanopore.yml | 48 +-- usegalaxy.org.au/none.yml | 58 ++-- usegalaxy.org.au/phylogenetics.yml | 94 +++--- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 12 +- usegalaxy.org.au/proteomics.yml | 200 ++++++------ usegalaxy.org.au/qiime_2.yml | 2 +- usegalaxy.org.au/rad_seq.yml | 74 ++--- usegalaxy.org.au/rna_seq.yml | 184 +++++------ usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 82 ++--- usegalaxy.org.au/send_data.yml | 8 +- usegalaxy.org.au/single_cell.yml | 242 +++++++-------- usegalaxy.org.au/statistics.yml | 32 +- usegalaxy.org.au/text_manipulation.yml | 38 +-- usegalaxy.org.au/variant_calling.yml | 34 +-- usegalaxy.org.au/vcfbcf.yml | 278 ++++++++--------- 99 files changed, 3038 insertions(+), 3055 deletions(-) diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 4a7dacd28..db75614ce 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -8139,3 +8139,12 @@ Update 220 20/11/24 03:19:15 quast False Tests failed iuc a3b35edea53a a3b35edea 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 +Update 221 27/11/24 01:50:18 abyss False Installed iuc db9b10824c61 db9b10824c61 3/3 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 221 27/11/24 02:02:53 infernal False Tests failed bgruening 3711f654044e 3711f654044e Staging Testing 6/12 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 221 27/11/24 02:10:14 krakentools_alpha_diversity False Tests failed iuc 78b69342c280 78b69342c280 Staging Testing 3/5 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 221 27/11/24 02:15:54 krakentools_beta_diversity False Installed iuc 4505d7643673 4505d7643673 3/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 221 27/11/24 02:16:35 krakentools_combine_kreports False Installed iuc 3d2cffa2c4ab 3d2cffa2c4ab Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 221 27/11/24 02:31:03 krakentools_extract_kraken_reads False Installed iuc 4bf1e2701504 4bf1e2701504 11/11 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 221 27/11/24 02:35:46 krakentools_kreport2krona False Installed iuc 02bbace216f2 02bbace216f2 2/2 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 221 27/11/24 02:41:27 krakentools_kreport2mpa False Installed iuc d33cf727ed94 d33cf727ed94 3/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 221 27/11/24 03:00:28 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_221/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 8f0340122..1b577ead9 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -4,23 +4,23 @@ tools: revisions: - 3f3e247c053d - 6e9aea89e388 - - c2ef298da409 - 4efdca267d51 + - c2ef298da409 - 78c75f134c16 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 owner: iuc revisions: - - 1dd7adc21b6d - 8dc7512c9dc9 + - 1dd7adc21b6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus @@ -40,16 +40,16 @@ tools: - name: annotatemyids owner: iuc revisions: - - 133f36c29579 - - fe3ca740a485 + - a79ee60b6926 - b5d8e5475247 + - fe3ca740a485 + - 4f2967b27e67 + - 1aae04680c4b + - 133f36c29579 - 3e1f6f6d557e - 44018dd6b447 - cd2480f35935 - - a79ee60b6926 - - 4f2967b27e67 - f29602ae449e - - 1aae04680c4b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,36 +62,36 @@ tools: - name: augustus_training owner: bgruening revisions: + - f1e653756174 + - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 - - 6519ebe25019 - - f1e653756174 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - bd0e53f3a891 - - 09855551d713 - 28433faa6e42 - ca6d970d931c + - bd0e53f3a891 + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: + - 92eee5f31117 + - 728dacaf08a9 - d77802fe76f7 - da5f1924bb2e - - 728dacaf08a9 - - 92eee5f31117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - fe48aa4ccd5e - 8fd427007e93 + - 7355bbf5e05f 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: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -125,8 +125,8 @@ tools: owner: galaxyp revisions: - 9d1fbff733cf - - d9c3016f7283 - 63662ae295d6 + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -156,12 +156,12 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 3bbe70fef6df + - b6b5cd37f2a2 - 14f588312c56 - 756376aeb1ae - - b6b5cd37f2a2 - 9f2455341fac - 9c15ca7e764e - - 3bbe70fef6df - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -169,48 +169,48 @@ tools: owner: iuc revisions: - a230ea445788 - - 0ffe5be70caf - - 1691af4a0d17 - - 73428a792541 - - 989f7c061f35 - 8e1ace8f77c6 + - 989f7c061f35 + - 73428a792541 + - 1691af4a0d17 - 30fb23d4c31c + - 0ffe5be70caf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 0418d28136de - 5a5ae61da69c - - 30f08d74024f - - 494f0bb4a993 - - 563a19373357 - e94187d661df + - 494f0bb4a993 + - 0418d28136de - 57c6718cbfcc + - 563a19373357 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - d6c7106b7b2e - f77d7b685bb3 + - 1bc5a03faf2e + - d6c7106b7b2e - f31125bb85ea - 2bba2ff070d9 - 4b96ced19f75 - - 1bc5a03faf2e - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - fed64e676186 - - d77fdcca400e - - 54961e026fe4 - b3cf4684e9c7 + - 520e30695ec3 - d3af38b9c7e1 + - 54961e026fe4 + - d77fdcca400e + - fed64e676186 - 52af33194019 - - 520e30695ec3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -222,8 +222,8 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 79261884facd + - 2aea122fbd25 - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -236,10 +236,10 @@ tools: - name: goseq owner: iuc revisions: + - ef2ad746b589 - 602de62d995b - - 43798b4caee0 - 8b3e3657034e - - ef2ad746b589 + - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -297,19 +297,19 @@ tools: - name: maker owner: iuc revisions: - - 370c210d9541 - d46d803ca6cc - 3c1a01127868 + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 033755194fe9 - b815ec682418 - - c8ac28e8ac44 - e95d52d295d7 + - c8ac28e8ac44 - 624606f7c996 + - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -352,10 +352,10 @@ tools: owner: crs4 revisions: - 8a22554cdde2 - - eaee459f3d69 - - bf68eb663bc3 - a17498c603ec - d643e3b03500 + - bf68eb663bc3 + - eaee459f3d69 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -367,15 +367,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -399,24 +399,23 @@ tools: - name: snpeff owner: iuc revisions: - - 8f92c2b26e6d - - ca2b512e8d7c - - c7275bd8b4d6 - - 268d162b9c49 - - 68693743661e - cfcf33df7fc0 + - 268d162b9c49 + - 5b80f544c67f - 6322be79bd8e + - 8f92c2b26e6d - 5a29ab10dba6 - - 5b80f544c67f + - 68693743661e + - c7275bd8b4d6 - 5c7b70713fb5 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: snptools @@ -441,25 +440,25 @@ tools: - name: tbprofiler owner: iuc revisions: - - 51dd22484644 - 45083d070fb8 - - 37213cf56392 - - ac8250086ac3 - - e1a9d6fd258d - - d03af1c7002c - 8cb134b8c1a5 - - 037a11682176 + - 4839e590cb26 + - ac8250086ac3 - 809dfc93d593 + - 51dd22484644 + - 037a11682176 - 200c378d85f3 - - 4839e590cb26 + - d03af1c7002c + - e1a9d6fd258d - ba6f87115e13 + - 37213cf56392 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/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 14bc5c417..ae1b3ce05 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,27 +2,28 @@ tools: - name: abyss owner: iuc revisions: - - 0124fce4654a - - 890b794c997d - - fa5259cc561b - - 7547fcab5d19 + - 0e93176640ac + - a929ce596a34 - 8f1b150a2487 + - db9b10824c61 + - 553bfe8bd0b5 + - fa5259cc561b - d6d5ccc2c581 - 841084c5fc46 - - 553bfe8bd0b5 - - a929ce596a34 - - 0e93176640ac + - 7547fcab5d19 + - 890b794c997d + - 0124fce4654a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - 94fe43e75ddc - - b2860df42e16 - - 067592b6b312 + - b9e31c5c01c7 - 21e491ad532a + - b2860df42e16 - ddddce450736 - - b9e31c5c01c7 + - 067592b6b312 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -37,8 +38,8 @@ tools: revisions: - 3371c5bdc17a - 5258e18bbe23 - - 22286dab5aa1 - a7f16f24e9a1 + - 22286dab5aa1 - faee8629b460 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -47,38 +48,37 @@ tools: revisions: - 53dd00a4ab68 - '392811378515' - - 8c2167481e72 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 1e62c28ba91d - - 1440ae06552f - - e824f5d958d0 - - ea8146ee148f + - f18f0b887c31 + - 0d243f458b53 + - cf13a1e03e5b - e5c372c91e46 + - e4bd1e99bacf + - 94170eee0ad8 + - 602fb8e63aa7 + - 2dd755c1c6ff - bb935709506a - 41030a6c03b7 - 46ae58b1d792 - - 0d243f458b53 - - 2dd755c1c6ff - - 602fb8e63aa7 + - 4048d82f0c88 + - 1440ae06552f - 5ecdeca79a0d - - 94170eee0ad8 + - 1e62c28ba91d + - e824f5d958d0 + - ea8146ee148f - 2babe6d5c561 - - f18f0b887c31 - - cf13a1e03e5b - - e4bd1e99bacf - - 4048d82f0c88 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - 5732f959936a - - c5b7390290b1 - 86f150c8019d + - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -90,32 +90,32 @@ tools: - name: flye owner: bgruening revisions: - - 8d4f03b5fe9d - - 3e4f8642c77e + - cb8dfd28c16f - 1ce9b1d72ec3 - 276f5d8712d5 - - e27815e82dd4 - 3ee0ef312022 - - 291923e6f276 - 1f0769f0b56b - - cb8dfd28c16f + - e27815e82dd4 + - 8d4f03b5fe9d + - 291923e6f276 + - 3e4f8642c77e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - 01210c4e9144 - - b2f674562a18 - 460fad600dce + - b2f674562a18 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 8b330a577046 - - 7348b69e5109 - 06bcf65179fb + - 7348b69e5109 + - 8b330a577046 - ba88bc5a6446 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -123,11 +123,11 @@ tools: owner: bgruening revisions: - 5127a713de83 - - 690c2caa367e + - 6ec1b853c8fd - 3ef480892a9f - - f4a3eff8ab85 - 3fba9c77550a - - 6ec1b853c8fd + - f4a3eff8ab85 + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -139,24 +139,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - 366a11d316a7 - - da9d8bf98802 - - 6505bd37670d - - 3f7be05a1597 - 60024a528cbd - - 5bec28269d95 - - 2061fb3b81b4 - - 5f625c63b8bc - - 9ef6920c3089 + - 045c7c3d8e59 + - 6505bd37670d + - 0ee0c3089254 + - df25d4fb79b7 + - 71740308d412 - 284a1cb82b61 - - 41cea2aa2dce + - 9ef6920c3089 - f3c89da3af16 - ec9e21e9c71b - - 71740308d412 - - 0ee0c3089254 - - 045c7c3d8e59 + - 3f7be05a1597 + - da9d8bf98802 + - 41cea2aa2dce + - 2061fb3b81b4 + - 5bec28269d95 + - 5f625c63b8bc + - 366a11d316a7 - 5161f204ba63 - - df25d4fb79b7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -174,8 +174,8 @@ tools: - name: megahit owner: iuc revisions: - - de387b2b2803 - a96f3ad4e0d8 + - de387b2b2803 - 14ddfc8ffb93 - 7518ee87b53d tool_panel_section_label: Assembly @@ -183,12 +183,12 @@ tools: - name: merqury owner: iuc revisions: - - 09c589057ee8 - - eb7b00ec347d - 39edec572bae - 9d79beb19ac3 - - f8113c25bc6b - d7edbc9c3a07 + - eb7b00ec347d + - f8113c25bc6b + - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl @@ -202,15 +202,15 @@ tools: - name: metaspades owner: nml revisions: + - f369ef5f210b - fd128c111ab0 + - 99ecfdafc64f - 3ca2d2a9068c - - f338e9942b27 + - eb7a370f6588 - 2ecf5a570907 - - 99ecfdafc64f - - f369ef5f210b - e731ea24e48d - 606b09cc9860 - - eb7a370f6588 + - f338e9942b27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -222,11 +222,11 @@ tools: - name: miniasm owner: iuc revisions: - - b799a615995d + - a7b889b90140 - 8dee0218ac7d + - b799a615995d - 8b6d0d85252b - 73a3846701e1 - - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -244,8 +244,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 7c2f5268d01c + - 64a1c751d99b - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -258,47 +258,48 @@ tools: - name: pretext_map owner: iuc revisions: - - dfb8a4497339 + - 02831bf9e95f - c6cec5ab35c1 - 2b16ba799da9 - - 8fef980d48b5 - - 02831bf9e95f - - d256a51a656b - 79b48f02db49 + - dfb8a4497339 - bbe19ef04a74 + - d256a51a656b + - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - 76d4cbefff85 + - e9bd16ba5ebd - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: + - 342a1d1fed7b - 875d0f36d66f + - a3b35edea53a - 72472698a2df - - 342a1d1fed7b - - 675488238c96 - - 6fcbee531de6 - - 3061c8b029e5 - 59db8ea8c845 + - 3061c8b029e5 - 7594365c546b - ebb0dcdb621a + - 675488238c96 + - 6fcbee531de6 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - aa39b19ca11e - - 39bed8de8017 - - 78c533842eeb - d865b62f501c - a199cd7ac344 + - cd06929b224b + - 39bed8de8017 + - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -316,12 +317,12 @@ tools: - name: raven owner: iuc revisions: - - 5c55448d0f33 - - 33b7d8481a76 - f8564b2d7f63 + - 33b7d8481a76 + - 5c55448d0f33 + - f11b994b7eb2 - 3edba9afc9bc - 2b2a352488fa - - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -334,13 +335,13 @@ tools: - name: rnaspades owner: iuc revisions: - - 1d06c8b38e77 - - 378e55aeeb25 - - 53c2bc8c2ae3 - e122f9101584 + - 28189050e437 - ef69617ecb42 + - 1d06c8b38e77 + - 53c2bc8c2ae3 + - 378e55aeeb25 - 5fc94b3a4704 - - 28189050e437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -352,80 +353,80 @@ tools: - name: shovill owner: iuc revisions: - - ad80238462c1 - d9f6a00b6db7 - - ee17a294d3a3 + - ad80238462c1 - 83ead2be47b2 - - f698c7604b3b - - 196a599ec43d + - ee17a294d3a3 - 865119fcb694 + - 196a599ec43d + - f698c7604b3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - 24e471d13fe9 - - 5e0825476fb7 - 015283de3004 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 1fc82fe7ebef - - 904bf932cf78 - 1bb12736175c - - 051fd2db8a27 - - c33a476f4001 + - 904bf932cf78 - 604782a8a53a - 7490b213baa9 + - 1fc82fe7ebef + - 051fd2db8a27 + - c33a476f4001 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - fee85957cebe - - 34305b013402 - - 9678993ca5bd - - d6e617c4e338 - - 808b3a0a6716 - ad8b536d1caa - 655fa188c3cc + - 808b3a0a6716 + - d6e617c4e338 + - 9678993ca5bd + - 34305b013402 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - e5a3b75a271f - - 6b5a5842531e - - 8d4b90bf9caf - 037f9927c4ff + - b8002c3f7141 - 21da31ed41a1 + - 8d4b90bf9caf - 7e27faaad80e - - b8002c3f7141 + - e5a3b75a271f + - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 9de69775f512 - - 2a10645aeadd - f1532cb33c75 - - 5b26685e5d3b - - 86f66ab58e14 + - 2a10645aeadd - 7922870efcca + - 9de69775f512 - 328aa71f0f3c + - 5b26685e5d3b + - 86f66ab58e14 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: + - 1708851f8804 - e41dcb0e913b - - 340bc17f49cf - - 85fb02c43042 - 8cc856b935ee - 6aad515a5270 - - 1708851f8804 + - 340bc17f49cf + - 85fb02c43042 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades @@ -433,59 +434,57 @@ tools: revisions: - de1260f8a300 - d5fb354f745d - - b3490b036c5a - - b65a43f70b99 - d159735a6a9f - - 6357b127161e - 249f6a28c751 + - b65a43f70b99 + - b3490b036c5a + - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - d5887ace0dd4 - - d2d1df21dfb9 + - 9006e5836729 - b7829778729f - - 7897763d14ec - - dd7ad84f3943 - 33368fec3b70 - - 9006e5836729 + - 7897763d14ec - a90db5dbaaf3 + - dd7ad84f3943 + - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ced385aa976d - - 505a9833ab5d + - 0368ac680e70 - 189e837009c9 - 6f4c8ad6ea01 - - ed2425b9fd27 - - 0368ac680e70 - 8f631679571f + - 505a9833ab5d + - ced385aa976d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 356afed970b4 + - a7ed21de23fe + - 19bdfd1e6fe3 - 9ded6109434a - d40ed4eb0c0e - - a7ed21de23fe - - f31d376ce725 - e59bee4565b3 - - 19bdfd1e6fe3 + - 356afed970b4 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 + - 6dd935e4984b + - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa @@ -493,54 +492,52 @@ tools: revisions: - ed312479d9eb - cb1e3db43020 - - bb11fefb23a3 - - b64696992ee9 + - 59bd28f6265d - 937ea677d437 - b5e35a2ca4f3 - - 59bd28f6265d + - b64696992ee9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - b9b0246a2be3 - - 2628f6790eda - 6015aa0303f2 - - cb4768eeca3b - - 6bfab4a4a988 - 383bb5ad32e2 - 05bd7504fdb2 + - 2628f6790eda + - b9b0246a2be3 + - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - 0a3a602cd1e3 + - 6e26c9afd301 - 9e3e80cc4ad4 - 8f9f06995f98 - - e022dff952df - 3e44ef016b45 + - e022dff952df - e92675014ac9 - - 0a3a602cd1e3 - - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 5da9a0e2fb2d - 08256557922f - - 8d09f8be269e - 920677cd220f + - 5da9a0e2fb2d + - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 0e2b4e3f9ca1 - 4a53b89fa703 - - 82398ba86ba7 - - 37d88f41c810 + - 0e2b4e3f9ca1 - d81360ea69d8 + - 37d88f41c810 + - 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 7303e3df5..fa5523c0e 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,9 +2,9 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - - 392f100eebcd - 4768f7f8e93f + - 392f100eebcd + - 1ae00120dd24 - bfd290fe1588 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: - - 31812e7a1315 + - 8e8dc9a1e3e5 - 1f5641a52664 + - 31812e7a1315 - ded48b36f3b7 - - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - 24a7a95867b0 - - 17fcac7ddf54 - 5c8ff92e38a9 + - 17fcac7ddf54 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 b2eeb315e..e064325a6 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,14 +2,14 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 159b04e36791 - a9c9d768b751 - - 204a131e47db - - 1c427e24fb79 - 0840ba83860c + - 1c427e24fb79 + - 204a131e47db + - d58c27d2c5a7 - 7beb76ffbc0f + - 159b04e36791 - d1f62024a08b - - d58c27d2c5a7 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge @@ -22,7 +22,7 @@ tools: - name: bbtools_tadpole owner: iuc revisions: - - 0ddf147d1897 - ce13b4678f18 + - 0ddf147d1897 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 3aa4c16c2..440c1e6ba 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: - - 589e7e57fd6d - - dde39ba9c031 - - 87ee588b3d45 - 64e2edfe7a2c - - 0a5c785ac6db + - ce3c7f062223 - a1a923cd89e8 - - a68aa6c1204a - - e19bebe96cd2 - a8eabd2838f6 - - b28e0cfa7ba1 - 07e8b80f278c - - ce3c7f062223 + - 0a5c785ac6db + - e19bebe96cd2 + - b28e0cfa7ba1 + - a68aa6c1204a + - 589e7e57fd6d + - 87ee588b3d45 + - dde39ba9c031 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 c5e1c8c39..cca989b34 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -9,9 +9,9 @@ tools: owner: bgruening revisions: - f921014aba5a - - 54f751e413f4 - - e8ac2b53f262 - 62c9df8382c2 + - e8ac2b53f262 + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - a52d2d93e595 - - d999e774072a - - acf4e47b734c - - 0e3cf9594bb7 - 2889433c7ae1 - - cbf3f518b668 + - 6f386c5dc4fb - e25d3acf6e68 + - acf4e47b734c + - 0e3cf9594bb7 - 5edc472ec434 - - 6f386c5dc4fb + - a52d2d93e595 + - cbf3f518b668 + - d999e774072a 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 bb52084eb..dfcecb47a 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -9,12 +9,12 @@ tools: owner: chemteam revisions: - 095ad4d096d1 - - 27ee142314a9 - - 6ca543ec1bf8 - - 710301bc46fa - da6bd1975a71 - - f4230f116196 - c8cdde00b105 + - 6ca543ec1bf8 + - 27ee142314a9 + - f4230f116196 + - 710301bc46fa tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -130,74 +130,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 3b8a9d5ced85 - - 88076940fa94 - bfb65cb551d8 + - 88076940fa94 - 0fac8e2afc13 - 79cfd9ead848 + - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - 55918daa5651 + - eb6564a60136 + - 715cd0e87781 - f5d979cb4b54 - d532b7e5f64b - b46d4b4d995c - - 715cd0e87781 - - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - f26afd1b7104 - 5579659312e6 + - d2f955aea23a - fdf2cc80adb5 + - f26afd1b7104 - 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 + - d1d0efda35c0 - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: + - ed736e6eee39 - 070e3ecc3fda + - 2c349b027a01 - cac1886249a2 - - ed736e6eee39 - 4da9ee404eab - - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - 73008ef1f487 - - c0c9a5024177 - - d1f803b5943c - - da8753545526 + - 2e219a2d9327 - 807aa4c9293d + - d1f803b5943c - f197e34c33a9 - 525ca7c8065f - - 2e219a2d9327 + - c0c9a5024177 + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: + - c4fbab8e03c5 - 61094e01eff9 - 1809414a9454 + - 2c8ed1b52bf7 - 7568ae18908a - - c4fbab8e03c5 - 27ea4e1a3f95 - - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: - - 730ef07b90ae - - 79e8ab8f1e81 + - ccfbd956a2d3 - d7ec25187599 - ba83f0923369 - - ccfbd956a2d3 + - 730ef07b90ae + - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -270,8 +270,8 @@ tools: revisions: - 4242b4d68e9c - b59c91adeac1 - - e6011617c748 - 1400d1977e7b + - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -304,8 +304,8 @@ tools: - name: qcxms_production_run owner: recetox revisions: - - e97bfe7ac906 - 356f7916ac07 + - e97bfe7ac906 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 + - 85fad59f8168 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 af06e8f9c..cea520d21 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 @@ -31,10 +31,10 @@ tools: owner: iuc revisions: - f5d67c722d67 - - 424aefbd7777 - 640d3af5d833 - 495a4173006f - 86e2413cf3f8 + - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -46,16 +46,16 @@ tools: - 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: - - 74c9214cc8e6 - - 4a14714649b4 - 5c2cc3b58c7d + - 4a14714649b4 + - 74c9214cc8e6 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 42d913203..27937c549 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -9,17 +9,17 @@ tools: - name: collapse_collections owner: nml revisions: - - 33151a38533a - - 830961c48e42 - 90981f86000f + - 830961c48e42 + - 33151a38533a - 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 @@ -31,10 +31,10 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - - baabc30154cd - 2dae863c8f42 + - baabc30154cd - 6cbe2f30c2d7 + - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 8fa70754e..c53d806d6 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -2,9 +2,9 @@ tools: - name: agat owner: bgruening revisions: - - e7449b2c14bf - d6ede73082da - abba05ead5d7 + - e7449b2c14bf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -16,39 +16,39 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 6ef0b5664c69 - - 367b1ed91207 - 3b6f97e7094c - - 5e1240a87bcb - - a3b86937ead6 - e3cbd2287f63 + - a3b86937ead6 + - 4a6ee918c13a + - 6ef0b5664c69 - ab9350a8ab4d - - 0b3c3ad92827 + - 5e1240a87bcb - f3a19509108a - - 4a6ee918c13a + - 367b1ed91207 + - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 501c21cce614 - - 584008e574b2 - - bd46669113b9 - - 1b5fc03380d4 - - 72ed72122deb - e525f9ffb9ac + - 091bb5922a82 + - 584008e574b2 + - d4d4e9febf5c - 54ccb7e1f49a + - 501c21cce614 - 33c99804a32f + - 1b5fc03380d4 + - 72ed72122deb + - bd46669113b9 - e177a8ea0bf1 - - d4d4e9febf5c - - 091bb5922a82 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - a0d092f27fdf - 11c3eb512633 + - a0d092f27fdf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -60,24 +60,24 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: + - 186b8d913e6c - 8979c288aefb - 77b41c89d856 - - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - - 4b347702c4aa - 43807a65369f + - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -103,8 +103,8 @@ tools: owner: devteam revisions: - 154d00cbbf2d - - 3e436657dcd0 - 4dea02886337 + - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -116,7 +116,6 @@ tools: - name: intermine_galaxy_exchange owner: iuc revisions: - - c24014d80001 - faef2b1622a3 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,26 +136,26 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0b4e36026794 - 0a7799698fe5 + - 0b4e36026794 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: + - 2dcfbbf9071a - 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 + - b9b385097f13 - 63769c4217a7 - - 26c6706bfb07 - 92ac8e086317 - - b9b385097f13 - - 19e45916daf9 + - 26c6706bfb07 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -168,9 +167,9 @@ 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 diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index e431f54a2..b9e12cb66 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,108 +2,108 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 5f6d123679f4 + - 268e91e540ee + - de72ba3ed6f2 - a1ca9bccc7f2 - e821645ef8fc - - 268e91e540ee - 29451af70c52 - - de72ba3ed6f2 + - 5f6d123679f4 - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e49b109abc2 - - bb1e4f63e0e6 + - 7a7fd0f5f15d - 0e143b4c3987 + - 0e49b109abc2 - 2d2cf5c1ea8a - - 5d11599b8a7d + - bb1e4f63e0e6 - 12af64f93288 - - 7a7fd0f5f15d + - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - dc059492a995 - - 7c1beb6d6eca - 195e98217334 - - c06951d10364 - 81b1e3e1fc6c + - c06951d10364 - 1d848bc4585f + - 7c1beb6d6eca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 07418a30ed01 + - 71aa86af6762 + - 3d211717a775 - a67ac707496a + - 93eb012d9eed + - 07418a30ed01 - bfff7454b59a - - 3d211717a775 - 26e7304d6737 - - 71aa86af6762 - - 93eb012d9eed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - dd0b7398bb96 - - b8858746dc1f - - 29fcfd36e90a - - 26983857c91a - 56d5b797ce84 - 5be24eba848d - 2bc10a9ca58b + - dd0b7398bb96 + - b8858746dc1f + - 26983857c91a + - 29fcfd36e90a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7e6bcd2e5128 - - e6d0bff01239 - - 9384cd033f30 - c3e012dfe21f - - 7ef978dc1b8a - ee3a1b0f45f1 - 72bfafe3330b + - 9384cd033f30 + - e6d0bff01239 + - 7ef978dc1b8a + - 7e6bcd2e5128 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: + - 514fa53b5efb + - fd1275e01605 + - 167788df3b46 - b73e213add0c - 9470f29702f8 - d9a637e83828 - a60c359ec43c - - 514fa53b5efb - - 167788df3b46 - fb9cf9c97ec4 - - fd1275e01605 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 5bffaa8354a1 - - e479c7ca5570 + - ca0616bb2cdf - 2c37ce318bc3 + - 5bffaa8354a1 - 86febdcc4283 - - ca0616bb2cdf - - c34d11ea4ba6 + - e479c7ca5570 - a02cfa31e9cb + - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 192ef85c0b0b - - 2d466b530754 - 78f405266706 - - 004aea905d4d + - 2d466b530754 - 1fcb7adc39b8 - 69a8621ca2f0 + - 192ef85c0b0b + - 004aea905d4d - 01fb6a7654e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,96 +111,96 @@ tools: owner: bgruening revisions: - d9ce4897dbb2 + - d580d6acd1df + - 3c9f0c486cca - 9ecba5e225a6 - - 137c4beed34b - db940c262830 - - 459cfa861f0b - - 3c9f0c486cca - 2f9e4843f480 - - d580d6acd1df + - 459cfa861f0b + - 137c4beed34b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: + - fd408d755394 + - bad3ca889618 + - bd7db9e2f2cb - 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: - - 9368fbc49c8b + - 4e12ea27f788 + - 56bce3c82278 - 3b9d990a0a0e - - 7fda5607e777 - 7e361d147872 - - 56bce3c82278 - - 4e12ea27f788 + - 7fda5607e777 + - 9368fbc49c8b - 231994413f89 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - ce4ce3316f74 - - b1779366c8e9 - 4431f39ede55 + - e65d16fb2724 + - b1779366c8e9 - c03c3384cd81 - 94ca68515826 + - ce4ce3316f74 - d9114ef1c8a5 - - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 4ed32329e0ed - - 23f7c5f1fdaf + - 2da482e408b8 - b88ebb3672a1 + - 23f7c5f1fdaf - f8fc4e5aff9d - - 793665fff0f8 + - 4ed32329e0ed - d57251071381 - - 2da482e408b8 + - 793665fff0f8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 010e58e9d822 - - 512155688d98 - - ba6efa77fb79 - e4c7985d4585 + - ba6efa77fb79 + - 010e58e9d822 + - a4dfb122e52b + - 25d830337d31 - c60570fa602f + - 512155688d98 - a7849312d328 - - 25d830337d31 - - a4dfb122e52b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: + - c899e0ccff8c - 4d678170d29b - - 443d9a9d6d11 - - 38e3f226248b - 00d869ea03a1 - - aa200e4f3939 - - c899e0ccff8c - 69264da0ce77 + - 38e3f226248b + - aa200e4f3939 + - 443d9a9d6d11 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - aac8444d6681 - - d806504e96d9 - - a2d70c4fd406 + - c361b12d207a - 6662b1a8d326 + - a2d70c4fd406 - 10301d137111 - - c361b12d207a + - d806504e96d9 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 79884cada..f16285954 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -2,15 +2,15 @@ tools: - name: obi_annotate owner: iuc revisions: - - d50dc96e3ce9 - 3021b9f5809f + - d50dc96e3ce9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -23,22 +23,22 @@ tools: - name: obi_grep owner: iuc revisions: - - 02bab5ff7c37 - e9e49cf06b42 + - 02bab5ff7c37 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 94f412098ac8 - 8cb6bd511879 + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -58,14 +58,14 @@ tools: - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 4cf47c504672 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - d4bea99366f9 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index 08bf8c016..b265e8fe5 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - dba489bfcd62 - - 63dd26468588 - 832c20329690 + - 63dd26468588 - 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 b7e7acbb2..18d5fa26d 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,9 +8,9 @@ tools: - name: bwameth owner: iuc revisions: + - d82648ad25a3 - cf1322aeb137 - 62f5fab76dfb - - d82648ad25a3 - 6da3972210ee - 29bdbc353f20 tool_panel_section_label: Epigenetics diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index ad180d118..4156fe1b9 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -9,25 +9,25 @@ tools: owner: lparsons revisions: - c053d4cad713 - - de6cebe3c043 - - 288f97432497 + - 49370cb85f0f + - 4e5056fefd88 + - 5eb7e84243f2 + - b1c926deaa2d + - 8665bcc8b847 - 660cffd8d92a - - c4b82dce8335 + - 44e2cc14f75b + - 8c0175e03cee - c5e2e5902201 - - b1c926deaa2d - 5915ea1ec9b1 + - de6cebe3c043 + - 64172f1c1202 - 093678460093 - - 8665bcc8b847 - 135b80fb1ac2 - - 48f587c13075 - - 49370cb85f0f - - 5eb7e84243f2 - - 64172f1c1202 - - 4e5056fefd88 - - e4691e1589d3 - - 8c0175e03cee - fe74900d6dc7 - - 44e2cc14f75b + - c4b82dce8335 + - e4691e1589d3 + - 48f587c13075 + - 288f97432497 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -40,8 +40,8 @@ tools: owner: devteam revisions: - f666895cbebd - - 9db07fd39f85 - 8889eb864cef + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -54,8 +54,8 @@ tools: owner: devteam revisions: - de2db1bdfbf8 - - 7d37cfda8e00 - 5cbde03c1103 + - 7d37cfda8e00 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: - - 25b8736c627a - 717aee069681 + - 25b8736c627a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -80,8 +80,8 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - 8cacfcf96a52 - e626b3ff9922 + - 8cacfcf96a52 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -101,16 +101,16 @@ tools: - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - f546e7278f04 - 2904d46167da + - f546e7278f04 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - f81d4362b6c1 - f773e98b26cf - ec0b5076173a + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -122,10 +122,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 0dbb995c7d35 - 56022eb50bbd - - 9c620a950d3a - cd0874854f51 + - 0dbb995c7d35 + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -137,14 +137,14 @@ tools: - name: fastp owner: iuc revisions: + - c59d48774d03 + - dbfc505896e9 + - a626e8c0e1ba + - d60c3f704da0 - 1d8fe9bc4cb0 - - 65b93b623c77 - dbf9c561ef29 - - a626e8c0e1ba - ecb9f4854617 - - dbfc505896e9 - - d60c3f704da0 - - c59d48774d03 + - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -156,9 +156,9 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - - f1dc2a761c30 - 9115b978ce10 + - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -170,9 +170,9 @@ tools: - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - - 10b75444feae - '144275714590' + - 10b75444feae + - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -184,9 +184,9 @@ tools: - name: fastq_groomer owner: devteam revisions: - - e9f8633db0a2 - - 47e5dbc3e790 - 8611b80a14d6 + - 47e5dbc3e790 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -212,8 +212,8 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 4e1d64e6385f - 9dfda4e310ed + - 4e1d64e6385f - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -227,8 +227,8 @@ tools: owner: devteam revisions: - 523c2aff0376 - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -240,9 +240,9 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - b41c2c1bcfbf - - 2ccb8dcabddc - 3e396e702cea + - 2ccb8dcabddc + - b41c2c1bcfbf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -254,9 +254,9 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - c885369b207b - - 8d958759cf2a - 09a2199cd356 + - 8d958759cf2a + - c885369b207b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -268,9 +268,9 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: + - 35e38452bb3f - e39cc71d3ed6 - 249c8393f2d4 - - 35e38452bb3f - 397dc333436b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -284,8 +284,8 @@ tools: owner: devteam revisions: - 74db4cffab1f - - 54053ea6c77e - 045f0e1043f7 + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -311,8 +311,8 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - 33794bdb7fe0 - f0b18efb97f1 + - 33794bdb7fe0 - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -332,10 +332,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - d5e9e83cd3d8 - - 567d5b3c52b1 - - 09070cacefd8 - 529bccd5e4a1 + - 09070cacefd8 + - 567d5b3c52b1 + - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -348,8 +348,8 @@ tools: owner: devteam revisions: - 8abdedf55101 - - 0b7ec11b3c7c - 4bedca26c133 + - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -362,9 +362,9 @@ tools: owner: devteam revisions: - 736b8f6ee456 + - 90858c306551 - bdf1ce174e39 - cb1e251cac37 - - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -390,10 +390,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - b29d37ca9e41 - - f984bb114520 + - 3599f5451ee2 - 02f8a17a4ebd + - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -405,10 +405,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - e246088b6e34 + - 177f0621c266 - 6027ef51ef91 + - e246088b6e34 - 0c2907307ba4 - - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -420,10 +420,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 377ac2829eac - 61b4cedc8934 - - 73194cdd4f57 - 547e8d00f11c + - 73194cdd4f57 + - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -447,10 +447,10 @@ tools: - name: pear owner: iuc revisions: + - f69501361cec - 037f0acc7830 - - b4c6f054210a - 2f804526f5fd - - f69501361cec + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -462,8 +462,8 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort @@ -477,16 +477,16 @@ tools: - name: seqkit_stats owner: iuc revisions: + - fe1ae2ebf63d - 795cd16de38f - 812705bcf39c - - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -513,9 +513,9 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - bf04bd405d5b - - d3f58a0dc09d - 71f649c23021 + - d3f58a0dc09d + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -527,11 +527,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - e654095ab143 - - 71ad4a56c40c - b557acca0b56 - - 24013bf85a6f + - 71ad4a56c40c - a535cf1e5da4 + - e654095ab143 + - 24013bf85a6f - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -551,14 +551,14 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 6a675c3aa610 - - 015cf18f4a15 - - 7a7e33d28f62 - - 7accf7407811 - 27ac32a22ad2 + - 7accf7407811 - 9fa7803d1c51 - - 828dba98cdb4 - f3759eec3018 + - 015cf18f4a15 + - 7a7e33d28f62 + - 6a675c3aa610 + - 828dba98cdb4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index cab5d247d..4460c17d5 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,30 +2,30 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - ce9cd02d5b88 + - e41385662e5e - 7b4468117008 + - ce9cd02d5b88 - 64e9a6afdd0c - - e41385662e5e 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: - - 2b0c9d9fc6ca - - f2e8552cf1d0 - - ff9530579d1f - - 2c64fded1286 - e7b2202befea - 3d0c7bdf12f5 + - ff9530579d1f - 5ec9f6bceaee + - 2c64fded1286 + - f2e8552cf1d0 - 9da02be9c6cc + - 2b0c9d9fc6ca tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -39,46 +39,46 @@ tools: owner: devteam revisions: - b6b54ba71bd8 - - ad116ae3f4d9 - 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 - 7306ec78632a + - 59003d0543cd - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 1f296803dfa3 - a72af9de6bf5 + - 1f296803dfa3 - 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 - - 9a913cdee30e + - 75c93c70d094 - 5e33b465d8d5 + - 3d93dd18d9f8 + - f7985e0479b9 - 1c2db0054039 - b2f1f75d49c4 - - f7985e0479b9 + - bf675f34b056 + - f7e2f1eb3a16 + - 9a913cdee30e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - - 949f01671246 - cd7e644cae1d + - 949f01671246 + - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control 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 b248d7a64..9243d596c 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 83a19df00eab - 141612f8c3e3 - 85ef5f5a0562 + - 83a19df00eab 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 a96c17603..95085422f 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 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: - 8f53b238a360 - - 0c8f7322f8fc - f2f3bc622a16 + - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets owner: iuc revisions: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 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: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -86,16 +86,16 @@ tools: - name: gemini_load owner: iuc revisions: - - 45296e47d565 - - b2c25142267e - cf61daf064fe + - b2c25142267e + - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors @@ -115,37 +115,37 @@ tools: - name: gemini_qc owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - da74170c55c7 - - 840fb4850be3 - 666f60a9331a + - 840fb4850be3 + - da74170c55c7 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: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -158,8 +158,8 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 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 aade5505c..2e186f768 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -9,15 +9,15 @@ tools: - 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 diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 690f919dc..dd2b28248 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -3,8 +3,8 @@ tools: owner: galaxyp revisions: - e9df53a75f3c - - 983bf725dfc2 - b39347891609 + - 983bf725dfc2 - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -17,53 +17,53 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 28587613264f - 1c58de56d587 + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - 516a54ddf218 - - f5ea3ce9b9b0 - - aad3885b3216 - - 734abc7ac21d - - 5e6237d58b0c - - 8848455c0270 - - 6591f049cf7e - - 9a776b080193 - 7068f48d0ef9 - - 1ec814014652 - - ba931a59dd59 - - 4317d3cb6cba + - e407b9da183a - 653e89d73fc4 + - 9a776b080193 + - 69ebb7f46e45 + - 83c7d564b128 + - 4317d3cb6cba - 4df8de2d0e48 - - c441583adae5 - - 1790dcf3c32d - - f8054ea1c365 - - 6ea73833cf67 + - aad3885b3216 + - 1ec814014652 - e08a7ad4378b - - 83c7d564b128 - - 69ebb7f46e45 - - e407b9da183a + - 6ea73833cf67 + - 734abc7ac21d + - f5ea3ce9b9b0 + - f8054ea1c365 + - 8848455c0270 + - 1790dcf3c32d + - c441583adae5 + - ba931a59dd59 + - 6591f049cf7e + - 5e6237d58b0c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 9aaa46d45472 - - 75b3b3d0adbf - 21a560af5913 - 34758ab8aaa4 + - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - 468c71dac78a - - bfdc6a7ffd3a - 054483e27a35 + - bfdc6a7ffd3a - 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 1a70aaa82..81420649f 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: - - 4b519282a05b - - 7f13dc906cb9 - c4bde687c846 + - a64dc31ab7f2 + - 4b519282a05b + - ae9994cf526f + - 740057a5126d - df7356989ac1 - fd59d783248a - - 740057a5126d + - 7f13dc906cb9 - 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: - - f95284aa2946 - 867ab348287d + - f95284aa2946 - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,56 +48,56 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - 374e9062d874 + - 48b42ee61bc5 + - 3b37b1b1c3a7 - '566197475670' - - ca7cb0eaad62 - 51c6ccaace7e - - 3b37b1b1c3a7 - - 48b42ee61bc5 + - ca7cb0eaad62 + - 53460afd5115 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 + - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - 6fc8bab811da - b0d96516e6a5 + - 6fc8bab811da tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca owner: iuc revisions: - - ae344ccf9d62 - b1268b7544d3 + - ae344ccf9d62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 + - 5fe1dc76176e - 299307abd804 + - d0fc8b746d57 - 5298e06f14f9 + - 1acf88921176 - e3a675da7fd0 - - 5fe1dc76176e - - d0fc8b746d57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 17b666467c32 - 0e7290688b50 + - 17b666467c32 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -116,15 +116,15 @@ tools: - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram owner: devteam revisions: - - cdb9e89e2970 - 6f134426c2b0 + - cdb9e89e2970 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse2 @@ -136,16 +136,16 @@ tools: - name: jbrowse owner: iuc revisions: - - 1cfc579079a6 - - 2bb2e07a7a21 - 6cd09d7b5f37 - - 4542035c1075 - 17359b808b01 - - 667e17248bfe + - 4542035c1075 + - 2bb2e07a7a21 + - 112eb40ba6cf + - ca2def38369c - 836d1aa3e89a - a6e57ff585c0 - - ca2def38369c - - 112eb40ba6cf + - 667e17248bfe + - 1cfc579079a6 - fd5dbf0f732e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -164,9 +164,9 @@ tools: - name: pathview owner: iuc revisions: - - 03c13085aecc - - f1691de443a7 - fe154a7af404 + - f1691de443a7 + - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -179,18 +179,18 @@ tools: - name: plot_ragtag_paf owner: galaxy-australia revisions: - - c1bed78b9ed5 - - 501dcf66c0ce - 94e0834ae4ed + - 501dcf66c0ce + - c1bed78b9ed5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - - f234e2e59d76 - 1c5dcef5ce0f - 62e3a4e8c54c + - 85da91bbdbfb + - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -209,11 +209,11 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 26f2fe7e53a1 - - 6c571966cfb9 - 7c9417381ad5 - 326098bc19cc - 44c66e8d21e6 + - 26f2fe7e53a1 + - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -225,22 +225,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 4ac4e7083b7e - - 326a3db8d9d1 - 7dd841a32245 - - 14e7c35f3d00 - - 36b848d5f3ec + - 326a3db8d9d1 + - 4ac4e7083b7e + - 2824d77cd8f8 - a1abfa420d9d + - 36b848d5f3ec + - 14e7c35f3d00 - 360df4999907 - - 2824d77cd8f8 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 83c573f2e73c - 2f557f6abbfb - 44608d0193ed - - 83c573f2e73c - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -253,7 +253,7 @@ tools: - name: xy_plot owner: devteam revisions: - - ecb437f1d298 - 319fa5a9fc1b + - ecb437f1d298 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 9274cfe21..795c95ffb 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: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 7779b9dcf040 - 22bd5861706d + - 7779b9dcf040 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells @@ -42,8 +42,8 @@ tools: - name: scanpy_filter_genes owner: ebi-gxa revisions: - - cc64914b0cf4 - 23d838d1569d + - cc64914b0cf4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster @@ -63,8 +63,8 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 79da59a0b180 - 64dd8bb151e1 + - 79da59a0b180 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -77,23 +77,23 @@ tools: - 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 owner: ebi-gxa revisions: - 94697510d55f - - 9a2f72d7dbd2 - ff6decc0f432 + - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -106,8 +106,8 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 28b1546857b0 - 3027cb62adbd + - 28b1546857b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -127,15 +127,15 @@ 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: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x @@ -148,8 +148,8 @@ tools: - name: scanpy_regress_variable owner: ebi-gxa revisions: - - d18ed15697bb - 0bab2ae44e7a + - d18ed15697bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap @@ -169,8 +169,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - 65c3ec07502b - be019b069e31 + - 65c3ec07502b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -197,8 +197,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - 0f98603d0116 + - 767a675b5254 - ea91cfd0444e 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 58b3331b4..6d1f18499 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: + - 9edf8894a22d - ed2cca6b5de4 + - 29f66c353bcb + - 0f611e7d7858 - a4c13ddcc8ee - 921a2da49a0c - - 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 + - 5746d61f0a91 - d404277cc87a + - 11de0d28ab30 + - 78fb5e286609 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - 977dc15add20 - - 03dd3c16ae4e - f72063d9426b - - 9e357a8b2ec3 - 11fa44ee0603 + - 03dd3c16ae4e - 4d511437b1e5 + - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - c3e5e2cf12b7 - - 77919cc3618e - - 41dbf4d162a2 - 3b5b54ed6392 - 1da5f169b491 + - 41dbf4d162a2 - 0ba4f56a3613 + - c3e5e2cf12b7 + - 77919cc3618e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e - 9939786dd9c9 - - f741330d4a71 - - 5308ca68ef3d + - b63363075c2e - 7babd8a46fe0 - 12d51d7be66f + - f741330d4a71 + - 5308ca68ef3d 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 0ec67decb..92ac914a1 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,29 +2,29 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 3df9f0a4bf34 - 7db4fc31dbee + - 699a5e9146b3 - 8bccb36e055a - 81f0cbca04a7 - 0c777d708acc - - 699a5e9146b3 + - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5bc8cdc17fd0 - - 0a53256b48c6 - - 5791a7f65275 - 2436a8807ad1 + - 5791a7f65275 + - 0a53256b48c6 + - 5bc8cdc17fd0 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - e576b73a2e2f - 6ad1d3cfdea1 - 9d47aabda459 + - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization @@ -38,19 +38,19 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - - d51310ab328a - f70b215d155c + - d51310ab328a + - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - 85edbb7a436b - - f3360fbeda64 - fcadded98e61 - - 10eed33aa9b2 + - f3360fbeda64 - b07f4839ca77 + - 10eed33aa9b2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -63,17 +63,17 @@ tools: - name: count_objects owner: imgteam revisions: - - 664232d2a3f7 - 5bf8eb50b280 - b58447a2eed2 + - 664232d2a3f7 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 @@ -86,49 +86,49 @@ tools: - name: cp_common owner: bgruening revisions: + - 670975e92458 - 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: - cdf8e3c57dae - - df3ad3ba5c6f - ef4aed1d34c4 + - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - 5d28ac336861 + - 6a7da2e5f696 - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e - 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 + - f24c370e5ea4 + - 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 @@ -150,65 +150,65 @@ tools: - name: cp_mask_image owner: bgruening revisions: - - 667a513e67e4 - b178453ea8d1 - 3a05117669cf + - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: + - ac5bea85a391 - 2564f461de62 - a1a961c46d4b - - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - 20dbb1f7ec7b - - a32c3f810ade - 91e03287f285 + - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: + - b64af54c5c09 - 8536b1ae0254 - 5499dc6f8ac1 - - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - 6f4715b8540a - - d3890df07463 - e972e07c7845 + - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - e52c75a28c4b - 407925835dd9 - 980aed9e8fd5 + - e52c75a28c4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - 79e10d12d90a - - d85f11570109 - acf3aa487283 + - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - b76841ee5560 - - 80b200ae516b - 035a58c7f54a + - 80b200ae516b 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 - - 8083a87d2fdf - 3a3033222f61 + - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - 33f4fa1413fb - - 4ecf93628f97 - 27edbb90ab2b + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -242,8 +242,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids @@ -256,8 +256,8 @@ tools: - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - f8b4eada923c + - 236ec78b2e53 - 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 e222ec1fc..2dc31a415 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: + - e4ee04da1c19 + - 40737febe339 + - 78bbd17d0703 - 3e4f434a69c6 - f362150bef41 - - 40737febe339 - a38934e303b9 - 1069f6db0a0e - d6e72da3ec35 - - e4ee04da1c19 - - 78bbd17d0703 - - 3a72fede57ce - e319b5b65879 + - 3a72fede57ce tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 618297d23022 + - f91cfb73d369 + - c88553ec696e - 0135f1d487a0 - - 2b95d5c04908 - - 7fe36019c073 + - 8f8df367470d - 72ddd32392cd - - 9537184d421f + - 7fe36019c073 - fcbeda41d0ac - - c88553ec696e - - 8f8df367470d - - f91cfb73d369 + - 9537184d421f + - 618297d23022 + - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 - - d7e79eb3bcb3 - - fafb3d685fa9 - 2cf4a1cafc16 + - fafb3d685fa9 + - d7e79eb3bcb3 + - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - bd2a7d1316b9 - - 43aac8d29685 - - 94df24c6bc00 - - a1c2aecd7a0d + - 28a6f1908fcc + - 9eaadf03e0df - 8d36959b000d + - 43aac8d29685 + - bd2a7d1316b9 - 6a1515bb0687 + - 7f1cfa4c0e32 + - 94df24c6bc00 - 3d18f8c3c0f6 + - ee29337f905c + - 5dc33613c288 - ee2beb764a7b - - 9eaadf03e0df - 8c05afb547fa - - 5dc33613c288 - - ee29337f905c - - 28a6f1908fcc - - 7f1cfa4c0e32 + - a1c2aecd7a0d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - a250929be21b - - db536ad45f28 - - 9f978da6528a - 5d6ed46cc101 + - 5671e1d3d5ee - 364f4ffec275 - - e3bb03cf207a - - cb903c9dc33d + - db536ad45f28 + - c092052ed673 - 8858fa037a15 + - 9f978da6528a - d37ede8589b2 - - 5671e1d3d5ee + - cb903c9dc33d + - e3bb03cf207a - 86a20ae274fc - - c092052ed673 - bcaa0d571ce2 + - a250929be21b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: + - 584beffa972b + - c5c9f02b6167 + - 194e3ceee923 - 230b05597996 - - f95f403841ad - - 12d66d0d05ac - 38b91a3190cd - - 194e3ceee923 - - e1a015876aa9 - - 584beffa972b - ed28dd32141c - - c5c9f02b6167 + - e1a015876aa9 + - abbc8041e8ec - 49236b03e4fd + - f95f403841ad + - 12d66d0d05ac - 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 fd641bd5b..84763b815 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -3,18 +3,18 @@ tools: owner: iuc revisions: - b8a457820315 - - 0f1724dd59d2 - - f198773344e4 - 17e3b698dd52 + - f198773344e4 + - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: + - a513e3fbb4c5 + - ac092723240d - 374cb875d38a - ba0c40780ecf - - ac092723240d - 22c2a1ac7ae3 - - 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 e0c11b2c9..af82722ed 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,36 +2,36 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 522137aaa9c4 - 772e0e89fc68 + - 522137aaa9c4 - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 8a794e6d3388 - - 4d81e3e2fb63 - f22a9297440f + - 4d81e3e2fb63 + - 8a794e6d3388 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - e1317b5502fa - b6ef6d0cb6b7 - - 818f9b69d8a0 - 2af1346e68c9 + - e1317b5502fa - f1b9a42d6809 + - 818f9b69d8a0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 1588f9076e32 - c80db5d6fd8c - - 947c2eacccb8 - 05143043ca13 + - 947c2eacccb8 + - 1588f9076e32 - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,62 +39,62 @@ tools: owner: bgruening revisions: - 9991c4ddde14 - - 29e4122c90de + - 25b46af53232 - 83228baae3c5 - 1552b8cb4a94 - - 25b46af53232 + - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 841a6cc5fc58 - f3dfa4bdf87e - - 53616c8b0865 + - 060ca94ac049 - a07ab242b0b5 + - 841a6cc5fc58 - 1a53edc4b438 - - 060ca94ac049 + - 53616c8b0865 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 927586a18553 - 40f4447733b2 - - 2fc89dcd41c8 + - 927586a18553 + - 91c4e3331208 - d4808d5b83da + - 2fc89dcd41c8 - dc4b5fd604a6 - - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 25ab6b4e376e - - e5a5ad882f1f + - 36e8d6d5d01b - 301e07345c93 - 7626ea9c2e1b - - 36e8d6d5d01b - c6ae57f774c6 + - 25ab6b4e376e + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 - - b7c3e9a3b954 - - 80852884053f - 4ed102b922cb + - 0630258dcf35 - 02d2be90dedb - f9639b488779 + - b7c3e9a3b954 + - 80852884053f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - ec69cbe34b73 + - caeb57858702 - 61634a87efc7 - 14180f9c831e - - caeb57858702 + - ec69cbe34b73 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 d8df6186f..ff607abf7 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 + - f6877ad76b00 - d5ceb9f3c25b - - 937aa69e715f + - 749c918495f7 + - cd659e8cc5fa - a6d65b0c67af - 03e9b2fbc005 + - 0d4acadabb04 + - 937aa69e715f - 17062a0decb7 - - f6877ad76b00 + - 3ba8d4563129 + - 017aba02828d tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: - - 2477830927ec - - dfd8b7f78c37 - e188dc7a68e6 - 53646aaaafef - - 3fe632431b68 - 64f11cf59c6e + - dfd8b7f78c37 + - 2477830927ec + - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - 60afcc2c1d05 + - 37b497aa133f - 3e1ea2facca6 - - 2ff111fac1d7 + - 60afcc2c1d05 - e7f19d6a9af8 - - 37b497aa133f + - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - b3eab4b67562 - - 8c6cd2650d1f - - c0c2d0941de8 - - 037c6e54df11 - - 11a0d50a54e6 - 53c0b7a1a0c3 - - 3f4d6399997b - - be1d967337e4 - - 77b2770508f6 + - 11a0d50a54e6 - 09b53c1d4ab1 + - 3f4d6399997b - 6b1e195506a3 + - c0c2d0941de8 + - be1d967337e4 + - b3eab4b67562 + - 037c6e54df11 - f54f5baedfdd + - 77b2770508f6 + - 8c6cd2650d1f - 5cc34c3f440d tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 13022c3d3076 - - b8f5f6e87f5c - - 79b885ce78d7 - - 1cd2511a396e - - ec9cbd6b9a49 - - 5ef7ec16b04f - - 45795f582ae9 - e403d27e8f24 + - 5ef7ec16b04f - 00fbfac99d39 + - 79b885ce78d7 - 178bdbdb6d24 + - 13022c3d3076 + - ec9cbd6b9a49 - 9ee34ba73ebf + - 1cd2511a396e - 42ce70172b72 + - 45795f582ae9 + - b8f5f6e87f5c tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index ee54516a1..ea13feabd 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 90dc951da294 - 6cd2a9e6ac49 + - 90dc951da294 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -63,8 +63,8 @@ tools: - name: isolib owner: recetox revisions: - - 2b1118bce0b1 - 6b0fef8a77c0 + - 2b1118bce0b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -95,49 +95,49 @@ tools: - 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 owner: recetox revisions: - - 83c4b4359ac4 - a177ac3c752c - 00e66c401366 + - 83c4b4359ac4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - 84af792d3a78 - - fd890f162ce6 - d7b517f2c5fe + - fd890f162ce6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - a5a5b147da70 - - 9e3c83d2afc3 - 1b09315a3f87 + - 9e3c83d2afc3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - 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: - 1d443ed476a1 - - 330b0dfae8da - 03bc9b7f40f6 + - 330b0dfae8da tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -150,23 +150,23 @@ tools: - name: matchms_networking owner: recetox revisions: - - 1d74ae228df3 - - f04b378325e5 - 8147d93d372d + - f04b378325e5 + - 1d74ae228df3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key owner: recetox revisions: - - 9d1b01d3fedd - fbdb2ae524df + - 9d1b01d3fedd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_spectra owner: recetox revisions: - - d50ce2f51fc0 - fbe335d27d25 + - d50ce2f51fc0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_similarity @@ -178,17 +178,17 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: + - 7627b40601f6 - 9ff95a1a2705 - 7ba589b01dbc - - 7627b40601f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - 500f473df7e4 - - 0cf68b536cd1 - ea6c5636c0cf + - 0cf68b536cd1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -256,40 +256,40 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - 5f2b58dadb39 - f2c1d0bbb074 + - 5f2b58dadb39 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr owner: recetox revisions: - - da7722f665f4 - 9b716db0a786 + - da7722f665f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - ec196e27a61a - c53a97599181 - 7b42ee54d757 + - ec196e27a61a - 79ad928a0dae tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: + - f3a18e020cdd - 18ec7635bac6 - - 149b9cc7499b - 59c393d35e0e - - f3a18e020cdd + - 149b9cc7499b tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - 134be5abb208 - 50b9918aeff2 + - 134be5abb208 - dfebc82ba1f0 - 481d769e2f7a tool_panel_section_label: Metabolomics @@ -297,29 +297,29 @@ tools: - name: recetox_aplcms_correct_time owner: recetox revisions: + - 501a232f3cd5 + - 30bf4e35da3e - a82db010c53e + - 51332c2520c7 - 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: - - b3413f335327 - - e7305ba0dd38 - b341cfd4baf8 + - e7305ba0dd38 - 89178a72388a + - b3413f335327 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 + - dd7bbc2b99d1 - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -328,16 +328,16 @@ tools: revisions: - d7f5878a98c3 - f92b1b64da93 - - 99d118321d5f - 24278c6b6d1c + - 99d118321d5f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ffbabefbd2e2 - - d90187b0f247 - ea0758b41473 + - d90187b0f247 + - ffbabefbd2e2 - 7acd11ddc061 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -400,8 +400,8 @@ tools: - name: use_theoretical_mz_annotations owner: recetox revisions: - - b3d41b1fcb18 - e0cac9994a72 + - b3d41b1fcb18 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 1de9b6ecf..e1ef2be8f 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,9 +8,9 @@ tools: - name: cat_bins owner: iuc revisions: + - 0e63d03c8790 - 0094893f5001 - 18676df0cb3a - - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -106,110 +106,110 @@ tools: owner: iuc revisions: - 00f5005840fa + - 96336c6a2bb7 - 1c35dadbe76f - 18a502a9d287 - 84fd33a60b35 - - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - a9f4a217dcd6 - addaf9d22850 - - f732237754fc - - e8fba04706d3 - 34e55239e68b + - e8fba04706d3 + - a9f4a217dcd6 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 5fe3edf19b9c + - 75403243703a - 0776d824d896 - 04c15826a0b8 - - 75403243703a - - 5fe3edf19b9c - 8c202e741d68 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 + - 43c99742158b + - e96bbb9e24ea + - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 84743da21318 - - 35176674168c + - 5c865a382933 - 306a40d4bb8f + - 84743da21318 - 1d75bd0595e2 - - 5c865a382933 + - 35176674168c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 78faebd0879c - - ac72310b038a - 555ccac8a4c5 - 8daf4564ccda + - 78faebd0879c + - ac72310b038a - 32c9ea835770 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - - 7b8cb2b02978 - cae017b76acb + - f947b4bb5107 - a58e4a43f49c + - 7b8cb2b02978 - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 073608a50ac3 - 04144473e59e + - 7f3b59dee073 + - 073608a50ac3 - 1bc3657cd694 - 7136e9ab70db - - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - d943081510da - 0a1224c4b781 + - d943081510da - 19299bb1c6af - - a7817705348e - 9058d8943303 + - a7817705348e 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 + - a68b985913ab + - f8f56dd6449f - 4d9445dff47b - 65d52c693b8e + - c4db8c4de66f - dbf1798c0dcc - - a68b985913ab - - f8f56dd6449f - 5c7ba3d85a01 - - c4db8c4de66f + - b907a3c0434f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -236,25 +236,25 @@ 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 - - b084117133af - d77397f09da1 + - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 7f208f1eb64f - 9704f1a3b32d - cad93abecac9 + - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -279,47 +279,47 @@ tools: - name: humann_join_tables owner: iuc revisions: - - f01ca38fb6c5 - 6bf703133209 + - f01ca38fb6c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - c409a495841f - - 79706f10d680 - 31c6d107e7a5 - - e88b731dad59 - 8237a0f225db + - c409a495841f + - e88b731dad59 + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 71ea608ddfa3 - - 172920f67a84 - 094ad9c068af - d24841f5c3d2 - - 714d5a28cc5c + - 71ea608ddfa3 + - 172920f67a84 - aabf8cfb8fef + - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a4d7148ccee4 - - 2bdd84912a2b - - a293a742194f - d7e9a3c41657 - - 12fb63b5f63f - 4137b492233e + - a293a742194f + - 2bdd84912a2b + - a4d7148ccee4 + - 12fb63b5f63f 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 + - cf87759761eb - 75bedfb2078b - - e2c71b852aba - a92c06a3afa7 - 97f7bb0851e7 - - cf87759761eb + - e2c71b852aba - 64bc7acc22a9 + - 6fcb8ac37a3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - e9d12c223a80 - 81c5dd1c777f + - e9d12c223a80 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -357,21 +357,21 @@ tools: owner: iuc revisions: - 080ea153677c - - 4e5e73d03f0d - - 5e5a999ffaa9 - c82508e76ad1 + - 4e5e73d03f0d - 4033827c76b8 - 2d35528d2141 + - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 6b7622dda516 - - c2803012bbb3 - fc6c328c292f - - 2cd76b089570 - 95bf7479d53c + - 2cd76b089570 + - c2803012bbb3 + - 6b7622dda516 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -403,8 +403,8 @@ tools: - name: khmer_abundance_distribution owner: iuc revisions: - - e699e2747356 - 7624945cacd3 + - e699e2747356 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median @@ -417,29 +417,29 @@ tools: - name: khmer_extract_partitions owner: iuc revisions: - - adb3dd5a899f - 1061711538c6 + - adb3dd5a899f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance owner: iuc revisions: - - 29a4d6e2ae9c - b86562b4f3fd + - 29a4d6e2ae9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 00f7064c564b - 19607c740d19 + - 00f7064c564b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median owner: iuc revisions: - - 4d23ab83ea29 - b1fe2ef3d244 + - 4d23ab83ea29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -458,17 +458,17 @@ tools: - name: kraken2 owner: iuc revisions: - - 328c607150ff - - 20e2f64aa1fe - cdee7158adf3 + - 20e2f64aa1fe - 4a9da2b6c2e3 + - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -480,15 +480,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 67236d921e83 - 5bee9adae474 + - 67236d921e83 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1c677354ab18 + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report @@ -521,19 +521,21 @@ tools: owner: iuc revisions: - c254d75b8b67 + - 4505d7643673 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_combine_kreports owner: iuc revisions: - - 4960abe31b4d - 073c867c5244 + - 3d2cffa2c4ab tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads owner: iuc revisions: - f329328da134 + - 4bf1e2701504 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona @@ -541,12 +543,14 @@ tools: revisions: - 2deaada69b14 - 88d274322340 + - 02bbace216f2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: - bb96a1e6583d + - d33cf727ed94 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -576,13 +580,13 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 4fd3b5d8706b - - 327d9f4cc95f - - 2cff76cf35c6 - - 27250f92a01a - e073891b2afc - - 3cc4a60615c0 + - 27250f92a01a + - 2cff76cf35c6 - 0270541aaf46 + - 327d9f4cc95f + - 4fd3b5d8706b + - 3cc4a60615c0 - 7f5d7b0e9884 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -665,18 +669,18 @@ tools: owner: iuc revisions: - ff8f55893e7d + - 6dee4abadccb + - 2131d7dca455 - 289b3807e80c - - ef65b083bd0c + - b89b0765695d + - a92a632c4d9b - fd69c607b43f - 1a6cdf55390f - a16313517e55 - - 2131d7dca455 - - 1a037928504c - - a92a632c4d9b - - b89b0765695d - - 740fd2d16a28 - - 6dee4abadccb - ec368db926f4 + - ef65b083bd0c + - 740fd2d16a28 + - 1a037928504c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -708,22 +712,22 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 709adbfcf308 - 415cb5d91168 + - 709adbfcf308 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline @@ -736,8 +740,8 @@ tools: - name: picrust2_place_seqs owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -813,20 +817,20 @@ tools: - 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: - - 4d83eccf5f81 - - 4b9a8031ab74 - - 3b22de20bd4b - 141afacabcfa + - aeaa20b96ef2 + - 4b9a8031ab74 - 2fd4d4c9c5c2 + - 4d83eccf5f81 + - 3b22de20bd4b - be818ae858e4 - - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -857,7 +861,7 @@ tools: owner: iuc revisions: - 576963db5f1b - - 9495df9dd6ef - b3c7199d8786 + - 9495df9dd6ef 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 dbd37638b..193493f23 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: - - bdb4a58a2025 - 12e856482d26 + - bdb4a58a2025 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: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 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/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 6864160cc..8e7561434 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: + - bdfbaf0c10aa + - a74dbfee5a86 + - 80f03df2e2ce + - 2263989660f5 - cd07731e4434 + - 6ae5a7b5a0a2 - 098506c54016 - - 8b67dd48fec1 - - 80f03df2e2ce - - 9eeb13a92d79 - - a74dbfee5a86 - 9baa871cb1d1 - - 48c13389050d - 9422c5a87ee2 - - bdfbaf0c10aa - 94b8c6013083 - - 6ae5a7b5a0a2 - - 2263989660f5 + - 9eeb13a92d79 + - 48c13389050d + - 8b67dd48fec1 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - '764845535798' - - 5abf2c2249aa - - be78f13134e2 - - 2e093badc689 - - d390fe1567dc - - f14193ec1f50 - - 4a60927aaca5 - - bc3831dd65c1 - f0af8936ed41 - - aaa0d6a8b808 - - 3ff17bad4006 - c18157c68134 + - 2e093badc689 - fc2e49f91e52 - - c44f824c051a + - 3ff17bad4006 + - 4a60927aaca5 + - be78f13134e2 + - d390fe1567dc + - aaa0d6a8b808 + - '764845535798' - d7ce0ec78e51 + - c44f824c051a + - bc3831dd65c1 + - f14193ec1f50 + - 5abf2c2249aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,15 +46,15 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -67,46 +67,46 @@ tools: - name: mafft owner: rnateam revisions: - - a65296ffb4a0 - - 8e649f27aa0d + - f0d493f8f84f - bf28a8cff401 - - c5908940967d - - 6f28e90db932 + - a65296ffb4a0 - f1a5908ea2cb + - 6f28e90db932 - 15974dd17515 - - f0d493f8f84f + - 8e649f27aa0d + - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - - e8fdceffea4c - b3acbb3a6af0 + - e8fdceffea4c + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 5561a1193611 - 60698466facd - c9685bc0407c + - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 57f042937ba7 - 48823c9635a4 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - fb43e8887350 - - 4fc0cb2ac8ae - ebe3b0f84de9 + - 4fc0cb2ac8ae + - fb43e8887350 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer @@ -120,8 +120,8 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 - 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 572644aad..d8ac29f47 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,11 +8,11 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: + - 9aa9d92c3c51 - 18a8d140ec6f + - 7c47b3c9e493 - 28928576e1ea - 1145758d2f0b - - 9aa9d92c3c51 - - 7c47b3c9e493 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -26,8 +26,8 @@ tools: revisions: - 63d8ecfcfab1 - 090ab4f31074 - - fc5b6491cf78 - 6942f170cc43 + - fc5b6491cf78 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -39,11 +39,11 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - 72b5e9dda577 - fc8804320156 - 79e9a869f40e - - a7228a7ea146 + - 72b5e9dda577 - cb34f00cc10f + - a7228a7ea146 - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -51,9 +51,9 @@ tools: 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: - - edf6d4003fad - - 0f5f4a208660 - - 2bf63b38ee9b + - 19f3b583a9b3 + - eb746fa6f514 - ec699520444c - cc36773a3681 - - 19f3b583a9b3 - 43815fa60f3a + - 2bf63b38ee9b + - 0f5f4a208660 + - edf6d4003fad - 222669c4afb6 - - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - c0fb573c1e8d - b833eff63b10 + - c0fb573c1e8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -93,79 +93,77 @@ tools: owner: iuc revisions: - a38bdcec9e4c - - 0f1c34698076 - edbb6c5028f5 - 645159bcee2d - - a3c4fe6f49ab - - a02b8b3f5a0c - 7b379e98b9a9 + - a02b8b3f5a0c + - a3c4fe6f49ab + - 0f1c34698076 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: - - a8d4be409446 - 90a922f32523 - be95355fef8d + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: + - d376944466bf - 449e9aeded2d - 4857d5bcce52 - - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: + - bec636361cfd - a3afc5f0a96c - de5b3d8f5b90 - - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - - 5f76b20953e5 - 93d623d9979c + - 5f76b20953e5 + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - daf8518d243a + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract owner: iuc revisions: - 08064da7b7fb - - 7e4f1ed70187 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: iuc revisions: - - a57b6350fd5d - 5c4fa65f5733 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -174,21 +172,19 @@ tools: revisions: - 336791b5665f - 0433aad600e9 - - 338d15b8d6fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist owner: iuc revisions: - - ae9060e764b5 - 72dfdbfab3cc tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 626b6c2be5c2 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle @@ -196,7 +192,6 @@ tools: revisions: - ce8af9373061 - 26e6c9362b7b - - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -208,7 +203,6 @@ tools: - name: poretools_tabular owner: iuc revisions: - - 2cb2feb94f0e - 5f5f1da94d7f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -221,15 +215,14 @@ tools: - name: poretools_winner owner: iuc revisions: - - 79c1ac92f31b - 6d93709247c7 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - 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/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index c95485b63..c4cc716b3 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: - - 592ef3959907 - a5921c09b7b7 + - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: annotation_profiler @@ -21,8 +21,8 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 71186bb66ca2 - 4e85a3a5dbd1 + - 71186bb66ca2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts @@ -60,17 +60,17 @@ tools: owner: iuc revisions: - baceff842902 - - 3e73c97f025d - 97b1b5ad1cda - adfd6bf710bd - d74850cf4e42 + - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 83da94c0e4a6 - 9dd107db92c2 + - 83da94c0e4a6 - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -83,19 +83,19 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 1e34d2e3d285 - - 2f27f3b86827 - - ed1518ce2237 - e9ee4d074d5d - - e4b4837f06f5 + - 2f27f3b86827 + - 1e34d2e3d285 - edacc4bcd3cb + - e4b4837f06f5 + - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 9e993022c762 - 46066df8813d + - 9e993022c762 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -114,16 +114,16 @@ 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: - - 5a0d0bee4f8d - 4a08b7b76b78 + - 5a0d0bee4f8d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -136,8 +136,8 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -164,16 +164,16 @@ tools: owner: iuc revisions: - 5bcf0e24f42c - - b4b2b284230a - 172815da3d41 + - b4b2b284230a - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - 10232d2b5062 - df84aaed4769 + - 10232d2b5062 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_hisat2_index_builder @@ -193,22 +193,22 @@ tools: owner: iuc revisions: - 87febc68b45b - - 19bbd19b74b3 - fea85c467896 + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 7776cb18fdf8 - 0df47f8552f6 + - 7776cb18fdf8 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 15c2fc266540 - 4c7ebbad42cf + - 15c2fc266540 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -226,19 +226,19 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 9c43baa60906 + - d8dc037e3c13 - 0cb27ea69dc1 + - 4ba60cb14cb0 - 2c61c30a57e7 - - 9c43baa60906 - 5fe20c915fa6 - - 4ba60cb14cb0 - - d8dc037e3c13 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 @@ -252,10 +252,10 @@ tools: - name: data_manager_pangolearn owner: iuc revisions: - - 6e24e79d3d69 + - df30a2f1db55 - 29c738066906 + - 6e24e79d3d69 - ed7a967cb11b - - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -273,9 +273,9 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: + - 1865e693d8b2 - 3e4d45aca422 - ad90c2da4f38 - - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -294,17 +294,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - c520a52b5174 - d63c1442407f + - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 94a50db37d1a - 625fd9476402 - 9946bc39c834 + - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1082,11 +1082,11 @@ tools: - name: salsa owner: iuc revisions: - - f77f7a7f3b83 - ab5b7f6b7198 + - 58a870ef434c - ba7b0f11e470 + - f77f7a7f3b83 - 9a22227bb6d0 - - 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 b142fda5b..56b173e9f 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -40,66 +40,65 @@ tools: owner: iuc revisions: - a6619171428e - - 3b8b5bde0bd9 - - b89cac5156ec - - 8834daeb9892 - - c78f3d7dd1db - - cce7b18495e4 - - 81e66674859e - - 3f59ebfbfe3d - - '841557158611' - f04a1264e2a2 - - d7c7ef3353fe - - 26de3a7b1cb9 - - 5a7c56a5cc08 + - 81e66674859e - 107d3ba7024a - - f73435dc282b - 6a457678efcb + - 5a7c56a5cc08 + - f73435dc282b + - '841557158611' + - d7c7ef3353fe + - 3b8b5bde0bd9 + - cce7b18495e4 + - 3f59ebfbfe3d + - b89cac5156ec - d033ffc1c161 + - 8834daeb9892 + - 26de3a7b1cb9 + - c78f3d7dd1db tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - 5fcd1ece3a6e - - b0af57c1a968 - - 6a726db04d4b - - e75442c7f4da - - 6283babe736e - - 3b96e92e8ec3 - 659517798cc4 - - a185b079b095 - - 7a2092844346 - - 4755f52427c4 - - 02b8758214b0 - - 6223845127ea - 5b777002c2de + - 02b8758214b0 - df47d4845b62 + - 6223845127ea + - b0af57c1a968 + - 7a2092844346 + - a185b079b095 + - 6a726db04d4b - aa8cc71438cf - 88c4aa435ded + - 6283babe736e + - 4755f52427c4 + - 3b96e92e8ec3 + - e75442c7f4da tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 111bd54f6bc4 - - 0878b7fd5260 - b8476e82ac20 - d1c340a5664b - 24d024316465 - - f87ac61981f0 - - 524d31add34a - - 70acec670c30 - f97743d52b87 + - 70acec670c30 + - 524d31add34a + - 111bd54f6bc4 + - f87ac61981f0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 9e10ba792be2 + - 4f6349228462 - feb40665d7cd + - 9e10ba792be2 - daddf188c13f - - 4f6349228462 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -111,33 +110,33 @@ tools: - name: pangolin owner: iuc revisions: - - a2099fb98cdb - - 437e28791761 - - 2fa9d4f1b48f - - abf6dbe8c9d7 - - 81804a978fc0 - - 7bb8726be37c - - 5f8727ff21e7 - ca337cce3888 + - 81804a978fc0 + - a2099fb98cdb - 42a174224817 - 14ae456b8cc5 - - 3a43c3982401 - - b6abccb1f25b + - 03ed9524dcd1 + - 5f8727ff21e7 + - 2f1019071464 + - abf6dbe8c9d7 - 83a69484cb87 + - 2fa9d4f1b48f - b7e297c2ede6 - 9d61d3fa046c - ca0d8cf80567 - - 36912871ccdc - - 03ed9524dcd1 - - 2f1019071464 - 8ad84c5753ea + - 36912871ccdc + - 3a43c3982401 + - 437e28791761 + - 7bb8726be37c + - b6abccb1f25b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 2bf47d57ebb5 - 7157a5b34a68 + - 2bf47d57ebb5 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -149,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: - - b1e68bbe4cef - - ba29b5e2a4be - - a4b71be30c3c - 29ff6a849eac - 73a469f7dc96 + - a4b71be30c3c - ea30d3089354 + - ba29b5e2a4be + - b1e68bbe4cef tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: + - 91887494eb97 + - dbe2b2204555 - e88a7de55d6e - - 9b2b122d0415 - f1ccc8a6eb05 - 809e42326fc2 + - 9b2b122d0415 - 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 d6eef1fee..56126436e 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: + - 3f254c5ced1d + - 1aac2a13842a + - f6ced08779c4 - a1f0b3f4b781 - fc288950c3b7 - - b502c227b5e6 - 7d34178f2812 - - 1aac2a13842a - - 881d7645d1bf - - 3f254c5ced1d - - f6ced08779c4 - f9242e01365a + - b502c227b5e6 + - 881d7645d1bf 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 e87b34b61..3116cefae 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -3,17 +3,17 @@ tools: owner: galaxy-australia revisions: - a58f7eb0df2c + - 3bd420ec162d + - e4a053d67e24 + - e7f1b552a695 + - eb085b3dbaf8 + - 5b85006245f3 - 7fbec959cf2b - - 2f7702fd0a4c - 6ab1a261520a + - 2f7702fd0a4c + - c0e71cb2bd1b + - ca90d17ff51b - 3f188450ca4f - - 3bd420ec162d - - 5b85006245f3 - d00e15139065 - - ca90d17ff51b - - c0e71cb2bd1b - - eb085b3dbaf8 - - e7f1b552a695 - - 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 e3d2b63c7..99a842d5a 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: - - b18329a8ac14 - - 277dc652246e - 0a18ac48ac53 - - f28ad96b76dc - - 4c177985028a - b574b84afc4d - ece627528a78 + - 4c177985028a + - 277dc652246e + - f28ad96b76dc + - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - e988563cc6e5 - e215f71d7983 - - b41107d8fe89 - - a9a28e46d54a - 525f201b86c1 - bf06d196e23d + - b41107d8fe89 + - e988563cc6e5 + - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 - - 56da27be956a - bb6397b94018 + - 56da27be956a + - 8da3511c9467 - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - - 890845926d4b + - b8c79e70516d - f23d67e28cc8 + - 528fb09022be - a8157342d9a3 - - b8c79e70516d + - 890845926d4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 - 25b83cbd596a - - a95a82eb4d50 - - ae304a72db7b - 80600735685d - a69865da6f80 + - ae304a72db7b + - 59e85306eae5 + - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 83aac7741200 + - 798da6bdff3d - 611d80c0e29d - - e0669b1854b1 - ed9ed1e6cca2 + - e0669b1854b1 + - 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 - d426a9107a6c + - 5a35e3a8d013 - a7fb9b395ddf + - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - cc430977c8ff - 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 + - d2483487e077 + - 043f9c91f686 - 1693b2126f30 - c5aa9fca18c6 - - d2483487e077 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: - - ff8c9e0e8a7b - - ae4dc0c041f9 - bf0728e000cd - 9fa3dbf06f17 + - ae4dc0c041f9 + - ff8c9e0e8a7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,24 +129,24 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - 0fa397f4f40b + - 1c5cbf8f79ce - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - fb192dd6658a - 36880dfd9fa7 + - fb192dd6658a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: - - 0d2e93e01e68 - - ce1a157a41bd - d6a4dfdad269 + - ce1a157a41bd + - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -158,8 +158,8 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - d286ff4600dd - 160538a890a6 + - d286ff4600dd - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -173,23 +173,23 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 3fc2116ac6d9 - 9cb7dcc07dae + - 3fc2116ac6d9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 1f39c833f65f - - 837224ad1694 - 4d17fcdeb8ff + - 1f39c833f65f + - f522c08e900c - 9c52362ae7bb - - 7f432d87c82c - - e42225f8a659 - 2133b0be850a + - 837224ad1694 + - 7f432d87c82c - 37d669de2828 - 97a7f34fcb6a - - f522c08e900c + - e42225f8a659 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,62 +201,62 @@ tools: - name: metaquantome_db owner: galaxyp revisions: + - 85b8866f06d7 - a72ac2c7cc5b - - 0ed07016d668 - e63db1aa82ee - - 85b8866f06d7 + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 1974224d63c2 - - 990b4560ead7 - 767c1d761aaf + - 990b4560ead7 + - 1974224d63c2 - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: + - 35cc7ca0bdc7 - deaf035bbe9f - - 99450519d727 - 4f359549383c - - 35cc7ca0bdc7 + - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - 06f6826d380c - c1343e3389ca - - e79958768a2c + - 06f6826d380c - c7745841de24 + - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 - da986f83631b - - d2eac53666f0 + - b9d453dca8d3 - d46d64e7964d + - d2eac53666f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 944b43462104 - 1199751329b0 - 9bf325045235 + - 944b43462104 - 8bd7734309f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - e0104a9f20f0 - 8295d959ca28 + - e0104a9f20f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert @@ -270,25 +270,25 @@ tools: owner: galaxyp revisions: - de7593c29499 - - 28434abe6c5c - - 593839e1f2c3 - 8212e342e482 + - 593839e1f2c3 + - 28434abe6c5c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - bd1535813cfe - a5e394b36d87 + - bd1535813cfe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - 01dbaf6a57e0 - - f4be248c3d47 - 4e77b8f12cd3 - 8960fb791701 + - f4be248c3d47 + - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -302,18 +302,18 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 518b1730cf2a - 6ccbf9a2072c - f7fef900f5b2 - - c9eff69a7c62 + - 518b1730cf2a - 9cdf15d3cfc8 + - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - ca88bd28f116 + - dff6c756eee5 - 9876bda3ec53 - 5e948629bc73 tool_panel_section_label: Proteomics @@ -321,111 +321,111 @@ tools: - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e + - 1595601708ec - 890025d6e426 + - 41859bbdc16e - 658494a2cb00 - - 1595601708ec tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 9b7977080f6d + - 6634cad7d797 - 2a93a25f0599 - 5ad0b5bf1deb - - 6634cad7d797 + - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - d6878d27f051 - 05d5e1ddc985 - - 0bb5056cb775 - fe4e4587d265 + - 0bb5056cb775 + - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 + - 4af67edd5aef - 52ba9695e752 + - 5ad830edc021 - febd569ad26f - - 4af67edd5aef tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - b2fc8da99bcc - 27cba4c5fc42 - - 39e8fde08881 - 92352a475eed + - 39e8fde08881 + - b2fc8da99bcc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - d3546bb9fd8e - - 9e26f5c770f8 - d413dc49d650 + - 9e26f5c770f8 - 0efbc235f314 + - d3546bb9fd8e 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: - - a5d785af0ad8 + - ca799a7246e7 + - c55dddc5844a - c427a8628cbe + - a5d785af0ad8 - 382cde407f81 - - c55dddc5844a - - ca799a7246e7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 8ddb7bab1138 - - b5d0905419da - adca857b4884 + - b5d0905419da - 39caaa778d2e + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: + - 1c5f31b8d632 - f817513840a9 - 8d4db262964c - - 1c5f31b8d632 - - 18f93351f8b6 - 34e7afee141d + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - 5d9f175dff81 - c69f69d7867a - 986e03d3201e - - 5d9f175dff81 - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - be74a8cd7d66 - - 0e52c85f3b15 - - 476b5e296979 - 4204882495f2 + - 476b5e296979 + - 0e52c85f3b15 + - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -438,25 +438,25 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - 2b2a7551a857 - f5ec766d80cf - - a407b6790342 - c18d8efa4474 + - a407b6790342 + - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 4e66c4e73909 - - 021fdb80f204 - d0304fb829c0 + - 021fdb80f204 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - 2735db4dd8d9 - ee860980edc6 + - 2735db4dd8d9 - bf32e0bcf554 - 8098330f6d91 tool_panel_section_label: Proteomics @@ -464,8 +464,8 @@ tools: - name: openms_openswathanalyzer owner: galaxyp revisions: - - 0ced5bc9f4dd - 08488066d588 + - 0ced5bc9f4dd - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -473,107 +473,107 @@ tools: owner: galaxyp revisions: - de7a553552a6 - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: + - c1809c05ae8c - 1bf940c18d93 - e8f64a7dc470 - - c1809c05ae8c 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 - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - d4396637b9f5 - - 0bddef8d144e - c99d5004b74f + - 0bddef8d144e + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - 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: - 05ec9fb05ed1 - - f82b320ceb90 - f9ed7e074900 + - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 18826fb8e5db - d31426ef20f6 + - 18826fb8e5db - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 4a7b96835140 - 2aebe58de46e - bc63b4d12779 + - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 3d8d4ada5405 - - 5ae104d0da6e - decc397c3b7e + - 5ae104d0da6e + - 3d8d4ada5405 - 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 + - dd173849c3d8 + - e039cc5c7aed + - d6aca689dd48 + - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - d426affe977c - - 8a45fd5a608a - 16026cdb1330 + - 8a45fd5a608a + - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 43b9ed22e8ce - - 9c70a651a53e - dd71e020e2aa + - 9c70a651a53e + - 43b9ed22e8ce 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 @@ -587,10 +587,10 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - c8b225c69a7f - 5c2a97a234d6 - 7f6a1f27553e + - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -609,21 +609,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - cb0378d2d487 - 5f49ffce52cb + - cb0378d2d487 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 3634c90301af - 7fdd9119cc4f - - 07ff622ec007 + - 3634c90301af - 3ec27b4cee7c - - a72c48001f7c + - 07ff622ec007 + - 1beff3ddce58 - da885ca16cb2 + - a72c48001f7c - 943a34df6047 - - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index de428bfcc..e37ccd9e1 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 - - 110a346daf36 - 2f1d464ebfd2 - - cd5f98911089 - e345aadf914f + - 110a346daf36 - 42201b90e3f4 + - cd5f98911089 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 0cd2df8af811 - - 8501601a118d - - c207119ba5f6 - - 42d9087b4789 - 0345dbaaa79b - fcce77c09289 + - 42d9087b4789 + - 8501601a118d + - 0cd2df8af811 + - c207119ba5f6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -38,10 +38,10 @@ tools: revisions: - 04db7fd6b238 - 421c33b8bf17 - - 405a212b32ab - 33486216eec0 - - ad5ab22ffe24 + - 405a212b32ab - 89eb29319bf4 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -54,11 +54,11 @@ tools: owner: iuc revisions: - f6e91108b7b1 + - fa51dc5e8386 + - 7b72fde3d27e - 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: - - a3e86cd9cac7 - - c9b77ced9a78 + - 8a55d29c8fcf - d30e36c48c93 - 3d70c2996730 - 1544278c272e - - 8a55d29c8fcf + - c9b77ced9a78 + - a3e86cd9cac7 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: - - 564c33e5c3e3 - b242deb58952 - - a5969aa9347e - 887cf585cafc + - a5969aa9347e - e2db212d64ad - 7b881f5f5ad5 + - 564c33e5c3e3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,10 +104,10 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - 8cff84759bf6 - e897c74a48bb - b4bab607eb05 - bd5ff77e2036 + - 8cff84759bf6 - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 6dafad990086 - - 33f0793edf93 - - 4f65e343ecdf - adc7a7610d4f + - 4f65e343ecdf - 5e10f396979e - 887e0991eb24 + - 6dafad990086 + - 33f0793edf93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - c5d7050e4ad7 - 17d39bf0a63a - - 97575d01f06b - 43e3eeb2e0ec - - c287418eb288 + - c5d7050e4ad7 - 4e280b27a831 + - 97575d01f06b + - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - 09b8edb56d80 - 0b8c84a7fdb5 - cd034465d4a4 - - d9bf483266a1 - - 9586f08634c0 - a819ec3b362d + - 9586f08634c0 + - 09b8edb56d80 + - d9bf483266a1 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: + - 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 - - 912f904a6e1e - cfb504394ae1 - - d1fda11e602f - bb0475c884ff + - 8a35a3bc6752 + - 912f904a6e1e + - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 22c3dace9..bd9946b8c 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,19 +2,19 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 31f8063eedea - - 7acb00fc980a - cf01dd6c6b1f - 2d4e3aff9dc7 + - 31f8063eedea + - 7acb00fc980a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 7a5a2d28c539 + - 32e542c2a773 - 703a2cb3fb38 - 125d20cb23d7 - - 32e542c2a773 + - 7a5a2d28c539 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -77,9 +77,9 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - - e66b9b5b8580 - ad5d061fbdf2 + - e66b9b5b8580 + - f648e5180e40 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffcompare @@ -91,9 +91,9 @@ tools: - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - d080005cffe1 - 6926716bbfb5 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -105,11 +105,11 @@ tools: - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a + - 86285ddd4512 - 6a6717a5f421 - 22cf48ad7b16 + - cf747d1bd79a - 04adc9db1581 - - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -135,8 +135,8 @@ tools: - name: cuffquant owner: devteam revisions: - - 679d93c99757 - 93148c05136f + - 679d93c99757 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -161,9 +161,9 @@ tools: owner: iuc revisions: - 3b36efd62b3e - - 0693ccd171c4 - - e3b16fd7dd08 - 8f0181aacb7a + - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -175,13 +175,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 6a3a025714d3 + - 9a882d108833 + - d027d1f4984e - cd9874cb9019 - - 24a09ca67621 - 8fe98f7094de - - d027d1f4984e - - 9a882d108833 - 0696db066a5b + - 24a09ca67621 + - 6a3a025714d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -193,10 +193,10 @@ tools: - name: dexseq owner: iuc revisions: - - 2872c633f07e + - 9a7c5b6d8f1e - df929f257179 - b47c006d90c5 - - 9a7c5b6d8f1e + - 2872c633f07e - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -209,18 +209,18 @@ tools: - name: edger owner: iuc revisions: - - 5bf899c13979 - - 334ce9b1bac5 + - f2843df56434 + - 3d89af8a44f0 - ae2aad0a6d50 - - a8305cf0c951 + - 334ce9b1bac5 + - 555659de7321 - 070900306913 + - a8305cf0c951 + - df0c8d0a5992 + - 0cb907a2a810 + - 5bf899c13979 - 6e53e565fc6a - 9bdff28ae1b1 - - 0cb907a2a810 - - 3d89af8a44f0 - - f2843df56434 - - df0c8d0a5992 - - 555659de7321 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -251,18 +251,18 @@ tools: - name: featurecounts owner: iuc revisions: - - ea04b737afa0 - - 6f66ae7c5f7a - - af814359d244 + - 1b851f87fbe0 - f3a5f075498f + - f9d49f5cb597 - a56fbe2d6ba7 + - ea04b737afa0 + - 38b6d12edc68 + - e6a2a912677a - 7db9d3ea71c9 - - 1b851f87fbe0 + - 6f66ae7c5f7a - a37612abf7f9 - - e6a2a912677a + - af814359d244 - 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: + - 0f710191a66d - 3c97c841a443 - 3c5e024a18cf - - 0f710191a66d 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: - - 26371a1df031 - - d4b55e2beb12 - - 6c19daec423d - f4af63aaf57a + - 6c19daec423d + - 26371a1df031 + - 3fb01a8c902d - a86e80d3c09c + - d4b55e2beb12 - 6ab42baa56e9 - - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -336,9 +336,9 @@ tools: - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - - 67b0b160903a - 4418229c501e + - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -357,10 +357,10 @@ tools: owner: iuc revisions: - 01247aaf0a10 - - 1c75aa5de15e - 5ae5c312d718 - - 87c11c05d238 + - 1c75aa5de15e - ce5d418183c5 + - 87c11c05d238 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -372,8 +372,8 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 4f9c4e6566e5 - c971db6f0fe5 + - 4f9c4e6566e5 - 10c98fab6c5a - 40985510cd98 tool_panel_section_label: RNA-seq @@ -387,14 +387,14 @@ tools: - name: limma_voom owner: iuc revisions: - - 0921444c832d - - 32511f586472 - - d6f5fa4ee473 - - 119b069fc845 + - e827f9aae031 - 58c35179ebf0 + - 32511f586472 - 97e06a4c7c75 + - d6f5fa4ee473 + - 0921444c832d - 708348a17fa1 - - e827f9aae031 + - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -443,8 +443,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - d696cf0a9622 - 72927fc9e9ed + - d696cf0a9622 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -462,21 +462,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 4014de1b6daf - - b0f2be869d6d - - c7c55b694974 - 980d2a2e1180 - - c772497b2c32 - 4074fc1940e2 - - 5ec75f5dae3c - - 3ea5a2a63fa2 - - 79de45b5069b - b9e04854e2bb + - 4df95e2d7f61 + - c772497b2c32 + - 79de45b5069b + - 5ec75f5dae3c + - b0f2be869d6d + - c7c55b694974 + - 7ed2edc1337f + - 4014de1b6daf - 0a563fd2f22e + - 3ea5a2a63fa2 - 99b17b74a8cd - - 4df95e2d7f61 - e132e7d02a3e - - 7ed2edc1337f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -500,14 +500,14 @@ tools: - name: salmon owner: bgruening revisions: - - 2c0ca397d302 - - e3d32471da11 + - cc05793bb896 - 15cd64d7c58b - 49121db48873 + - e3d32471da11 - ebab418107f5 - f4d5237a84f6 - - cc05793bb896 - 53e9709776a0 + - 2c0ca397d302 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -519,23 +519,23 @@ tools: - name: seurat owner: iuc revisions: - - c0fd285eb553 + - 8c28affc7c48 - fab6ff46e019 - 56242ff81c84 - - 8c28affc7c48 + - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: + - cef79931dda5 + - 1ebd14235b92 - 914cfcba0ec8 - - 258d696dbd7e - dd4df992d93d + - ae618321f34a - 76d290331481 + - 258d696dbd7e - cbf488da3b2c - - cef79931dda5 - - ae618321f34a - - 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: - - d0d4cef4f967 - - c6334cb383ff - 0db979fead3a + - d0d4cef4f967 - ffd1300599a1 + - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -586,10 +586,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - bcc5f03f1900 - d6a479fd4281 - - ba3720d7e68b - 74217fbfba4d - - bcc5f03f1900 + - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -601,10 +601,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - 2fb4ee002432 - - c2b82a94493e + - 478f36effca1 - 56162e446004 + - c2b82a94493e 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: - - fab23c3b5258 - - 9ff3765e7172 - 3f4094b6a565 + - 9ff3765e7172 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -630,10 +630,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e - - 4687ecf0eb2d - 34a018cbee9c - be3f26533209 + - 870ac06dff8e + - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -645,11 +645,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 65e7dea767ea + - c5fbddcac63a - 5192f657f305 + - 65e7dea767ea - 05ab8d5e04a2 - 33406f5a445c - - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -661,9 +661,9 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - a35cba31d904 - 6f0fb35b799c + - 1fdb25a8384d - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -677,9 +677,9 @@ tools: owner: iuc revisions: - c2c039e421af - - 7c7fbf13aadd - - 964b7efe2639 - 37a1129c89d2 + - 964b7efe2639 + - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -691,8 +691,8 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 047c22569787 - 1d689e4e1caf + - 047c22569787 - 24e94d84adc9 - eafea3083352 tool_panel_section_label: RNA-seq @@ -707,8 +707,8 @@ tools: owner: iuc revisions: - 3a4ac03d1266 - - 04bb8bb7c198 - 9871104ea630 + - 04bb8bb7c198 - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -734,14 +734,14 @@ tools: owner: iuc revisions: - d2bc35f3d1c5 - - 8f1c3df4dd49 - - db1f362cca3e - - d84caa5a98ad - - 32b86cd8eb50 - - 48636f857c4b - - 9fa24d5aac68 - c9cfec002f71 + - d84caa5a98ad - cee61b3fcf78 + - 9fa24d5aac68 + - 48636f857c4b + - 32b86cd8eb50 + - 8f1c3df4dd49 + - db1f362cca3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -753,8 +753,8 @@ tools: - name: trinotate owner: iuc revisions: - - 6fd16fad465d - 4383070d29ed + - 6fd16fad465d - 2b093007fab9 - 9e61bc67866f tool_panel_section_label: RNA-seq diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index a0868c72e..13cadf889 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 1a052c827e88 - 080fd5739bb4 - - 473382134e56 + - 1a052c827e88 - 27e16a30667a + - 473382134e56 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 b013b0844..04dd20584 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - 10184eaa85fc - - 3c661e57a88f - 88eedb4abea0 + - 3c661e57a88f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,10 +16,10 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - - 1dfd95ee241e - 108db6635177 + - cb20f99fd45b - 993b19f20c76 + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -37,8 +37,8 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 75d5afa09972 - 5325e44297b9 + - 75d5afa09972 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - 9c1c0b947e46 - ef11139d4545 + - 9c1c0b947e46 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -83,9 +83,9 @@ tools: owner: iuc revisions: - 5f8e69cc4c6e - - e7fd6754d093 - - 30a201c9c310 - 19ece8afbaab + - 30a201c9c310 + - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -110,8 +110,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -163,10 +163,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - 6856f8a01905 - - 9149ad20699a - 46c6639921f1 + - 12749212f61b + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -180,8 +180,8 @@ tools: revisions: - 33208952b99d - 92ec40abcdcf - - 26b4f9f98aca - 06dc50b7b711 + - 26b4f9f98aca tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -205,11 +205,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 66e23b11feae - a8d69aee190e - 720217c23995 - - b3d99709fe1a - b906586a6596 + - b3d99709fe1a + - 66e23b11feae 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: + - db17d5321bad + - 22970df7a40e - fe34990e5ce7 - fefd89ab563c - cc61ade70eb8 - - db17d5321bad - - 22970df7a40e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -245,10 +245,10 @@ tools: owner: devteam revisions: - 811fc2d75ad4 - - 88b8c2916784 - - 7a6034296ae9 - - fa5d3e61e429 - 7def34e6cf4d + - fa5d3e61e429 + - 7a6034296ae9 + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -267,21 +267,21 @@ tools: - name: samtools_merge owner: iuc revisions: - - 36677f429310 - - 740ce0a18f0d - b40e2d865d52 - 65a38e8c8e2a + - 740ce0a18f0d + - 36677f429310 - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: + - 329deb17a9f7 + - fa7ad9b89f4a - 583abf29fc8e - 9da0311ab1dd - - 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: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -306,8 +306,8 @@ tools: - name: samtools_reheader owner: devteam revisions: - - 30388d878f81 - 85e38b31e8b3 + - 30388d878f81 - db000c6007a0 - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM @@ -327,9 +327,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - a4a10c7924d1 - b8beef827165 - 344fc91e1bfd + - a4a10c7924d1 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 + - 6c2c1836728b - cab3f8d35989 + - d54a4df48867 - e613c1ad4c4c - - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -357,11 +357,11 @@ tools: owner: devteam revisions: - 818030fa6bbf - - 135c85f4cfaf - - bd850490c7f1 - - 5d9ae78f34d3 - b7f7826ef1cd - bcedabb53ddf + - bd850490c7f1 + - 5d9ae78f34d3 + - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -374,10 +374,10 @@ tools: owner: devteam revisions: - 541082d03bef - - 5a08c09b9311 + - 145f6d74ff5e - 1cc79f49b8d5 - 24c5d43cb545 - - 145f6d74ff5e + - 5a08c09b9311 - 3a0efe14891f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - b72793637686 + - b01db2684fa5 + - 32dc5f781059 + - 6be888be75f9 + - 5826298f6a73 - 0dbf49c414ae + - b72793637686 - bf328cec6a42 - - 6be888be75f9 + - c370440f901e - 350bbc5c2ffd - - b01db2684fa5 - 2dce91e11ca7 - - c370440f901e - - 32dc5f781059 - - 5826298f6a73 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 b4ce72ad6..2ebe2c208 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: - - 4aab5ae907b6 - - 6f6537780379 - a62c4a11a67d - - 5cb6146337d8 - - 59bb6d34fca6 - ea5e944f447d - - d147d6455873 + - 5cb6146337d8 - 480d9e9d156b + - d147d6455873 + - 4aab5ae907b6 + - 6f6537780379 + - 59bb6d34fca6 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 ae3c0c7c6..799a6b31e 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,21 +8,21 @@ tools: - name: alevin owner: bgruening revisions: - - e32b215b7c04 - - e4c01dcece8b - - b0fe3e482cb7 - - ecb9ea6269ee - c9944a2600f1 + - ecb9ea6269ee + - e32b215b7c04 - f2000bc73102 + - b0fe3e482cb7 + - e4c01dcece8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - c0b037b12765 - 7a6655aa6eb2 - - 707023fa62fe - e1c3c2f2a834 + - c0b037b12765 + - 707023fa62fe tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -30,10 +30,10 @@ tools: revisions: - 6f143dfe902a - 55e35e9203cf - - 32e547223c9e - - 93dd15e13e6a - - 00712416fdaa - cfc3f5a57dc6 + - 00712416fdaa + - 93dd15e13e6a + - 32e547223c9e - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -46,13 +46,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 39e945f0b2c1 - - 6f0d0c784f09 - b9fac48532eb + - 14c576ea6148 + - 6f0d0c784f09 + - 038e32885fec - 688357ad5e61 - ee98d611afc6 - - 038e32885fec - - 14c576ea6148 + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -64,61 +64,61 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - d4af736e7b83 - 9bd945a03d7b - - c4209ea387d4 - b85871dd69f9 - - 3d748954434b + - c4209ea387d4 - 43cb7b5a6fe7 - ed4996a16f7f + - 3d748954434b + - d4af736e7b83 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 7e8c677a7b71 + - c4209ea387d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: + - 2e8022f1923c - a4774b7b2e85 - fe75d2414dc0 - - 2e8022f1923c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: + - 0e70b2dfe4be + - 4fff5a293013 - 769d815e4b0d - 02b1fe7aed76 - - 4fff5a293013 - - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - aa4a6f0916b4 - - c29e7bb492bf - 344c2af50552 - a90f8efe08b4 + - aa4a6f0916b4 + - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - c32347702e12 - - 050cf43887d3 - - 5b7c81b35b89 - b13d3e4c48e1 + - 5b7c81b35b89 + - 050cf43887d3 + - c32347702e12 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 1d77986f9ddc - 239193b96d72 + - 1d77986f9ddc - 02fc39c8610d - ae969fdb8442 tool_panel_section_label: Single-cell @@ -156,11 +156,11 @@ tools: - name: dropletutils owner: iuc revisions: - - 8855361fcfc5 - - a9caad671439 + - cfe1e6c28d95 - 2c1200fba922 - cdf4443d5625 - - cfe1e6c28d95 + - 8855361fcfc5 + - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -196,48 +196,48 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 952abbc4b1de - - fb7068d30ec9 - 01c37e54e86e + - fb7068d30ec9 + - 952abbc4b1de tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: + - 57aeaf6b237d - 9d42a6133690 - f1c35f3f310d - - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - cab616fe7e64 - - 23b8d6b8960c - 163fd744e235 + - 23b8d6b8960c + - cab616fe7e64 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - b9ab56aecd18 - - f47ac4a0b337 - 013e53ccc7ac + - f47ac4a0b337 + - b9ab56aecd18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: + - a63e9713c39d - 9ea228a9afc8 - b892fa1fcaec - - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 640e0e45518a - f8320df1866b + - 640e0e45518a - 45a386d18509 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -245,8 +245,8 @@ tools: owner: bgruening revisions: - f963c251ac77 - - c354255ff705 - 9d02f1819e81 + - c354255ff705 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint @@ -260,9 +260,9 @@ tools: - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - 2dccb6bb0add - 782bdcb775fb - e06265d204f6 + - 2dccb6bb0add tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts @@ -276,9 +276,9 @@ tools: - 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 @@ -292,65 +292,65 @@ tools: - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: + - a315574104c6 - 4401ed529d2c - 3a6a5381db36 - - a315574104c6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - c0737631eea1 - - 2ba6cee8e4db - a83732c79949 + - 2ba6cee8e4db + - c0737631eea1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 30d7390bc918 - ea19190ce5e0 - 62b720dceb56 + - 30d7390bc918 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2b4d6a8dab36 - 2786a931cad2 - cd40ca76865a + - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - 0410b6aada45 - ffc33339cd3e - bf9379529c3e + - 0410b6aada45 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: + - 07dd436ea686 - 77d8e0fd162a - 5dfba24d7bdd - - 07dd436ea686 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - f1b3902f8baf - 972dcccb5bbc + - f1b3902f8baf - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: + - 7f7c6ead2d0d - 409396ea5cf0 - bb8849fca57c - - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo @@ -364,8 +364,8 @@ tools: - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 55b013e59018 - c261b6b05ee3 + - 55b013e59018 - 32173084d53f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -373,72 +373,72 @@ tools: owner: bgruening revisions: - 4b194e675916 - - b376ef118807 - b6b8c8672756 + - b376ef118807 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1511a8ebe906 - ed900cd4a0a9 + - 1511a8ebe906 - 910c6a1c3a27 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - 2aa5b6b65197 - 6d042c96aceb + - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - ea5d67ec94ab - - 9b383d429659 - dd9988943f53 + - 9b383d429659 + - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: + - 06ced663d24f - 11f39d7f6c64 - 6326cd29c1c3 - - 06ced663d24f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 - 337705015ee8 + - b4e780e93c91 - beb5b5917d2f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: + - 58de3c7c8e89 - e285920f8585 - 8d203e74869b - - 58de3c7c8e89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: + - 21d859ad4502 - ea8fb5e899e8 - 5cbd7a902a8d - - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - f81750434d70 - - 1d6af10874d5 - 36dfa2825a59 + - 1d6af10874d5 + - f81750434d70 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -456,9 +456,9 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 27fe5cd1729c - - 1de2276f633f - f36828ebdc54 + - 1de2276f633f + - 27fe5cd1729c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations @@ -472,27 +472,25 @@ tools: - name: modify_loom owner: iuc revisions: - - e98619de2776 - - 4b0adaa31c95 - - 7784821452ac - db575b4c8b22 - - eeab712b0b99 + - 7784821452ac - 59be31ac9dc3 - - 0f1aaff9b22d + - eeab712b0b99 + - e98619de2776 + - 4b0adaa31c95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare owner: bgruening revisions: - - 4447ed460308 - d817b3807562 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 2cfd0db49bbc + - 7ffaa0968da3 - 48f0fb3061b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -506,8 +504,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - fde4c972e7c5 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -525,8 +523,8 @@ tools: - name: raceid_clustering owner: iuc revisions: - - f911a64454fb - 7e014059a88d + - f911a64454fb - c4f39bf4a068 - a4b734cd253b - 49776718ae90 @@ -541,10 +539,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - 8b917923f7d4 - - 43c146e25a43 - 7608d5faee41 + - 8b917923f7d4 - d45f092caf24 + - 43c146e25a43 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -556,9 +554,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - - c7ddb719554d - 2b0d3e2f402a + - c7ddb719554d + - 37a47c4fd84d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -570,31 +568,31 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 6e90c8adf84f - df8e4e54d367 - 69018f285aa3 + - 6e90c8adf84f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory owner: iuc revisions: - - a6821f856a1e + - 6e90c8adf84f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 - - e93b008c637a - - 2bfd55b87af3 - 44b935f2271b + - c92d0f9338c5 - 72979cac22b2 + - 2bfd55b87af3 + - e93b008c637a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - 2af7c5086a96 + - 2bfd55b87af3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -612,17 +610,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 6f83f8fd381f - - b2df381a6004 - - aaa5da8e73a9 - - 38db3fef7aad + - 8983e7a04ba7 - 4d8f983cd751 + - aaa5da8e73a9 + - 6acb08931836 - 77b91b9bdf52 + - 38db3fef7aad + - b2df381a6004 - edec35114f72 - - 8983e7a04ba7 - - 6acb08931836 - - cb43c5d3acd3 + - 6f83f8fd381f - f9353ee6a0d4 + - cb43c5d3acd3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -634,15 +632,15 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 8cb783c81905 - - d636ce5cde16 - - fc0321c000a3 - - 72a6bebab2a5 + - a97abb8cd15b - 64388be6d510 - 277313130da5 - - a03ff8633507 - b409c2486353 - - a97abb8cd15b + - a03ff8633507 + - 8cb783c81905 + - 72a6bebab2a5 + - d636ce5cde16 + - fc0321c000a3 - 3c86f71498bc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -655,39 +653,39 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - c0a80a16560f - - 18262103fa61 - - f54f0f0598ad - 5e9171dc8244 + - c5d3684f7c4c + - f54f0f0598ad + - 18262103fa61 + - d86cb2ce311b - 6bd82ed14acd - cc0deb593fc8 + - 3081ff5c84a3 - 6c145a6868cc - 5c3ebe2adc77 - - 3081ff5c84a3 - - c5d3684f7c4c - - d86cb2ce311b + - c0a80a16560f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - d1cd8c147809 + - d86cb2ce311b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - 9f354c7c8c92 - - 7b9fafe32c86 - - 146ae5d70b47 - - 3bcd5445cd7a - 94c19fb1281c - - 4bda4412b8c2 + - d844935c906c + - 7b9fafe32c86 - c9cb76cf8d6c + - 3bcd5445cd7a - 56c0d4acef02 - - a407e7f8bdc1 - - d844935c906c - ab55fe8030b6 + - a407e7f8bdc1 + - 4bda4412b8c2 + - 146ae5d70b47 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -699,18 +697,18 @@ tools: - name: scanpy_plot owner: iuc revisions: - - dbbe1ea8ecb1 - - 6adf98e782f3 - - aa0c474463c2 - 0185bd174ea0 + - 40812a65a78b - f7446fd8d5e7 + - 6adf98e782f3 - 9b0cdb8cf6be - - 62acdd96d4a0 - 6f5349dd5c49 + - 7647e5cd1b8b + - 62acdd96d4a0 + - dbbe1ea8ecb1 + - aa0c474463c2 - 95777145cb92 - 1072ce66b426 - - 40812a65a78b - - 7647e5cd1b8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -722,17 +720,17 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: + - fe8f16c594ec - a39040ae0a38 - 9fb627495ec2 - - d18e7a6e5cd4 - - fe8f16c594ec - - 73ab2ac53d06 - f2f6c703da06 + - 73ab2ac53d06 + - d18e7a6e5cd4 - c65fce500915 - - c5541bfb8feb + - 458e8f43a775 - 215733a383f2 + - c5541bfb8feb - bf2017df9837 - - 458e8f43a775 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -744,8 +742,8 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - fd808de478b1 - b834074a9aff + - fd808de478b1 - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -758,8 +756,8 @@ tools: - name: scater_filter owner: iuc revisions: - - 7a365ec81b52 - b7ea9f09c02f + - 7a365ec81b52 - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -778,8 +776,8 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - ef4c80837bc5 - 2e41b35b5bdd + - ef4c80837bc5 - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -799,8 +797,8 @@ tools: owner: iuc revisions: - c99ba278dfa9 - - 9e5c0bb18d08 - 46fc6751d746 + - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -1029,8 +1027,8 @@ tools: - name: sinto_fragments owner: iuc revisions: - - 29e6bfb2cf49 - 6f66f523a9b7 + - 29e6bfb2cf49 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image @@ -1051,7 +1049,6 @@ tools: revisions: - 64fa083411f1 - 588c811fdd48 - - 88192fe25375 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting @@ -1077,8 +1074,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 883c33ef3372 - 90e95e9ee190 + - 883c33ef3372 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index d668d08cf..22868a413 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,11 +32,11 @@ tools: - name: datamash_ops owner: iuc revisions: - - 746e8e4bf929 - - 4c07ddedc198 - 2f3c6f2dcf39 - - 562f3c677828 + - 4c07ddedc198 - 419027d822d6 + - 562f3c677828 + - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - cb1c59d69557 - 6c29c7e347e8 - 7a15159140d1 + - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,11 +120,11 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 840f29aad145 - - 4c4ec859c31a - 7442b94d6a1e - - aef56d0e7a61 + - 4c4ec859c31a - 9c3e1d3235c8 + - 840f29aad145 + - aef56d0e7a61 - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -133,30 +133,30 @@ tools: revisions: - 9fda0b82f419 - d0352e8b4c10 - - 07843f917990 - 375bbd555f4a - 30d21a6041f6 + - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 2c58b83c9bad - 7ae443e6217d - - cd02bf168d23 - 8b1b2b91f8d0 - 4cc980df6265 + - cd02bf168d23 + - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 4bbaf77573ef + - ad7e0b4291ee - bb9fc9d46ea4 + - 4bbaf77573ef + - 1dd433d2c92c - 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 227445c45..0c66317e2 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: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 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: - - f18f67056946 - 6c6d26ff01ff + - f18f67056946 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 + - aff5135563c6 + - 464b9305180e + - 6e8d94597139 - 9cd341095afd + - 13b6f0007d9e - 02026300aa45 - 626658afe4cb - - 6e8d94597139 + - be25c075ed54 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: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -80,10 +80,10 @@ tools: owner: iuc revisions: - 37cde8134c6a - - 34d29339abab - - 557ec8d7087d - 90f657745fea + - 557ec8d7087d - 9cc411a62277 + - 34d29339abab tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -115,22 +115,22 @@ tools: - name: query_tabular owner: iuc revisions: - - 623f3eb7aa48 - - 83069b38aa85 - - 2e8f945f7285 - - cf34c344508d - 3a6b78c39dca - - 33d61c89fb8d - - cf4397560712 + - 2e8f945f7285 - 1ea4e668bf73 + - 623f3eb7aa48 + - cf4397560712 + - 33d61c89fb8d + - cf34c344508d + - 83069b38aa85 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - 399da6b5ec21 - - 503bcd6ebe4b - ae8c4b2488e7 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -142,10 +142,10 @@ 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 @@ -158,15 +158,15 @@ tools: - name: text_processing owner: bgruening revisions: - - fbf99087e067 - - 0a8c6b61f0f4 - - d698c222f354 + - 86755160afbf - ddf54b12c295 - - 9ff72e942410 - 74a8bef53a00 - - 86755160afbf + - 9ff72e942410 + - d698c222f354 + - fbf99087e067 - f46f0e4f75c4 - a6f147a050a2 - 12615d397df7 + - 0a8c6b61f0f4 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 7760d5d72..d5e410e0c 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -14,9 +14,9 @@ tools: - name: breseq owner: iuc revisions: - - 0d18a3ba2d1c - 82fb5e3bb93e - 85c57cc9b558 + - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -36,32 +36,32 @@ tools: - name: freebayes owner: devteam revisions: - - a5937157062f - - ef2c525bd8cd - 156b60c1530f + - 04fa42777df9 - 57def2d7c093 + - ef2c525bd8cd - 3e954e7125bf - - 04fa42777df9 + - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 09d6e4693887 - - e61c9ac190ad - 791f73caa0c8 + - 09d6e4693887 - 435b157bed6d + - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - dfadc322b065 - - 4805fe3d8fda - 65432c3abf6c - - 074d44697036 - b11e8e9c23bf + - dfadc322b065 + - 4805fe3d8fda - 3b4b2121842f + - 074d44697036 - e1461b5c52a0 - 03627f24605f tool_panel_section_label: Variant Calling @@ -69,8 +69,8 @@ tools: - name: lofreq_filter owner: iuc revisions: - - 9cb929f21cfa - 701d134358ad + - 9cb929f21cfa - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,16 +78,16 @@ tools: owner: iuc revisions: - f4473557ffc7 - - 426d707dfc47 - - 971e07ca4456 - c27549b9aa1f + - 971e07ca4456 + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - aa35ee7f3ab2 - cdaab621d454 + - aa35ee7f3ab2 - dbd9f2db9ed8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -101,18 +101,18 @@ tools: owner: iuc revisions: - 93c4b04a0769 - - ceff2f6a5368 - 43fffeed243f + - ceff2f6a5368 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: - - 9bccc8404a3c - 5bbf9eada9c2 + - c9a8ef2aa380 - fa016f1eea1a - d220115f882b - - c9a8ef2aa380 + - 9bccc8404a3c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -154,21 +154,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - 32f14a2723ec - 40f0591deda0 - - e7aff4a85df5 - ee4a90760848 + - e7aff4a85df5 - 3b1e7c170b10 - - 32f14a2723ec tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - adc0645b945c - 42818629ec4c - - 9793bc5d741b - - 4934c0ac6197 + - adc0645b945c - 02d81b994ef5 + - 4934c0ac6197 + - 9793bc5d741b 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 881130939..826250d9b 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: + - 265fe0f9ea64 - 6a88248893c4 - - b7ea370b8f5d - - 8a2e296c07ef - 2c372041ed8c - - e075b1be5abb - ebe5fc018e72 + - b7ea370b8f5d + - 8a2e296c07ef - 95815a0bb307 - - 265fe0f9ea64 + - e075b1be5abb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -21,13 +21,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 21687e35f066 - - c37b684e7f4e + - b03984136ce4 + - 22637b1a55bf - 0fba2c15b40d - 1001172b5089 + - 21687e35f066 + - c37b684e7f4e - 544cb432072b - - 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: - - 8408bffd5616 - - 3a7084316a6e - - 8627b2b383b4 - - 8ca3647c90fd + - bf1f4994f104 - 01d6b7d6365e + - 0238f68ad641 - ccb83bf54de0 - 143796b504eb - - bf1f4994f104 - - 0238f68ad641 + - 3a7084316a6e + - 8ca3647c90fd + - 8627b2b383b4 + - 8408bffd5616 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,14 +59,14 @@ tools: - name: bcftools_concat owner: iuc revisions: - - 6b6c992d3a14 + - d144af39073a - 62ca6da715bf - - 03e0645395d2 - - 81426b3cf18b + - 6b6c992d3a14 - f430a1ec7ee4 - - d144af39073a - - abd489215f73 + - 03e0645395d2 - 9b5abbf50d23 + - abd489215f73 + - 81426b3cf18b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - d3081540d175 - - d37e313a41be - - 1829900b5dcd - 2363ef414c9b + - d37e313a41be - 1171446da5db - - 95c6f3f4c77f + - d3081540d175 - e522022137f6 - 8aa352093d73 + - 1829900b5dcd + - 95c6f3f4c77f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - d58d2e8c7a57 - - 1137ce8efc1e - - b14ff40958cb - - 92c0aff8b53e - 348cd212dbad - 09f37afb3621 + - 1137ce8efc1e + - d58d2e8c7a57 - 012656fd329f + - 92c0aff8b53e - 9b29129fb491 + - b14ff40958cb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - de68c11034f6 - - cfd81f17580b - 367ba501b6eb - 1f2183a23823 - - 55c0e906c14c - ecc9192912b8 + - 55c0e906c14c - 7291189e98b4 + - de68c11034f6 + - cfd81f17580b 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: - - e6f4badbe6f3 + - ae68ceb4cca3 - 7cbf3c66d4ad - 039ea3f1dea9 - - 6c790a091c7c - - ae68ceb4cca3 - - 64a8f7dae3ad - d237eaef451f + - e6f4badbe6f3 + - 64a8f7dae3ad + - 6c790a091c7c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -152,14 +152,14 @@ tools: - name: bcftools_filter owner: iuc revisions: - - cdb7b4927742 - - 6ea7170a016d - - 277719af4dd7 + - 46fcafba49ec - 5d6653c989cb - 33bd9301568c - - 46fcafba49ec - - 963a3635b2e1 - e7452697afd9 + - 6ea7170a016d + - 963a3635b2e1 + - 277719af4dd7 + - cdb7b4927742 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 91c1e57d5c7f - - a29a2f40b665 - a1213a0b7b66 - - 26d97cdd5410 - 501bfb078342 - - b7f0f59baa7e + - a29a2f40b665 - 5a321fab1fe4 + - 91c1e57d5c7f + - b7f0f59baa7e - 7b4454382d39 + - 26d97cdd5410 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -192,13 +192,13 @@ tools: revisions: - c803c34361e0 - 15da1ddcfeff - - 39bca000353d - - 5f27e814a119 - - 709dd8291b83 - - 97d19c008d15 - 768d04526638 - - 81e4014fa809 + - 5f27e814a119 - d7d1663559e9 + - 81e4014fa809 + - 97d19c008d15 + - 709dd8291b83 + - 39bca000353d 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 - - b84fda8ebef0 - 86296490704e - - 2215287d5cc9 - 7ba36babba2d + - b84fda8ebef0 + - 2215287d5cc9 + - 85ee7e6c4204 + - b1eba148b35b + - 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: - - 4e1d23e5c691 - - 37757ffb4c5f - - 31ea13dfe5e6 - - ce9396ddcb2b - f506df85c652 - - cf06b44624c7 - - 9c711df3258d - - 0a5dcc9a8ec2 - 5660b21a0dbd - 56556e1267de + - 9c711df3258d + - ce9396ddcb2b + - 0a5dcc9a8ec2 + - 4e1d23e5c691 + - 31ea13dfe5e6 + - 37757ffb4c5f + - cf06b44624c7 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: - - 021693fdadaa - 1ca7418e46ee - - 48291658fdf6 - - 6deb4d549bc9 - a404f786a94c - 19905c025d2a + - 48291658fdf6 - 271965b55437 + - 6deb4d549bc9 + - 021693fdadaa 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: - - 71c78e0eea52 - - 3f6fadf8b8ff - - f7879f1e77f9 - - c450406f722b - dadbd61dc4cf - 97e8145d7e30 - - 5ad5d4243987 + - c450406f722b + - 3f6fadf8b8ff - 69d8b7567281 + - f7879f1e77f9 + - 71c78e0eea52 + - 5ad5d4243987 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,12 +287,12 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - d31a2e310a52 - - 0fe007201caf - 79f7a1acc2cd - 2514e684f8a3 - - cc7f9a4e186b - 283911fe7e1a + - 0fe007201caf + - d31a2e310a52 + - cc7f9a4e186b - 6cf13a657cf6 - 52f9e4a660e3 tool_panel_section_label: VCF/BCF @@ -307,13 +307,13 @@ tools: owner: iuc revisions: - 75ddd081f608 - - 1411bef27a75 - 80e6e399ccd0 - - 230e424bde67 - - 0a62420cb9cd - a12844ca467a - 026a989b7cee + - 230e424bde67 - 6963a6841d22 + - 1411bef27a75 + - 0a62420cb9cd 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: + - b10d1510fa84 - 5acfca5a76af - - 450a265f92e8 - bca7ce81688f - - b10d1510fa84 - - e493702b19eb - - ba20340426fe - 5808f77b2bb6 + - e493702b19eb + - 450a265f92e8 - 444e6a756c35 + - ba20340426fe 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: - - d52b8947b269 - dd72ff87cfd0 - - 157ffcdd3fa7 + - 68fec03a63b7 + - c43399f161f4 - f2482aa4862e + - 157ffcdd3fa7 - 12152af85697 - 4d236c696844 - - 68fec03a63b7 - - c43399f161f4 + - d52b8947b269 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 - - 75becf493cd3 - cbe39e530cbf - 29ba253e2e05 - 8f2fc0ab30fb + - 75becf493cd3 + - 8dbce095986c + - 0e5d11004815 + - 6f8e223f78f3 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: - - e0a856def0b0 + - a8630d4fbaf8 - 88bb477f45f7 - - 3ff5654b4e7d - - a367a15c6de5 - - f544f71adb73 - 8f5962c43868 - - a8630d4fbaf8 + - a367a15c6de5 + - e0a856def0b0 - 9708e3086f32 + - 3ff5654b4e7d + - f544f71adb73 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: - - 8b260d252ff4 - - 6ce175385dd9 - 03e30f06f15f + - 8b260d252ff4 - 5c9729d54721 + - 31c096c6b156 + - 4ed46189d6c6 - 96d0145c041a + - 6ce175385dd9 - 34dc0bbc7e93 - - 4ed46189d6c6 - - 31c096c6b156 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: - - 11af7fce71cf - - a730269af659 - - 681bdf1e22ff - - 2c4941386820 + - 46eb13bc2c73 - 40daf124be88 - - 09f5e45a8212 - a1aad8b559c6 - - 46eb13bc2c73 + - 2c4941386820 + - 681bdf1e22ff + - 11af7fce71cf + - 09f5e45a8212 + - a730269af659 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: + - f272b8ba0983 + - b74b8cbfc1f1 + - 8cb121b6a1d2 - 0594ea1417c8 - 12038f59c0f4 - 3897eaadfbff - - f272b8ba0983 - - 8cb121b6a1d2 - - 743cd1472aeb - 6cbb9c47795c - - b74b8cbfc1f1 - 882b2e649602 + - 743cd1472aeb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -458,12 +458,12 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - adee7e8b746f + - a9826db86d9a + - 238f78e38a8b - cced6715f926 - eccb508bb678 + - adee7e8b746f - 18cf9de1cf73 - - a9826db86d9a - - 238f78e38a8b - dba06328556a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: - - 9f36041495a3 - e53501abf992 - - 3ce32adc55b2 - f64e7ca2efd2 - c9935c9e8a24 - - fdec14f69010 - - 31a1b89eab9b + - 9f36041495a3 + - 3ce32adc55b2 - e0ad88dec40d + - 31a1b89eab9b + - fdec14f69010 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - d68c43202172 - 4db0695a6fc7 - 3b7b1fe7b937 - - fd3539749127 - - d43eb39b989e + - b7be725976b6 - 79489d5685dd - 2331ddcbd5aa - - b7be725976b6 + - d43eb39b989e + - d68c43202172 + - fd3539749127 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 - - 5296d26b0373 - - 1ccf0e7fb4f6 - b0d39ef600a7 + - 5296d26b0373 + - 1a989b4110da - 6a636d58dfc2 + - 1ccf0e7fb4f6 + - 78cd8b69da4c + - 58091e1be01b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: + - baa8823f8073 - 591cc8518033 - - b17394940c7a - - '388983871932' - - 4d3ce9dc1525 - - b641062a2587 - bf8325a07ce7 + - b641062a2587 - e8af591435d1 - - baa8823f8073 + - '388983871932' + - 4d3ce9dc1525 + - b17394940c7a 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: - - 3ca3de4e5291 - - 59fa8742285e - - 3a233c8eb814 - - 38d75661c235 - - d1f8f55f564d - - 1a2ef636f48e - c2ab91a0d506 + - 1a2ef636f48e + - 59fa8742285e + - 3ca3de4e5291 - e6b5cbbf449b + - d1f8f55f564d + - 38d75661c235 + - 3a233c8eb814 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: - - a8a4f94aa321 - 57a16b310fe8 + - a8a4f94aa321 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 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: - - aea8e90ad788 - 9edfe5145ba8 + - aea8e90ad788 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -619,8 +619,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -647,10 +647,9 @@ tools: - name: vcffilter owner: devteam revisions: - - eae7c08ebb6f - 4bdc111b2470 - 6b935ab36d7b - - fa24bf0598f4 + - eae7c08ebb6f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -670,29 +669,29 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom owner: devteam revisions: - - 8254e0fe7358 - b07ef36cf7e6 + - 8254e0fe7358 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign owner: devteam revisions: - - 29f9b782727e - d2406f98a782 + - 29f9b782727e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers @@ -705,8 +704,8 @@ tools: - name: vcfrandomsample owner: devteam revisions: - - 6257ee3b50d3 - 12b570dd0bc5 + - 6257ee3b50d3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples @@ -721,7 +720,6 @@ tools: revisions: - ee60203e68d9 - 5b7120c66efc - - f0580efedada tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate @@ -751,7 +749,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 6f6bf10618d7 - 166c4f50525f + - 6f6bf10618d7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index c5195c086..fba91387c 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,8 +2,8 @@ tools: - name: abricate owner: iuc revisions: - - 78c75f134c16 - 3f3e247c053d + - 78c75f134c16 - c2ef298da409 - 6e9aea89e388 - 4efdca267d51 @@ -19,62 +19,62 @@ 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: - - 1fdc517743e6 - c4ac24510b55 + - 1fdc517743e6 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: + - fe3ca740a485 + - 133f36c29579 + - 4f2967b27e67 + - 44018dd6b447 - 3e1f6f6d557e + - cd2480f35935 - 1aae04680c4b - f29602ae449e - - cd2480f35935 - - 44018dd6b447 - a79ee60b6926 - - fe3ca740a485 - b5d8e5475247 - - 4f2967b27e67 - - 133f36c29579 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - - 7be22100e5e1 - - dc027fa56d55 - f1e653756174 + - dc027fa56d55 + - 7be22100e5e1 - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: + - 09855551d713 + - ca6d970d931c - bd0e53f3a891 - 28433faa6e42 - - ca6d970d931c - - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -89,9 +89,9 @@ tools: - name: barrnap owner: iuc revisions: + - 8fd427007e93 - fe48aa4ccd5e - 7355bbf5e05f - - 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: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -116,17 +116,17 @@ tools: - name: cpat owner: bgruening revisions: - - 1ac12c0cc7a0 - 8e9e228c54c4 - 7ccc6234b54e + - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf - d9c3016f7283 - 63662ae295d6 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -157,60 +157,60 @@ tools: owner: iuc revisions: - 3bbe70fef6df - - 756376aeb1ae - - 582fd74dc2a1 - - 9c15ca7e764e - - b6b5cd37f2a2 - 9f2455341fac + - b6b5cd37f2a2 + - 9c15ca7e764e - 14f588312c56 + - 582fd74dc2a1 + - 756376aeb1ae tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 30fb23d4c31c - - 73428a792541 - a230ea445788 + - 73428a792541 - 8e1ace8f77c6 - - 989f7c061f35 - - 1691af4a0d17 - 0ffe5be70caf + - 1691af4a0d17 + - 30fb23d4c31c + - 989f7c061f35 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 30f08d74024f - - e94187d661df - - 57c6718cbfcc - 5a5ae61da69c - - 563a19373357 - 494f0bb4a993 - 0418d28136de + - 563a19373357 + - 30f08d74024f + - 57c6718cbfcc + - e94187d661df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - f77d7b685bb3 - - f31125bb85ea - - d6c7106b7b2e - - 4b96ced19f75 - - 7abc5f6dd595 - 2bba2ff070d9 - 1bc5a03faf2e + - 4b96ced19f75 + - d6c7106b7b2e + - 7abc5f6dd595 + - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 52af33194019 - d3af38b9c7e1 - b3cf4684e9c7 - - d77fdcca400e - - 54961e026fe4 - 520e30695ec3 + - d77fdcca400e - fed64e676186 + - 54961e026fe4 + - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -236,10 +236,10 @@ tools: - name: goseq owner: iuc revisions: - - 8b3e3657034e - 602de62d995b - - 43798b4caee0 + - 8b3e3657034e - ef2ad746b589 + - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -263,15 +263,15 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - - 74810db257cc - 98cafcbd2578 + - 74810db257cc - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -297,19 +297,19 @@ tools: - name: maker owner: iuc revisions: + - d46d803ca6cc - 370c210d9541 - 3c1a01127868 - - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 033755194fe9 - - b815ec682418 - e95d52d295d7 - 624606f7c996 - c8ac28e8ac44 + - b815ec682418 + - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -357,10 +357,10 @@ tools: - name: prokka owner: crs4 revisions: - - 8a22554cdde2 - bf68eb663bc3 - - a17498c603ec - d643e3b03500 + - 8a22554cdde2 + - a17498c603ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -372,15 +372,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - 3f987772e283 - ba6d2c32f797 + - 3f987772e283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -404,23 +404,23 @@ tools: - name: snpeff owner: iuc revisions: - - cfcf33df7fc0 - - 8f92c2b26e6d - - 5a29ab10dba6 - 68693743661e - 5c7b70713fb5 - - 268d162b9c49 - 5b80f544c67f + - 5a29ab10dba6 + - cfcf33df7fc0 - 6322be79bd8e + - 8f92c2b26e6d - c7275bd8b4d6 + - 268d162b9c49 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - - 5fab4f81391d - 09d6806c609e + - 5fab4f81391d + - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna @@ -439,18 +439,18 @@ tools: - name: tbprofiler owner: iuc revisions: - - 51dd22484644 - - ba6f87115e13 - - 200c378d85f3 - - 4839e590cb26 - - 037a11682176 - 809dfc93d593 + - 037a11682176 - ac8250086ac3 - - 45083d070fb8 - - 37213cf56392 - - d03af1c7002c + - 51dd22484644 - e1a9d6fd258d + - d03af1c7002c + - 45083d070fb8 + - 200c378d85f3 + - 4839e590cb26 - 8cb134b8c1a5 + - 37213cf56392 + - ba6f87115e13 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 1962c83ad..c28a2f149 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,27 +2,28 @@ tools: - name: abyss owner: iuc revisions: + - a929ce596a34 - 890b794c997d - - d6d5ccc2c581 - - fa5259cc561b - - 553bfe8bd0b5 - - 0124fce4654a - 841084c5fc46 - - a929ce596a34 - 8f1b150a2487 - - 7547fcab5d19 + - d6d5ccc2c581 + - 553bfe8bd0b5 - 0e93176640ac + - db9b10824c61 + - 7547fcab5d19 + - 0124fce4654a + - fa5259cc561b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b2860df42e16 - - ddddce450736 - 21e491ad532a - - 067592b6b312 - 94fe43e75ddc - b9e31c5c01c7 + - b2860df42e16 + - ddddce450736 + - 067592b6b312 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -35,9 +36,9 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 3371c5bdc17a - - 22286dab5aa1 - a7f16f24e9a1 + - 22286dab5aa1 + - 3371c5bdc17a - faee8629b460 - 5258e18bbe23 tool_panel_section_label: Assembly @@ -45,39 +46,38 @@ tools: - name: blobtoolkit owner: bgruening revisions: - - 8c2167481e72 - - 53dd00a4ab68 - '392811378515' + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 4048d82f0c88 + - 94170eee0ad8 - 41030a6c03b7 - - 5ecdeca79a0d - e4bd1e99bacf - - 1e62c28ba91d - - ea8146ee148f - 2dd755c1c6ff - - 46ae58b1d792 - - 0d243f458b53 - - 602fb8e63aa7 - 2babe6d5c561 - - e824f5d958d0 + - 602fb8e63aa7 + - 4048d82f0c88 + - 5ecdeca79a0d + - ea8146ee148f - 1440ae06552f - - cf13a1e03e5b - e5c372c91e46 + - 46ae58b1d792 + - cf13a1e03e5b + - e824f5d958d0 - bb935709506a - - 94170eee0ad8 + - 1e62c28ba91d + - 0d243f458b53 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 86f150c8019d - - c5b7390290b1 - 5732f959936a + - c5b7390290b1 + - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -89,44 +89,44 @@ tools: - name: flye owner: bgruening revisions: + - 3e4f8642c77e + - cb8dfd28c16f - 276f5d8712d5 + - 1f0769f0b56b + - e27815e82dd4 - 1ce9b1d72ec3 - 8d4f03b5fe9d - - e27815e82dd4 - - 1f0769f0b56b - - 3e4f8642c77e - - cb8dfd28c16f - - 291923e6f276 - 3ee0ef312022 + - 291923e6f276 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - b2f674562a18 - 01210c4e9144 - 460fad600dce - 3169a38c2656 - - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 7348b69e5109 - - ba88bc5a6446 - 8b330a577046 + - ba88bc5a6446 - 06bcf65179fb + - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: + - 690c2caa367e + - f4a3eff8ab85 - 3fba9c77550a + - 6ec1b853c8fd - 3ef480892a9f - 5127a713de83 - - f4a3eff8ab85 - - 6ec1b853c8fd - - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -139,23 +139,23 @@ tools: owner: bgruening revisions: - 60024a528cbd - - f3c89da3af16 - - ec9e21e9c71b - - da9d8bf98802 + - 5161f204ba63 + - 0ee0c3089254 + - 71740308d412 - 284a1cb82b61 - - 5f625c63b8bc + - 5bec28269d95 - 3f7be05a1597 - - 045c7c3d8e59 + - ec9e21e9c71b - 9ef6920c3089 - - 5bec28269d95 + - 045c7c3d8e59 + - 366a11d316a7 - 41cea2aa2dce + - f3c89da3af16 + - 5f625c63b8bc + - da9d8bf98802 - 2061fb3b81b4 - df25d4fb79b7 - - 366a11d316a7 - - 71740308d412 - 6505bd37670d - - 0ee0c3089254 - - 5161f204ba63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -179,21 +179,21 @@ tools: - name: megahit owner: iuc revisions: + - de387b2b2803 - 7518ee87b53d - a96f3ad4e0d8 - 14ddfc8ffb93 - - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 9d79beb19ac3 + - 39edec572bae + - 09c589057ee8 - eb7b00ec347d - - f8113c25bc6b + - 9d79beb19ac3 - d7edbc9c3a07 - - 09c589057ee8 - - 39edec572bae + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl @@ -207,15 +207,15 @@ tools: - name: metaspades owner: nml revisions: - - 606b09cc9860 - - f338e9942b27 - - 99ecfdafc64f - f369ef5f210b - - e731ea24e48d + - 606b09cc9860 - 2ecf5a570907 - - 3ca2d2a9068c + - 99ecfdafc64f - eb7a370f6588 + - e731ea24e48d + - f338e9942b27 - fd128c111ab0 + - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -227,11 +227,11 @@ tools: - name: miniasm owner: iuc revisions: - - b799a615995d - - 73a3846701e1 - 8b6d0d85252b + - b799a615995d - a7b889b90140 - 8dee0218ac7d + - 73a3846701e1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -249,8 +249,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - 15200570e926 + - 7c2f5268d01c - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -263,13 +263,12 @@ tools: - name: pretext_map owner: iuc revisions: - - 2b16ba799da9 - - dfb8a4497339 - 8fef980d48b5 - - 79b48f02db49 + - d256a51a656b + - dfb8a4497339 + - 2b16ba799da9 - c6cec5ab35c1 - bbe19ef04a74 - - d256a51a656b - 02831bf9e95f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -284,24 +283,24 @@ tools: - name: quast owner: iuc revisions: - - 875d0f36d66f - - 3061c8b029e5 - - 59db8ea8c845 - 342a1d1fed7b - - ebb0dcdb621a - 675488238c96 + - 3061c8b029e5 + - 72472698a2df + - ebb0dcdb621a - 7594365c546b + - 59db8ea8c845 + - 875d0f36d66f - 6fcbee531de6 - - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - d865b62f501c - - cd06929b224b - - a199cd7ac344 - 78c533842eeb + - a199cd7ac344 + - cd06929b224b - aa39b19ca11e - 39bed8de8017 tool_panel_section_label: Assembly @@ -315,31 +314,31 @@ tools: - name: raven owner: iuc revisions: - - f8564b2d7f63 + - 2b2a352488fa - f11b994b7eb2 - 3edba9afc9bc - - 2b2a352488fa - - 5c55448d0f33 - 33b7d8481a76 + - f8564b2d7f63 + - 5c55448d0f33 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: - - 1d06c8b38e77 - 28189050e437 - - ef69617ecb42 - 5fc94b3a4704 + - 378e55aeeb25 - 53c2bc8c2ae3 - e122f9101584 - - 378e55aeeb25 + - 1d06c8b38e77 + - ef69617ecb42 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -351,158 +350,158 @@ tools: - name: shovill owner: iuc revisions: + - 83ead2be47b2 + - 865119fcb694 - ee17a294d3a3 - ad80238462c1 - - 83ead2be47b2 - - 196a599ec43d - f698c7604b3b - d9f6a00b6db7 - - 865119fcb694 + - 196a599ec43d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - 24e471d13fe9 - - 015283de3004 - 5e0825476fb7 + - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 7490b213baa9 + - 1bb12736175c - 604782a8a53a - c33a476f4001 - - 051fd2db8a27 - - 1bb12736175c - 1fc82fe7ebef + - 051fd2db8a27 - 904bf932cf78 + - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - 9678993ca5bd - - d6e617c4e338 - - 808b3a0a6716 - 655fa188c3cc - - fee85957cebe + - 808b3a0a6716 - ad8b536d1caa + - d6e617c4e338 + - fee85957cebe - 34305b013402 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 21da31ed41a1 - - 037f9927c4ff - - b8002c3f7141 - 8d4b90bf9caf - e5a3b75a271f - - 6b5a5842531e + - 037f9927c4ff - 7e27faaad80e + - 21da31ed41a1 + - b8002c3f7141 + - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 5b26685e5d3b + - 9de69775f512 - 328aa71f0f3c - 86f66ab58e14 - - 9de69775f512 - - 7922870efcca - - 2a10645aeadd - f1532cb33c75 + - 2a10645aeadd + - 5b26685e5d3b + - 7922870efcca tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 340bc17f49cf - - 6aad515a5270 - - 1708851f8804 - - 8cc856b935ee - e41dcb0e913b + - 8cc856b935ee + - 6aad515a5270 - 85fb02c43042 + - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - d159735a6a9f - - b3490b036c5a - de1260f8a300 - - d5fb354f745d - - 6357b127161e - b65a43f70b99 - 249f6a28c751 + - b3490b036c5a + - d5fb354f745d + - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: + - a90db5dbaaf3 + - dd7ad84f3943 + - d5887ace0dd4 + - d2d1df21dfb9 - 7897763d14ec - 9006e5836729 - - dd7ad84f3943 - 33368fec3b70 - b7829778729f - - d5887ace0dd4 - - d2d1df21dfb9 - - a90db5dbaaf3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ced385aa976d - - 6f4c8ad6ea01 - - 0368ac680e70 - 505a9833ab5d - 8f631679571f + - ced385aa976d - 189e837009c9 + - 0368ac680e70 + - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: + - a7ed21de23fe - 9ded6109434a - - e59bee4565b3 + - d40ed4eb0c0e - 19bdfd1e6fe3 - 356afed970b4 - - a7ed21de23fe - - d40ed4eb0c0e + - e59bee4565b3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 80a17897564d - ebd801e712bc - - 7673a6c920b2 - 4688ae3b49b5 - b23249f81bc4 - 6dd935e4984b + - 7673a6c920b2 + - 80a17897564d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - ed312479d9eb - - 59bd28f6265d - cb1e3db43020 - - b64696992ee9 - b5e35a2ca4f3 - 937ea677d437 + - ed312479d9eb + - b64696992ee9 + - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 383bb5ad32e2 - 6015aa0303f2 - - cb4768eeca3b - b9b0246a2be3 + - 383bb5ad32e2 + - cb4768eeca3b - 05bd7504fdb2 - 2628f6790eda tool_panel_section_label: Assembly @@ -510,29 +509,29 @@ tools: - name: unicycler owner: iuc revisions: - - 8f9f06995f98 + - e92675014ac9 - 3e44ef016b45 - 0a3a602cd1e3 - - e92675014ac9 - e022dff952df - - 9e3e80cc4ad4 - 6e26c9afd301 + - 9e3e80cc4ad4 + - 8f9f06995f98 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 8d09f8be269e - 5da9a0e2fb2d - 920677cd220f + - 8d09f8be269e - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 4a53b89fa703 - 82398ba86ba7 + - 4a53b89fa703 - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -545,8 +544,8 @@ tools: - name: yahs owner: iuc revisions: - - 39495e107274 - - ff4031bfaa22 - 425e63adcc5d + - ff4031bfaa22 + - 39495e107274 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 9a6a526bc..d6977d7c5 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -3,25 +3,25 @@ tools: owner: iuc revisions: - bfd290fe1588 + - 392f100eebcd - 4768f7f8e93f - 1ae00120dd24 - - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 1f5641a52664 - - 31812e7a1315 - 8e8dc9a1e3e5 + - 1f5641a52664 - ded48b36f3b7 + - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: + - 17fcac7ddf54 - 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 5d199212a..7f5958101 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,21 +2,21 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 0840ba83860c - 159b04e36791 + - 0840ba83860c - 204a131e47db - a9c9d768b751 - - d58c27d2c5a7 - 1c427e24fb79 - - d1f62024a08b - 7beb76ffbc0f + - d58c27d2c5a7 + - d1f62024a08b tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge owner: iuc revisions: - - cab19c0452c4 - 1bb2b5b52030 + - cab19c0452c4 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_tadpole diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index cae2567e8..b00adf5d0 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 589e7e57fd6d - - a8eabd2838f6 - - e19bebe96cd2 - - b28e0cfa7ba1 - - 87ee588b3d45 - - dde39ba9c031 - - 64e2edfe7a2c - - a1a923cd89e8 - 07e8b80f278c + - dde39ba9c031 + - 87ee588b3d45 - ce3c7f062223 + - a1a923cd89e8 - a68aa6c1204a + - e19bebe96cd2 - 0a5c785ac6db + - b28e0cfa7ba1 + - 64e2edfe7a2c + - a8eabd2838f6 + - 589e7e57fd6d 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 06ecde584..f713f1ea1 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,24 +8,24 @@ tools: - name: diamond owner: bgruening revisions: + - 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 + - d999e774072a - 0e3cf9594bb7 - 2889433c7ae1 + - cbf3f518b668 + - a52d2d93e595 - e25d3acf6e68 - - d999e774072a + - 5edc472ec434 - 6f386c5dc4fb + - acf4e47b734c tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 396353400..d631d2de7 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 095ad4d096d1 - - 27ee142314a9 - da6bd1975a71 - - 710301bc46fa - - f4230f116196 - 6ca543ec1bf8 + - 095ad4d096d1 + - f4230f116196 - c8cdde00b105 + - 710301bc46fa + - 27ee142314a9 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: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 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: - - 0fac8e2afc13 - - bfb65cb551d8 - - 3b8a9d5ced85 - 88076940fa94 + - bfb65cb551d8 - 79cfd9ead848 + - 3b8a9d5ced85 + - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - eb6564a60136 - f5d979cb4b54 - - 715cd0e87781 + - 55918daa5651 - d532b7e5f64b + - 715cd0e87781 - b46d4b4d995c - - 55918daa5651 + - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - dae135dfd519 - 5579659312e6 + - dae135dfd519 + - fdf2cc80adb5 - d2f955aea23a - f26afd1b7104 - - fdf2cc80adb5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - bc31d02be922 - - 319a28774da9 - d1d0efda35c0 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 4da9ee404eab - ed736e6eee39 + - 4da9ee404eab - 070e3ecc3fda - - 2c349b027a01 - cac1886249a2 + - 2c349b027a01 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 + - c0c9a5024177 + - 73008ef1f487 - 807aa4c9293d - 2e219a2d9327 - - da8753545526 + - 525ca7c8065f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: + - 61094e01eff9 + - 2c8ed1b52bf7 - c4fbab8e03c5 - 1809414a9454 - 7568ae18908a - - 61094e01eff9 - - 2c8ed1b52bf7 - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -210,10 +210,10 @@ tools: owner: chemteam revisions: - 730ef07b90ae - - 79e8ab8f1e81 - - ba83f0923369 - ccfbd956a2d3 + - ba83f0923369 - d7ec25187599 + - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -269,9 +269,9 @@ tools: owner: bgruening revisions: - e6011617c748 - - b59c91adeac1 - 4242b4d68e9c - e2c36f62e22f + - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -351,9 +351,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - d4c67ced6abc - 85fad59f8168 - 9b48456a96fe + - d4c67ced6abc - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 7782bf53d..557a1b727 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -3,10 +3,10 @@ tools: owner: bgruening revisions: - fa56d93f7980 - - f907216064f6 + - c97a786e8fb5 - 2605cbdaa7d8 - 163688bb8f73 - - c97a786e8fb5 + - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -25,11 +25,11 @@ tools: - name: macs2 owner: iuc revisions: - - 86e2413cf3f8 - - 495a4173006f + - 640d3af5d833 - 424aefbd7777 - f5d67c722d67 - - 640d3af5d833 + - 495a4173006f + - 86e2413cf3f8 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator @@ -42,7 +42,7 @@ tools: - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 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 ae0baaae9..bae34340c 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - 705ebd286b57 - cd6da887a5f4 + - 705ebd286b57 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 830961c48e42 - 33151a38533a - 90981f86000f - 25136a2b0cfe + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,8 +31,8 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 6cbe2f30c2d7 - 0046692724f9 + - 6cbe2f30c2d7 - 2dae863c8f42 - baabc30154cd tool_panel_section_label: Collection Operations @@ -40,7 +40,7 @@ tools: - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b 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 c26d239e9..1f1446695 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 - 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: - - 5e1240a87bcb + - 6ef0b5664c69 + - 4a6ee918c13a - 367b1ed91207 - - 3b6f97e7094c - a3b86937ead6 - - ab9350a8ab4d - - 6ef0b5664c69 + - 5e1240a87bcb + - 3b6f97e7094c - e3cbd2287f63 + - ab9350a8ab4d - f3a19509108a - 0b3c3ad92827 - - 4a6ee918c13a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 091bb5922a82 - - e525f9ffb9ac - - d4d4e9febf5c - - 54ccb7e1f49a - - 584008e574b2 - bd46669113b9 - - 1b5fc03380d4 + - e525f9ffb9ac - 72ed72122deb - 501c21cce614 - - 33c99804a32f + - 1b5fc03380d4 + - 54ccb7e1f49a + - d4d4e9febf5c + - 584008e574b2 - e177a8ea0bf1 + - 091bb5922a82 + - 33c99804a32f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -67,8 +67,8 @@ tools: owner: devteam revisions: - 77b41c89d856 - - 186b8d913e6c - 8979c288aefb + - 186b8d913e6c 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: - - 4dea02886337 - 3e436657dcd0 - 154d00cbbf2d + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -136,15 +136,15 @@ tools: owner: devteam revisions: - 78fb18899c99 - - 68f57cc8fad0 - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 26c6706bfb07 - 63769c4217a7 + - 26c6706bfb07 - b9b385097f13 - 92ac8e086317 - 19e45916daf9 @@ -168,8 +168,8 @@ tools: owner: iuc revisions: - 98704d357ede - - fa49730d1d4b - a2f83a375bf2 + - fa49730d1d4b tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 784fdcd82..e63dcfccf 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: - - 29451af70c52 - - e821645ef8fc - - de72ba3ed6f2 - - c929a006727f - 5f6d123679f4 - - a1ca9bccc7f2 - 268e91e540ee + - a1ca9bccc7f2 + - c929a006727f + - 29451af70c52 + - de72ba3ed6f2 + - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e49b109abc2 - - bb1e4f63e0e6 - - 12af64f93288 - 5d11599b8a7d + - bb1e4f63e0e6 + - 0e49b109abc2 - 0e143b4c3987 - 7a7fd0f5f15d - 2d2cf5c1ea8a + - 12af64f93288 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - c06951d10364 - - 7c1beb6d6eca - 81b1e3e1fc6c - - dc059492a995 - 1d848bc4585f + - 7c1beb6d6eca + - dc059492a995 - 195e98217334 + - c06951d10364 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - a67ac707496a - 07418a30ed01 - - 71aa86af6762 + - 26e7304d6737 + - 3d211717a775 + - a67ac707496a - 93eb012d9eed + - 71aa86af6762 - bfff7454b59a - - 3d211717a775 - - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 29fcfd36e90a - 2bc10a9ca58b + - 5be24eba848d + - b8858746dc1f - dd0b7398bb96 - 56d5b797ce84 - - 5be24eba848d - 26983857c91a - - b8858746dc1f - - 29fcfd36e90a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7e6bcd2e5128 - - 72bfafe3330b - - 9384cd033f30 - - 7ef978dc1b8a - - e6d0bff01239 - ee3a1b0f45f1 + - 7ef978dc1b8a - c3e012dfe21f + - 72bfafe3330b + - e6d0bff01239 + - 9384cd033f30 + - 7e6bcd2e5128 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: + - fd1275e01605 - 9470f29702f8 - - d9a637e83828 - 167788df3b46 - - b73e213add0c - - fd1275e01605 - - 514fa53b5efb - a60c359ec43c - fb9cf9c97ec4 + - b73e213add0c + - 514fa53b5efb + - d9a637e83828 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 - - a02cfa31e9cb - e479c7ca5570 + - 2c37ce318bc3 + - ca0616bb2cdf + - a02cfa31e9cb - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 2d466b530754 - 01fb6a7654e6 - - 69a8621ca2f0 + - 2d466b530754 - 78f405266706 - - 192ef85c0b0b - - 004aea905d4d - 1fcb7adc39b8 + - 69a8621ca2f0 + - 004aea905d4d + - 192ef85c0b0b 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 + - db940c262830 + - 137c4beed34b + - d9ce4897dbb2 + - 2f9e4843f480 - 459cfa861f0b + - 3c9f0c486cca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fbe773640707 - - 2c66e43f1c86 - 32e451def88c - - f264afa9fa6f - - bd7db9e2f2cb - bad3ca889618 + - f264afa9fa6f - fd408d755394 + - bd7db9e2f2cb + - fbe773640707 + - 2c66e43f1c86 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 7fda5607e777 - - 231994413f89 + - 7e361d147872 - 3b9d990a0a0e + - 231994413f89 + - 7fda5607e777 - 56bce3c82278 - - 7e361d147872 - - 9368fbc49c8b - 4e12ea27f788 + - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 4431f39ede55 - c03c3384cd81 - - d9114ef1c8a5 - - e65d16fb2724 - - b1779366c8e9 - ce4ce3316f74 - 94ca68515826 + - d9114ef1c8a5 + - 4431f39ede55 + - b1779366c8e9 + - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - d57251071381 - - 793665fff0f8 - - 23f7c5f1fdaf - - 4ed32329e0ed - b88ebb3672a1 + - 4ed32329e0ed - f8fc4e5aff9d - 2da482e408b8 + - d57251071381 + - 793665fff0f8 + - 23f7c5f1fdaf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a7849312d328 + - 010e58e9d822 + - e4c7985d4585 - a4dfb122e52b + - a7849312d328 - c60570fa602f - 25d830337d31 - - 010e58e9d822 - - e4c7985d4585 - - ba6efa77fb79 - 512155688d98 + - ba6efa77fb79 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - c899e0ccff8c - - 4d678170d29b - - 69264da0ce77 - 38e3f226248b - - 00d869ea03a1 + - 69264da0ce77 - 443d9a9d6d11 + - 4d678170d29b + - c899e0ccff8c - aa200e4f3939 + - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - aac8444d6681 - - a2d70c4fd406 - - d806504e96d9 - 10301d137111 - - c361b12d207a + - d806504e96d9 + - a2d70c4fd406 - 6662b1a8d326 + - c361b12d207a 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 c8e193153..2d0c0d41c 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -2,43 +2,43 @@ 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 owner: iuc revisions: - - 94f412098ac8 - 8cb6bd511879 + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -65,7 +65,7 @@ tools: - name: obi_uniq owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index e9a6db869..42a614fb1 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -4,7 +4,7 @@ tools: revisions: - ce385837c160 - dba489bfcd62 - - 63dd26468588 - 832c20329690 + - 63dd26468588 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 d52d1276e..3e90a2b6c 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - cf1322aeb137 - 6da3972210ee - - 62f5fab76dfb + - cf1322aeb137 - d82648ad25a3 - 29bdbc353f20 + - 62f5fab76dfb tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index a243c0d38..7f5e93015 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: + - e4691e1589d3 - fe74900d6dc7 - - 5915ea1ec9b1 + - c053d4cad713 + - 64172f1c1202 - 660cffd8d92a - - de6cebe3c043 - - e4691e1589d3 + - 5915ea1ec9b1 - 8c0175e03cee - - 44e2cc14f75b - - 49370cb85f0f - - 5eb7e84243f2 - c5e2e5902201 - - c4b82dce8335 - 8665bcc8b847 - - 64172f1c1202 - - 093678460093 + - c4b82dce8335 - 288f97432497 + - 4e5056fefd88 + - 44e2cc14f75b + - 135b80fb1ac2 + - de6cebe3c043 + - 5eb7e84243f2 - 48f587c13075 - b1c926deaa2d - - 135b80fb1ac2 - - 4e5056fefd88 - - c053d4cad713 + - 093678460093 + - 49370cb85f0f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -41,9 +41,9 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - - 5cbde03c1103 - de2db1bdfbf8 + - 5cbde03c1103 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -61,24 +61,24 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 9457a20156db - - 516b97a23d7e - 859422bcb689 + - 516b97a23d7e + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a - f773e98b26cf - f81d4362b6c1 + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -86,37 +86,37 @@ tools: revisions: - 9c620a950d3a - cd0874854f51 - - 56022eb50bbd - 0dbb995c7d35 + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - ecb9f4854617 - - a626e8c0e1ba + - dbfc505896e9 - c59d48774d03 + - ecb9f4854617 + - 65b93b623c77 - d60c3f704da0 - - dbfc505896e9 - 1d8fe9bc4cb0 - - 65b93b623c77 + - a626e8c0e1ba - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - f1dc2a761c30 - - b05e39b9c170 - 9115b978ce10 + - b05e39b9c170 + - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: + - '144275714590' - 10b75444feae - 81a9090d6df3 - - '144275714590' tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -138,8 +138,8 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -154,50 +154,50 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 3e396e702cea - b41c2c1bcfbf + - 3e396e702cea - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - c885369b207b - 8d958759cf2a + - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - - e39cc71d3ed6 - 397dc333436b - 249c8393f2d4 + - e39cc71d3ed6 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - - 045f0e1043f7 - 54053ea6c77e + - 045f0e1043f7 - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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_trimmer owner: devteam revisions: - 33794bdb7fe0 - - b63b2bfb3ea3 - f0b18efb97f1 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -210,26 +210,26 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: + - 529bccd5e4a1 - 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 - 8abdedf55101 - 0b7ec11b3c7c + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: + - 90858c306551 - 736b8f6ee456 - cb1e251cac37 - - 90858c306551 - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -244,28 +244,28 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 02f8a17a4ebd + - 3599f5451ee2 - b29d37ca9e41 + - 02f8a17a4ebd - f984bb114520 - - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - 0c2907307ba4 - 177f0621c266 + - 6027ef51ef91 - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: + - 547e8d00f11c - 377ac2829eac - 61b4cedc8934 - 73194cdd4f57 - - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -278,39 +278,39 @@ tools: owner: iuc revisions: - 037f0acc7830 - - f69501361cec - 2f804526f5fd + - f69501361cec - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: - - 61eb4cfc7313 - 29ef2c5ec205 + - 61eb4cfc7313 - 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: - - 3da72230c066 - 4b494533146a + - 3da72230c066 - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -324,40 +324,40 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - 71f649c23021 - d3f58a0dc09d - bf04bd405d5b + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - e654095ab143 - - a535cf1e5da4 - 71ad4a56c40c - - 24013bf85a6f - b557acca0b56 - 8250ea3a1501 + - a535cf1e5da4 + - 24013bf85a6f + - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 27ac32a22ad2 - - 9fa7803d1c51 - - 015cf18f4a15 - - 828dba98cdb4 - 7a7e33d28f62 - - f3759eec3018 - 6a675c3aa610 - 7accf7407811 + - 27ac32a22ad2 + - f3759eec3018 + - 828dba98cdb4 + - 015cf18f4a15 + - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group @@ -370,8 +370,8 @@ tools: - name: umi_tools_whitelist owner: iuc revisions: - - 4c8a1c7d3608 - e4e12f0b3af1 - 953b4821b183 + - 4c8a1c7d3608 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 400eb94a8..a6ba2d6ce 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,38 +2,38 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - e41385662e5e - - 64e9a6afdd0c - ce9cd02d5b88 + - 64e9a6afdd0c + - e41385662e5e - 7b4468117008 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - 5ec9f6bceaee - - ff9530579d1f - - 2b0c9d9fc6ca - - 9da02be9c6cc - - 3d0c7bdf12f5 - f2e8552cf1d0 + - ff9530579d1f - 2c64fded1286 - e7b2202befea + - 9da02be9c6cc + - 3d0c7bdf12f5 + - 2b0c9d9fc6ca tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - c1a33f603da2 - 89d299153577 - a252d8415583 + - c1a33f603da2 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution @@ -47,39 +47,39 @@ tools: - name: fastx_quality_statistics owner: devteam revisions: - - 59003d0543cd - - 7306ec78632a - cc0fd298cc17 + - 7306ec78632a + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - a72af9de6bf5 - 1f296803dfa3 - 8880fb74ef56 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 9a913cdee30e - - 1c2db0054039 - - f7e2f1eb3a16 - - b2f1f75d49c4 - - 75c93c70d094 - - bf675f34b056 - 5e33b465d8d5 + - 75c93c70d094 - c1a4b5f3b432 - - abfd8a6544d7 + - 9a913cdee30e - 3d93dd18d9f8 + - bf675f34b056 + - b2f1f75d49c4 + - f7e2f1eb3a16 + - abfd8a6544d7 + - 1c2db0054039 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 949f01671246 - - cd7e644cae1d - 084bbd8ba7b8 + - cd7e644cae1d + - 949f01671246 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 c01999d90..0dfc5355c 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: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f 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 2d183e1d1..1545a9f2d 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -9,15 +9,15 @@ tools: - name: sample_seqs owner: peterjc revisions: - - 7c40a1fbc82e - bdaefd241921 + - 7c40a1fbc82e tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_filter_by_id owner: peterjc revisions: - - 83a19df00eab - - 85ef5f5a0562 - 141612f8c3e3 + - 85ef5f5a0562 + - 83a19df00eab 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 1dd47cff5..d90b0a808 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -16,16 +16,16 @@ tools: - name: gemini_annotate owner: iuc revisions: - - 0c8f7322f8fc - - f2f3bc622a16 - 8f53b238a360 + - f2f3bc622a16 + - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -38,15 +38,15 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,15 +59,15 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,23 +86,23 @@ 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 owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 61343646155c - 00c2734b3bea + - 61343646155c tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -115,16 +115,16 @@ tools: - name: gemini_qc owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - 840fb4850be3 - da74170c55c7 - 666f60a9331a + - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,15 +137,15 @@ tools: - name: gemini_region owner: iuc revisions: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 9844ff03b..061f295f2 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -16,21 +16,21 @@ 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 owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 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 4ebeec7e0..21b103b41 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -3,9 +3,9 @@ tools: owner: galaxyp revisions: - b39347891609 - - e9df53a75f3c - 983bf725dfc2 - c1b437242fee + - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,54 +17,54 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 1c58de56d587 - e063168e0a81 - 28587613264f + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: + - 4df8de2d0e48 + - 6ea73833cf67 + - 516a54ddf218 + - 8848455c0270 + - 653e89d73fc4 + - 69ebb7f46e45 - aad3885b3216 - - ba931a59dd59 - - 6591f049cf7e + - 1790dcf3c32d - 4317d3cb6cba - - 7068f48d0ef9 - - 69ebb7f46e45 - - 9a776b080193 - - 8848455c0270 - - 5e6237d58b0c - - e08a7ad4378b - - c441583adae5 + - ba931a59dd59 - 83c7d564b128 - 734abc7ac21d + - e08a7ad4378b + - c441583adae5 + - 9a776b080193 + - f8054ea1c365 + - f5ea3ce9b9b0 + - 7068f48d0ef9 + - 5e6237d58b0c - 1ec814014652 + - 6591f049cf7e - e407b9da183a - - 6ea73833cf67 - - 516a54ddf218 - - f5ea3ce9b9b0 - - 1790dcf3c32d - - 653e89d73fc4 - - f8054ea1c365 - - 4df8de2d0e48 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 - - 75b3b3d0adbf - 21a560af5913 - 34758ab8aaa4 + - 75b3b3d0adbf + - 9aaa46d45472 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 468c71dac78a - - 95fb5712344f + - af5eccf83605 - bfdc6a7ffd3a - 054483e27a35 - - af5eccf83605 + - 468c71dac78a + - 95fb5712344f 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 764add73f..9663756ba 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,14 +2,14 @@ tools: - name: circos owner: iuc revisions: - - 290a11559985 - - df7356989ac1 - - 4b519282a05b - - 740057a5126d - 7f13dc906cb9 - - ae9994cf526f - a64dc31ab7f2 + - 4b519282a05b + - df7356989ac1 + - 290a11559985 + - 740057a5126d - fd59d783248a + - ae9994cf526f - c4bde687c846 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -29,8 +29,8 @@ tools: owner: devteam revisions: - 7cf5b1d072b5 - - f95284aa2946 - 867ab348287d + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,24 +42,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - 3b37b1b1c3a7 + - ca7cb0eaad62 + - '566197475670' - 51c6ccaace7e - 48b42ee61bc5 - 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 - - 1a72f938213e - 3d059e9c2fba + - 1a72f938213e + - 10515715c940 - da4c086cff5b + - d3a9e32672ec 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: - - 299307abd804 - - 5298e06f14f9 + - 1acf88921176 - 5fe1dc76176e - e3a675da7fd0 - - 1acf88921176 + - 5298e06f14f9 - d0fc8b746d57 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -103,15 +103,15 @@ 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 owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f 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: - - 112eb40ba6cf - - a6e57ff585c0 + - fd5dbf0f732e + - 4542035c1075 - 1cfc579079a6 + - 667e17248bfe + - 6cd09d7b5f37 - 2bb2e07a7a21 - - ca2def38369c + - a6e57ff585c0 - 17359b808b01 - - 667e17248bfe + - ca2def38369c - 836d1aa3e89a - - 4542035c1075 - - 6cd09d7b5f37 - - fd5dbf0f732e + - 112eb40ba6cf tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -157,9 +157,9 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - - fe154a7af404 - 03c13085aecc + - fe154a7af404 + - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -179,17 +179,17 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 1c5dcef5ce0f + - 85da91bbdbfb - 62e3a4e8c54c - f234e2e59d76 - - 85da91bbdbfb + - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 9958188c6195 - 7b21a9b5922f + - 9958188c6195 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -201,11 +201,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 26f2fe7e53a1 - - 7c9417381ad5 - - 326098bc19cc - 44c66e8d21e6 + - 7c9417381ad5 - 6c571966cfb9 + - 26f2fe7e53a1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -217,23 +216,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 326a3db8d9d1 - - 7dd841a32245 - 36b848d5f3ec + - 360df4999907 - 14e7c35f3d00 - - 2824d77cd8f8 - - 4ac4e7083b7e - a1abfa420d9d - - 360df4999907 + - 4ac4e7083b7e + - 7dd841a32245 + - 326a3db8d9d1 + - 2824d77cd8f8 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - 73b8cb5bddcd + - 83c573f2e73c - 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 169e09a7a..1661eb404 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -42,8 +42,8 @@ tools: - name: scanpy_filter_genes owner: ebi-gxa revisions: - - cc64914b0cf4 - 23d838d1569d + - cc64914b0cf4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster @@ -56,15 +56,15 @@ tools: - name: scanpy_find_markers owner: ebi-gxa revisions: - - d8f5224005bb - 0a8e527d1517 + - d8f5224005bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 79da59a0b180 - 64dd8bb151e1 + - 79da59a0b180 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -77,23 +77,23 @@ 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 owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: + - 94697510d55f - 9a2f72d7dbd2 - ff6decc0f432 - - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -127,8 +127,8 @@ tools: - 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 @@ -141,15 +141,15 @@ tools: - name: scanpy_read_10x owner: ebi-gxa revisions: - - 287503c35cb4 - 078aa23c9374 + - 287503c35cb4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable owner: ebi-gxa revisions: - - d18ed15697bb - 0bab2ae44e7a + - d18ed15697bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap @@ -169,8 +169,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - be019b069e31 - 65c3ec07502b + - be019b069e31 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -190,22 +190,22 @@ tools: - name: scanpy_run_tsne owner: ebi-gxa revisions: - - abdb61e4afa3 - 3fb53f5e46ea + - abdb61e4afa3 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - 0f98603d0116 - ea91cfd0444e + - 767a675b5254 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/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index efcda67d6..c67fb63bf 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -4,42 +4,42 @@ tools: revisions: - 9edf8894a22d - 29f66c353bcb - - ed2cca6b5de4 - - 921a2da49a0c - - a4c13ddcc8ee - 0f611e7d7858 + - a4c13ddcc8ee + - 921a2da49a0c + - ed2cca6b5de4 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 11de0d28ab30 + - 755df866ad0c - d404277cc87a - - ec4b948dc6f0 - - 78fb5e286609 - 5746d61f0a91 - - 755df866ad0c + - 78fb5e286609 + - ec4b948dc6f0 + - 11de0d28ab30 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 11fa44ee0603 + - 4d511437b1e5 + - 9e357a8b2ec3 - 977dc15add20 + - 11fa44ee0603 - 03dd3c16ae4e - - 9e357a8b2ec3 - - 4d511437b1e5 - f72063d9426b tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 77919cc3618e - - 0ba4f56a3613 - - 1da5f169b491 - 3b5b54ed6392 - 41dbf4d162a2 + - 1da5f169b491 + - 0ba4f56a3613 + - 77919cc3618e - c3e5e2cf12b7 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu @@ -47,11 +47,11 @@ tools: owner: bgruening revisions: - 9939786dd9c9 - - 12d51d7be66f - f741330d4a71 - - b63363075c2e - - 7babd8a46fe0 - 5308ca68ef3d + - 7babd8a46fe0 + - 12d51d7be66f + - b63363075c2e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index 598e74c9f..bc8cc7135 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,19 +2,19 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 7db4fc31dbee - - 81f0cbca04a7 - 699a5e9146b3 - - 3df9f0a4bf34 - - 0c777d708acc - 8bccb36e055a + - 0c777d708acc + - 3df9f0a4bf34 + - 7db4fc31dbee + - 81f0cbca04a7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - 5bc8cdc17fd0 + - 5791a7f65275 - 2436a8807ad1 - 0a53256b48c6 tool_panel_section_label: Imaging @@ -22,25 +22,25 @@ tools: - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 9d47aabda459 - e576b73a2e2f + - 9d47aabda459 - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - 77f7159d775a - 70316d792fc9 - b1c2c210813c + - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - d51310ab328a - - f70b215d155c - dba87c4b32d3 + - f70b215d155c + - d51310ab328a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_split_binaryimage_by_watershed @@ -52,10 +52,10 @@ tools: - name: bfconvert owner: imgteam revisions: - - 10eed33aa9b2 - - 85edbb7a436b - f3360fbeda64 + - 10eed33aa9b2 - b07f4839ca77 + - 85edbb7a436b - fcadded98e61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -69,17 +69,17 @@ tools: - name: count_objects owner: imgteam revisions: - - 664232d2a3f7 - 5bf8eb50b280 - b58447a2eed2 + - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - 0e4dccaafef5 - - eb6c08714244 - e917a2424690 + - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -93,88 +93,88 @@ tools: owner: bgruening revisions: - 6070780813d9 - - e7273daa5ae2 - 670975e92458 + - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: + - df3ad3ba5c6f - ef4aed1d34c4 - cdf8e3c57dae - - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - 5d28ac336861 - 2484086dee41 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - f2ed92b011a9 - - bace5a93a97c - 11f177b1a59e + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f24c370e5ea4 - - f8fa0f6718a3 - d0178bdcd00e + - f8fa0f6718a3 + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 3245681b2f6d - 31d195bedf6d + - 3245681b2f6d - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: + - 993faa34333b - 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 + - ff1a86a87364 + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - 667a513e67e4 - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - 2564f461de62 - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: + - 20dbb1f7ec7b - 91e03287f285 - a32c3f810ade - - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity @@ -188,9 +188,9 @@ tools: - 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 @@ -204,17 +204,17 @@ tools: - name: cp_measure_object_size_shape owner: bgruening revisions: - - acf3aa487283 - d85f11570109 - 79e10d12d90a + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 80b200ae516b - b76841ee5560 - 035a58c7f54a + - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -227,17 +227,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - 8083a87d2fdf - 3a3033222f61 + - 48102a685037 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 @@ -249,8 +249,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids @@ -264,8 +264,8 @@ tools: owner: imgteam revisions: - 7b6d9412c7f8 - - f8b4eada923c - 236ec78b2e53 + - f8b4eada923c 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 1cac3c429..ce5e53638 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 1069f6db0a0e - - 3a72fede57ce - 78bbd17d0703 - - 40737febe339 - - f362150bef41 + - 3e4f434a69c6 - e319b5b65879 + - f362150bef41 - e4ee04da1c19 - - 3e4f434a69c6 - - d6e72da3ec35 + - 3a72fede57ce - a38934e303b9 + - 40737febe339 + - 1069f6db0a0e + - d6e72da3ec35 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 9537184d421f - - 7fe36019c073 - - 8f8df367470d - 0135f1d487a0 - - 72ddd32392cd + - 9537184d421f + - fcbeda41d0ac - 618297d23022 - - f91cfb73d369 - c88553ec696e - - fcbeda41d0ac + - 8f8df367470d + - 7fe36019c073 - 2b95d5c04908 + - f91cfb73d369 + - 72ddd32392cd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 - - fafb3d685fa9 - d7e79eb3bcb3 + - fafb3d685fa9 - 2cf4a1cafc16 + - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 7f1cfa4c0e32 - - a1c2aecd7a0d + - 8c05afb547fa - bd2a7d1316b9 - - 9eaadf03e0df - - 6a1515bb0687 + - 3d18f8c3c0f6 - ee29337f905c - - ee2beb764a7b - - 8d36959b000d - - 43aac8d29685 - 5dc33613c288 + - ee2beb764a7b - 94df24c6bc00 - - 3d18f8c3c0f6 - - 8c05afb547fa + - a1c2aecd7a0d - 28a6f1908fcc + - 6a1515bb0687 + - 7f1cfa4c0e32 + - 8d36959b000d + - 9eaadf03e0df + - 43aac8d29685 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - e3bb03cf207a + - 364f4ffec275 - a250929be21b - - bcaa0d571ce2 + - c092052ed673 + - db536ad45f28 + - cb903c9dc33d - 5671e1d3d5ee - - e3bb03cf207a + - 5d6ed46cc101 - 86a20ae274fc - - 9f978da6528a - 8858fa037a15 - - cb903c9dc33d - - c092052ed673 - - 5d6ed46cc101 - - 364f4ffec275 - - db536ad45f28 + - 9f978da6528a + - bcaa0d571ce2 - d37ede8589b2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: + - c5c9f02b6167 + - abbc8041e8ec - f95f403841ad - e1a015876aa9 + - 3b6a16d82c1b - 38b91a3190cd - - c5c9f02b6167 - - 12d66d0d05ac + - 230b05597996 - 49236b03e4fd - - 194e3ceee923 - - abbc8041e8ec - - 3b6a16d82c1b + - 12d66d0d05ac - ed28dd32141c + - 194e3ceee923 - 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 09ead8e2c..b346142a2 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 + - 0f1724dd59d2 + - 17e3b698dd52 - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: + - 374cb875d38a - 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 737bbc5e2..e61d24cc2 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -19,9 +19,9 @@ tools: owner: bgruening revisions: - f1b9a42d6809 + - e1317b5502fa - 818f9b69d8a0 - b6ef6d0cb6b7 - - e1317b5502fa - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -29,19 +29,19 @@ tools: owner: bgruening revisions: - c80db5d6fd8c - - 947c2eacccb8 - - 8334dc98c48e - 1588f9076e32 + - 8334dc98c48e + - 947c2eacccb8 - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 83228baae3c5 - - 1552b8cb4a94 - 9991c4ddde14 - 29e4122c90de + - 1552b8cb4a94 + - 83228baae3c5 - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -50,50 +50,50 @@ tools: revisions: - 1a53edc4b438 - 060ca94ac049 - - a07ab242b0b5 - 53616c8b0865 - f3dfa4bdf87e - 841a6cc5fc58 + - a07ab242b0b5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - 91c4e3331208 + - d4808d5b83da + - dc4b5fd604a6 - 2fc89dcd41c8 - 40f4447733b2 - - d4808d5b83da - 927586a18553 - - dc4b5fd604a6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - 7626ea9c2e1b - - 36e8d6d5d01b - - c6ae57f774c6 - - e5a5ad882f1f - 301e07345c93 + - e5a5ad882f1f - 25ab6b4e376e + - c6ae57f774c6 + - 36e8d6d5d01b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - b7c3e9a3b954 - - f9639b488779 - 80852884053f + - f9639b488779 + - 02d2be90dedb + - b7c3e9a3b954 - 0630258dcf35 - 4ed102b922cb - - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 61634a87efc7 - 14180f9c831e + - 61634a87efc7 - caeb57858702 - ec69cbe34b73 tool_panel_section_label: Machine Learning diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 1940d40d3..8bfc99abe 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - cd659e8cc5fa - - 03e9b2fbc005 - - d5ceb9f3c25b - - 937aa69e715f - 749c918495f7 - - 0d4acadabb04 - - f6877ad76b00 + - d5ceb9f3c25b + - a6d65b0c67af - 017aba02828d - 17062a0decb7 - - a6d65b0c67af + - f6877ad76b00 + - 0d4acadabb04 - 3ba8d4563129 + - cd659e8cc5fa + - 937aa69e715f + - 03e9b2fbc005 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: - - dfd8b7f78c37 - - e188dc7a68e6 - - 2477830927ec - 64f11cf59c6e - - 53646aaaafef + - e188dc7a68e6 - 3fe632431b68 + - 53646aaaafef + - 2477830927ec + - dfd8b7f78c37 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - e7f19d6a9af8 - - 60afcc2c1d05 - 3e1ea2facca6 + - e7f19d6a9af8 - 37b497aa133f - 2ff111fac1d7 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 53c0b7a1a0c3 + - 11a0d50a54e6 + - c0c2d0941de8 - b3eab4b67562 - - 5cc34c3f440d - - 3f4d6399997b - be1d967337e4 - - 11a0d50a54e6 - - 037c6e54df11 - - 09b53c1d4ab1 - 6b1e195506a3 - - c0c2d0941de8 + - 5cc34c3f440d + - 09b53c1d4ab1 - f54f5baedfdd - - 77b2770508f6 + - 037c6e54df11 - 8c6cd2650d1f + - 77b2770508f6 + - 3f4d6399997b + - 53c0b7a1a0c3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: + - e403d27e8f24 + - 5ef7ec16b04f - 00fbfac99d39 - - 79b885ce78d7 - 1cd2511a396e - - 178bdbdb6d24 - - 42ce70172b72 - - e403d27e8f24 - ec9cbd6b9a49 - - 5ef7ec16b04f - - 9ee34ba73ebf + - 45795f582ae9 - b8f5f6e87f5c + - 9ee34ba73ebf - 13022c3d3076 - - 45795f582ae9 + - 79b885ce78d7 + - 178bdbdb6d24 + - 42ce70172b72 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 74813531a..09d1b9ad5 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 90dc951da294 - 6cd2a9e6ac49 + - 90dc951da294 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -57,8 +57,8 @@ tools: - name: isolib owner: recetox revisions: - - 6b0fef8a77c0 - 2b1118bce0b1 + - 6b0fef8a77c0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -71,23 +71,20 @@ tools: owner: recetox revisions: - a5d41764722d - - 1d10d32fa3b3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_convert owner: recetox revisions: - - 9e83636da9d3 - - c990df6afc24 - b9cc12600553 + - 9e83636da9d3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - 00e66c401366 - - a177ac3c752c - 83c4b4359ac4 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -95,29 +92,25 @@ tools: revisions: - fd890f162ce6 - 84af792d3a78 - - d7b517f2c5fe tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - - 9e3c83d2afc3 - - a5a5b147da70 - 1b09315a3f87 + - a5a5b147da70 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export owner: recetox revisions: - - 8832425b1ff6 - f04610d25411 - - b576ed720711 + - 8832425b1ff6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: - - 1d443ed476a1 - 330b0dfae8da - 03bc9b7f40f6 tool_panel_section_label: Metabolomics @@ -125,22 +118,19 @@ tools: - 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: - - f04b378325e5 - 8147d93d372d - - 1d74ae228df3 + - f04b378325e5 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 @@ -148,7 +138,6 @@ tools: owner: recetox revisions: - d50ce2f51fc0 - - fbe335d27d25 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_similarity @@ -160,15 +149,13 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 9ff95a1a2705 - - 7627b40601f6 - 7ba589b01dbc + - 9ff95a1a2705 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - - 500f473df7e4 - 0cf68b536cd1 - ea6c5636c0cf tool_panel_section_label: Metabolomics @@ -176,7 +163,6 @@ tools: - name: matchms_subsetting owner: recetox revisions: - - 6d2f2c565431 - 5bbd1a8404f5 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -239,34 +225,34 @@ tools: - name: ramclustr owner: recetox revisions: - - 9b716db0a786 - da7722f665f4 + - 9b716db0a786 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - 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: + - 149b9cc7499b - 18ec7635bac6 - - 59c393d35e0e - f3a18e020cdd - - 149b9cc7499b + - 59c393d35e0e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: + - 134be5abb208 - 50b9918aeff2 - 481d769e2f7a - - 134be5abb208 - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -274,20 +260,20 @@ tools: owner: recetox revisions: - a82db010c53e - - 9064aecc78a7 - - 501a232f3cd5 + - 51332c2520c7 - 02c772a49998 + - 9064aecc78a7 - 30bf4e35da3e - - 51332c2520c7 + - 501a232f3cd5 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 - b341cfd4baf8 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table @@ -302,19 +288,19 @@ tools: - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - d7f5878a98c3 - - 99d118321d5f - f92b1b64da93 - 24278c6b6d1c + - d7f5878a98c3 + - 99d118321d5f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ffbabefbd2e2 - - 7acd11ddc061 - ea0758b41473 + - ffbabefbd2e2 - d90187b0f247 + - 7acd11ddc061 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -326,8 +312,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 6b5dec818827 - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -345,8 +331,8 @@ tools: - name: rmassbank owner: recetox revisions: - - 0b28816c1c2c - 5a6bb93ec656 + - 0b28816c1c2c 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 a45e0a520..9095a339c 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,16 +2,16 @@ tools: - name: bracken owner: iuc revisions: - - 0c7b6eb7e752 - 1d4bd12f01cf + - 0c7b6eb7e752 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_bins owner: iuc revisions: - - 0094893f5001 - - 18676df0cb3a - 0e63d03c8790 + - 18676df0cb3a + - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -90,101 +90,101 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 7c2100246a2f - - 65db807336bc - 76d3d2b10738 - - 5b5a7af9fbb4 - 63f86089423e + - 65db807336bc + - 7c2100246a2f + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 1c35dadbe76f - 18a502a9d287 + - 00f5005840fa - 96336c6a2bb7 - 84fd33a60b35 - - 00f5005840fa + - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - 34e55239e68b - - a9f4a217dcd6 - - e8fba04706d3 - addaf9d22850 + - a9f4a217dcd6 + - 34e55239e68b - f732237754fc + - e8fba04706d3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 04c15826a0b8 - 0776d824d896 - 5fe3edf19b9c - - 04c15826a0b8 - - 75403243703a - 8c202e741d68 + - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 43c99742158b - - 75c8945b0da2 - e96bbb9e24ea - 8470de786d47 - 1c9b3bcd4261 + - 43c99742158b + - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 84743da21318 - 306a40d4bb8f - 5c865a382933 - 35176674168c - 1d75bd0595e2 - - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a - - 555ccac8a4c5 - - 78faebd0879c - 32c9ea835770 + - 78faebd0879c + - 555ccac8a4c5 + - ac72310b038a - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - 7b8cb2b02978 - - a58e4a43f49c - f947b4bb5107 - d60df8727f59 - cae017b76acb + - a58e4a43f49c + - 7b8cb2b02978 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7f3b59dee073 - - 7136e9ab70db - 04144473e59e - - 073608a50ac3 + - 7136e9ab70db + - 7f3b59dee073 - 1bc3657cd694 + - 073608a50ac3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - a7817705348e + - d943081510da + - 19299bb1c6af - 0a1224c4b781 - 9058d8943303 - - 19299bb1c6af - - d943081510da + - a7817705348e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -197,13 +197,13 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - b907a3c0434f - - f8f56dd6449f - a68b985913ab - - 5c7ba3d85a01 - - 65d52c693b8e + - f8f56dd6449f - 4d9445dff47b - c4db8c4de66f + - b907a3c0434f + - 65d52c693b8e + - 5c7ba3d85a01 - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -217,9 +217,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6c84982ee6f7 - - 6d364c65c946 - 654548ae1357 + - 6d364c65c946 + - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -231,25 +231,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - bd7a9c6efb10 - 6aad8ca3918b - e66ab198ec15 - - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - b084117133af - - d77397f09da1 - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - cad93abecac9 - - 9704f1a3b32d - 7f208f1eb64f + - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -288,33 +288,33 @@ tools: - name: humann_regroup_table owner: iuc revisions: + - 31c6d107e7a5 - e88b731dad59 - 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: - - aabf8cfb8fef - - d24841f5c3d2 - - 71ea608ddfa3 - 094ad9c068af - - 172920f67a84 - 714d5a28cc5c + - 71ea608ddfa3 + - 172920f67a84 + - aabf8cfb8fef + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a4d7148ccee4 - 12fb63b5f63f - - 4137b492233e - - d7e9a3c41657 - - a293a742194f - 2bdd84912a2b + - a293a742194f + - a4d7148ccee4 + - d7e9a3c41657 + - 4137b492233e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -327,19 +327,19 @@ tools: owner: iuc revisions: - 75bedfb2078b + - 6fcb8ac37a3e - cf87759761eb - - 97f7bb0851e7 + - 64bc7acc22a9 - e2c71b852aba - a92c06a3afa7 - - 6fcb8ac37a3e - - 64bc7acc22a9 + - 97f7bb0851e7 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 @@ -352,21 +352,21 @@ tools: owner: iuc revisions: - 5e5a999ffaa9 - - 080ea153677c + - 4033827c76b8 - 4e5e73d03f0d - c82508e76ad1 - 2d35528d2141 - - 4033827c76b8 + - 080ea153677c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - 6b7622dda516 - - fc6c328c292f - - c2803012bbb3 - 95bf7479d53c + - fc6c328c292f - 2cd76b089570 + - c2803012bbb3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: itsx @@ -378,15 +378,15 @@ 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 owner: iuc revisions: - - 385a965c6f87 - 65b382bf9b7c + - 385a965c6f87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution @@ -406,15 +406,15 @@ tools: - name: khmer_extract_partitions owner: iuc revisions: - - adb3dd5a899f - 1061711538c6 + - adb3dd5a899f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance owner: iuc revisions: - - b86562b4f3fd - 29a4d6e2ae9c + - b86562b4f3fd tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_below_abundance_cutoff @@ -434,8 +434,8 @@ tools: - name: khmer_partition owner: iuc revisions: - - 8388fe31d604 - 5a0fa29951ae + - 8388fe31d604 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: - - 20e2f64aa1fe - cdee7158adf3 - - 328c607150ff + - 20e2f64aa1fe - 4a9da2b6c2e3 + - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -469,15 +469,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1c677354ab18 - 6c09bed3444f + - 1c677354ab18 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report @@ -510,19 +510,21 @@ tools: owner: iuc revisions: - c254d75b8b67 + - 4505d7643673 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_combine_kreports owner: iuc revisions: + - 3d2cffa2c4ab - 073c867c5244 - - 4960abe31b4d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads owner: iuc revisions: - f329328da134 + - 4bf1e2701504 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona @@ -530,11 +532,13 @@ tools: revisions: - 2deaada69b14 - 88d274322340 + - 02bbace216f2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: + - d33cf727ed94 - bb96a1e6583d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -565,22 +569,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - e073891b2afc - 0270541aaf46 - - 27250f92a01a - - 7f5d7b0e9884 - 327d9f4cc95f - - 4fd3b5d8706b - - 2cff76cf35c6 - 3cc4a60615c0 + - 7f5d7b0e9884 + - 2cff76cf35c6 + - e073891b2afc + - 27250f92a01a + - 4fd3b5d8706b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - 76bc4efa1aeb - eb50e7eca3dc - 708abf08a626 - - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -653,26 +657,26 @@ tools: - name: metaphlan owner: iuc revisions: - - 1a037928504c - - ec368db926f4 - - ff8f55893e7d - - 2131d7dca455 - - fd69c607b43f - - b89b0765695d - - ef65b083bd0c + - 740fd2d16a28 - 289b3807e80c - - 1a6cdf55390f - 6dee4abadccb - - a16313517e55 - - 740fd2d16a28 + - 1a037928504c - a92a632c4d9b + - 1a6cdf55390f + - a16313517e55 + - b89b0765695d + - fd69c607b43f + - 2131d7dca455 + - ff8f55893e7d + - ec368db926f4 + - ef65b083bd0c 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 @@ -696,29 +700,29 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 2f47a294ef49 - 6034c3f3ecf0 + - 2f47a294ef49 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 709adbfcf308 - 415cb5d91168 + - 709adbfcf308 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline @@ -731,15 +735,15 @@ tools: - name: picrust2_place_seqs owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions owner: iuc revisions: - - 677f3c8db525 - 881f2faa5fe7 + - 677f3c8db525 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -770,8 +774,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 2e62e32d4f33 - 65e5f9caefcc + - 2e62e32d4f33 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -789,27 +793,27 @@ tools: - name: polypolish owner: iuc revisions: - - f355085dd2aa - 915637bd1d1a + - f355085dd2aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 4b9a8031ab74 + - be818ae858e4 - 2fd4d4c9c5c2 + - aeaa20b96ef2 + - 3b22de20bd4b - 141afacabcfa - - be818ae858e4 - 4d83eccf5f81 - - 3b22de20bd4b - - aeaa20b96ef2 + - 4b9a8031ab74 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 f3b33a02e..8869ba2d6 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: - - bdb4a58a2025 - 12e856482d26 + - bdb4a58a2025 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 14940925c..7cb3d6291 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: + - 9422c5a87ee2 + - 8b67dd48fec1 + - 9baa871cb1d1 - 6ae5a7b5a0a2 - - a74dbfee5a86 - - 48c13389050d - - 80f03df2e2ce - - 94b8c6013083 - 2263989660f5 - - 9422c5a87ee2 - 098506c54016 - - 9eeb13a92d79 - cd07731e4434 - - 8b67dd48fec1 - - 9baa871cb1d1 + - 80f03df2e2ce + - 9eeb13a92d79 - bdfbaf0c10aa + - 48c13389050d + - 94b8c6013083 + - a74dbfee5a86 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 4a60927aaca5 - - c18157c68134 - - 2e093badc689 - - d390fe1567dc - 3ff17bad4006 - '764845535798' - - f14193ec1f50 + - c18157c68134 + - fc2e49f91e52 + - 4a60927aaca5 + - 5abf2c2249aa - be78f13134e2 - - bc3831dd65c1 - - f0af8936ed41 + - f14193ec1f50 + - 2e093badc689 - d7ce0ec78e51 - - 5abf2c2249aa + - bc3831dd65c1 + - d390fe1567dc - aaa0d6a8b808 + - f0af8936ed41 - c44f824c051a - - fc2e49f91e52 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -67,61 +67,61 @@ tools: - name: mafft owner: rnateam revisions: - - bf28a8cff401 + - f0d493f8f84f - a65296ffb4a0 - 15974dd17515 - - 6f28e90db932 - 8e649f27aa0d - - f0d493f8f84f - - c5908940967d + - bf28a8cff401 - f1a5908ea2cb + - c5908940967d + - 6f28e90db932 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - e8fdceffea4c - b3acbb3a6af0 + - fbca557a4847 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: - 48823c9635a4 - - 57f042937ba7 - bcd65de9725b + - 57f042937ba7 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - fb43e8887350 - - 4fc0cb2ac8ae - ebe3b0f84de9 + - 4fc0cb2ac8ae + - fb43e8887350 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 636b049e6141 - 7cd7a55a678d + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - 959c1f8dae95 - cf3c9489c088 + - b4124df98b26 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 c28def525..d9cfc60de 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -9,9 +9,9 @@ tools: owner: galaxy-australia revisions: - 9aa9d92c3c51 + - 18a8d140ec6f - 28928576e1ea - 7c47b3c9e493 - - 18a8d140ec6f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -24,28 +24,28 @@ tools: owner: galaxy-australia revisions: - 6942f170cc43 + - 63d8ecfcfab1 - fc5b6491cf78 - 99c9427219d3 - - 63d8ecfcfab1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - - 79e9a869f40e - - 72b5e9dda577 - - a7228a7ea146 - fc8804320156 + - 72b5e9dda577 - 0e9e7fcdd543 + - 79e9a869f40e + - a7228a7ea146 + - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - d6cddc06aeae - - 18505fe2bdb1 - fa11aa8103b2 + - 18505fe2bdb1 - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -58,15 +58,15 @@ tools: - name: medaka_variant owner: iuc revisions: + - 0f5f4a208660 + - 43815fa60f3a - cc36773a3681 - - ec699520444c + - 19f3b583a9b3 - 222669c4afb6 - - 0f5f4a208660 - eb746fa6f514 + - ec699520444c - 2bf63b38ee9b - edf6d4003fad - - 43815fa60f3a - - 19f3b583a9b3 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -85,60 +85,60 @@ tools: - name: nanoplot owner: iuc revisions: - - 645159bcee2d - edbb6c5028f5 - - a38bdcec9e4c - - 0f1c34698076 - a3c4fe6f49ab - 7b379e98b9a9 - a02b8b3f5a0c + - 0f1c34698076 + - a38bdcec9e4c + - 645159bcee2d 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: - - be95355fef8d - a8d4be409446 - 90a922f32523 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - - 4857d5bcce52 - 449e9aeded2d + - 4857d5bcce52 + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - - a3afc5f0a96c - de5b3d8f5b90 + - a3afc5f0a96c + - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 5f76b20953e5 - 93d623d9979c - 543cbeef3949 + - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - daf8518d243a + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -176,15 +176,15 @@ tools: - 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: - - 26e6c9362b7b - ce8af9373061 + - 26e6c9362b7b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index cb135e3df..248a14891 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -30,16 +30,16 @@ tools: - d74850cf4e42 - 3e73c97f025d - 97b1b5ad1cda - - baceff842902 - adfd6bf710bd + - baceff842902 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 + - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -51,20 +51,20 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - e9ee4d074d5d + - 2f27f3b86827 - 19b6a2f0dbe2 - ed1518ce2237 - - 2f27f3b86827 - - 1e34d2e3d285 - 13851aefa67a + - 1e34d2e3d285 + - e9ee4d074d5d - e4b4837f06f5 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 9e993022c762 - 46066df8813d + - 9e993022c762 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -83,9 +83,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 38ccd4589990 - 5711fc06a63e - 48a42ca61006 - - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -105,8 +105,8 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -125,17 +125,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: + - 27a6a256cd23 - 52b6a4d98009 - - 172815da3d41 - b4b2b284230a - - 27a6a256cd23 + - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -147,8 +147,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d210e1f185bd - d74c740bdb25 + - d210e1f185bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -160,23 +160,23 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - fea85c467896 - 87febc68b45b + - fea85c467896 - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 7776cb18fdf8 - 0df47f8552f6 + - 7776cb18fdf8 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 4c7ebbad42cf - 15c2fc266540 + - 4c7ebbad42cf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -194,19 +194,19 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 5fe20c915fa6 - d8dc037e3c13 - 4ba60cb14cb0 - - 2c61c30a57e7 - - 0cb27ea69dc1 - 9c43baa60906 + - 0cb27ea69dc1 + - 2c61c30a57e7 + - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite @@ -220,10 +220,10 @@ tools: - name: data_manager_pangolearn owner: iuc revisions: + - df30a2f1db55 + - ed7a967cb11b - 29c738066906 - 6e24e79d3d69 - - ed7a967cb11b - - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -241,9 +241,9 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - 1865e693d8b2 - ad90c2da4f38 - 3e4d45aca422 + - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -263,16 +263,16 @@ tools: owner: iuc revisions: - 64deddb6a8ec - - d63c1442407f - c520a52b5174 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 9946bc39c834 - - 94a50db37d1a - 625fd9476402 + - 94a50db37d1a + - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -326,8 +326,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 @@ -783,8 +783,8 @@ 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: rsem_datatypes @@ -796,11 +796,11 @@ tools: - name: salsa owner: iuc revisions: + - 58a870ef434c - 9a22227bb6d0 - - ab5b7f6b7198 - ba7b0f11e470 - f77f7a7f3b83 - - 58a870ef434c + - ab5b7f6b7198 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 09e37cbee..7a596d2fd 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,65 +33,65 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 8834daeb9892 - 107d3ba7024a + - 5a7c56a5cc08 + - 6a457678efcb - c78f3d7dd1db + - 26de3a7b1cb9 - 3f59ebfbfe3d - - 3b8b5bde0bd9 - - 6a457678efcb - - 81e66674859e - - 5a7c56a5cc08 - - cce7b18495e4 - d7c7ef3353fe - - a6619171428e - f04a1264e2a2 - f73435dc282b - - 26de3a7b1cb9 + - 8834daeb9892 - b89cac5156ec + - cce7b18495e4 + - 81e66674859e + - a6619171428e - '841557158611' - d033ffc1c161 + - 3b8b5bde0bd9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 6223845127ea - - 5b777002c2de - - df47d4845b62 - - b0af57c1a968 - - 4755f52427c4 + - 3b96e92e8ec3 - 7a2092844346 - - 88c4aa435ded + - 4755f52427c4 + - aa8cc71438cf + - 5b777002c2de + - 659517798cc4 + - 6283babe736e - e75442c7f4da - 02b8758214b0 - - 659517798cc4 + - df47d4845b62 + - 6223845127ea + - 5fcd1ece3a6e + - 88c4aa435ded - a185b079b095 - - 3b96e92e8ec3 - 6a726db04d4b - - 6283babe736e - - aa8cc71438cf - - 5fcd1ece3a6e + - b0af57c1a968 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 70acec670c30 - - 111bd54f6bc4 - - c1d53e95327f + - f97743d52b87 - f87ac61981f0 + - c1d53e95327f + - 24d024316465 - b8476e82ac20 + - 111bd54f6bc4 + - 70acec670c30 - d1c340a5664b - - 24d024316465 - - f97743d52b87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: + - feb40665d7cd - 9e10ba792be2 - 4f6349228462 - - feb40665d7cd - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -104,33 +104,33 @@ tools: - name: pangolin owner: iuc revisions: - - b6abccb1f25b - - 42a174224817 - - a2099fb98cdb - - 81804a978fc0 - - 9d61d3fa046c - - 437e28791761 - 2fa9d4f1b48f - - 5f8727ff21e7 - - 36912871ccdc - - 03ed9524dcd1 - abf6dbe8c9d7 - 3a43c3982401 - - b7e297c2ede6 + - 437e28791761 + - 81804a978fc0 + - 36912871ccdc - 2f1019071464 + - 7bb8726be37c - ca0d8cf80567 - - ca337cce3888 - 14ae456b8cc5 - - 8ad84c5753ea + - 42a174224817 + - b7e297c2ede6 + - 9d61d3fa046c + - a2099fb98cdb + - ca337cce3888 - 83a69484cb87 - - 7bb8726be37c + - b6abccb1f25b + - 8ad84c5753ea + - 5f8727ff21e7 + - 03ed9524dcd1 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 2bf47d57ebb5 - 7157a5b34a68 + - 2bf47d57ebb5 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -143,22 +143,22 @@ tools: owner: iuc revisions: - b1e68bbe4cef - - ea30d3089354 - - ba29b5e2a4be - - 73a469f7dc96 - a4b71be30c3c + - 73a469f7dc96 + - ea30d3089354 - 29ff6a849eac + - ba29b5e2a4be tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - dbe2b2204555 - - 809e42326fc2 - 91887494eb97 - - e88a7de55d6e + - 9b2b122d0415 + - 809e42326fc2 - f1ccc8a6eb05 + - dbe2b2204555 + - e88a7de55d6e - 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 f65c5a041..1483f4cec 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - fc288950c3b7 - - 7d34178f2812 + - 1aac2a13842a - f6ced08779c4 - - 3f254c5ced1d - - b502c227b5e6 + - fc288950c3b7 - 881d7645d1bf + - 3f254c5ced1d - a1f0b3f4b781 - - 1aac2a13842a + - b502c227b5e6 + - 7d34178f2812 - 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 09f26f36b..5714dac72 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,18 +2,18 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - 5b85006245f3 - - d00e15139065 - - 3f188450ca4f - 2f7702fd0a4c + - d00e15139065 + - e7f1b552a695 - 7fbec959cf2b + - 5b85006245f3 + - 3f188450ca4f - c0e71cb2bd1b + - eb085b3dbaf8 - e4a053d67e24 - ca90d17ff51b + - 3bd420ec162d - 6ab1a261520a - a58f7eb0df2c - - 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 219438464..96f93c12a 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,32 +2,32 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - ece627528a78 + - b18329a8ac14 - b574b84afc4d - f28ad96b76dc - 277dc652246e - 0a18ac48ac53 + - ece627528a78 - 4c177985028a - - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - 525f201b86c1 - b41107d8fe89 - - bf06d196e23d - a9a28e46d54a - e988563cc6e5 - e215f71d7983 + - bf06d196e23d + - 525f201b86c1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 - 56da27be956a - bb6397b94018 + - 8da3511c9467 - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -35,9 +35,9 @@ tools: owner: galaxyp revisions: - b8c79e70516d + - 528fb09022be - a8157342d9a3 - 890845926d4b - - 528fb09022be - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -46,50 +46,50 @@ tools: revisions: - a69865da6f80 - 80600735685d + - 59e85306eae5 - 25b83cbd596a - ae304a72db7b - a95a82eb4d50 - - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 798da6bdff3d - - 83aac7741200 - - ed9ed1e6cca2 - - f1897eb07081 - - e0669b1854b1 - 611d80c0e29d + - e0669b1854b1 + - f1897eb07081 + - ed9ed1e6cca2 + - 83aac7741200 + - 798da6bdff3d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - d426a9107a6c - a7fb9b395ddf - 74b61bf5bc4b + - d426a9107a6c - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - df2187f9013b - - cc430977c8ff - 82f6c2f4332d + - cc430977c8ff + - df2187f9013b - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: + - 10566783d718 + - ba92b59cd529 - 1693b2126f30 + - d2483487e077 - c5aa9fca18c6 - 043f9c91f686 - - ba92b59cd529 - - d2483487e077 - - 10566783d718 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -108,9 +108,9 @@ tools: owner: galaxyp revisions: - bf0728e000cd - - ae4dc0c041f9 - 9fa3dbf06f17 - ff8c9e0e8a7b + - ae4dc0c041f9 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: + - d263296cd73e - eac99effe86f - d0ea7589e95f - - d263296cd73e 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 @@ -160,8 +160,8 @@ tools: owner: galaxyp revisions: - d286ff4600dd - - e66f552a3c47 - 160538a890a6 + - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -174,23 +174,23 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 3fc2116ac6d9 - 9cb7dcc07dae + - 3fc2116ac6d9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 9c52362ae7bb - - 837224ad1694 - 4d17fcdeb8ff + - 9c52362ae7bb - 2133b0be850a - - 97a7f34fcb6a - 1f39c833f65f - 7f432d87c82c - - 37d669de2828 - - e42225f8a659 - f522c08e900c + - e42225f8a659 + - 97a7f34fcb6a + - 37d669de2828 + - 837224ad1694 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,55 +202,55 @@ tools: - name: metaquantome_db owner: galaxyp revisions: + - e63db1aa82ee - 85b8866f06d7 - a72ac2c7cc5b - - e63db1aa82ee - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: + - 1974224d63c2 - 352b37c66d97 - 767c1d761aaf - - 1974224d63c2 - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: + - deaf035bbe9f + - 4f359549383c - 35cc7ca0bdc7 - 99450519d727 - - 4f359549383c - - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - 06f6826d380c + - c1343e3389ca - c7745841de24 - e79958768a2c - - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 - - d46d64e7964d - da986f83631b - b9d453dca8d3 + - d2eac53666f0 + - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 1199751329b0 - 9bf325045235 - - 944b43462104 - 8bd7734309f6 + - 1199751329b0 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -263,50 +263,50 @@ tools: - name: msconvert owner: galaxyp revisions: - - ab6c14374bc0 - 6153e8ada1ee + - ab6c14374bc0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats owner: galaxyp revisions: + - 28434abe6c5c - 593839e1f2c3 - de7593c29499 - - 28434abe6c5c - 8212e342e482 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - bd1535813cfe - a5e394b36d87 + - bd1535813cfe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: + - f4be248c3d47 - 01dbaf6a57e0 - 8960fb791701 - 4e77b8f12cd3 - - f4be248c3d47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 06cca574e337 - 25529df60a81 - 370141bc0da3 + - 06cca574e337 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 6ccbf9a2072c - - c9eff69a7c62 - 9cdf15d3cfc8 + - c9eff69a7c62 - f7fef900f5b2 + - 6ccbf9a2072c - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -314,16 +314,16 @@ tools: owner: galaxyp revisions: - ca88bd28f116 - - 9876bda3ec53 - dff6c756eee5 - 5e948629bc73 + - 9876bda3ec53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 658494a2cb00 - 890025d6e426 + - 658494a2cb00 - 41859bbdc16e - 1595601708ec tool_panel_section_label: Proteomics @@ -331,128 +331,128 @@ tools: - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 + - 9b7977080f6d - 5ad0b5bf1deb - 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toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a - 5d9f175dff81 - 111c3a00136d - 986e03d3201e + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 4204882495f2 - be74a8cd7d66 - - 0e52c85f3b15 - 476b5e296979 + - 0e52c85f3b15 + - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - f5ec766d80cf - - a407b6790342 - 2b2a7551a857 - c18d8efa4474 + - a407b6790342 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: + - 021fdb80f204 - 4e66c4e73909 - d0304fb829c0 - - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - 8098330f6d91 - ee860980edc6 - - bf32e0bcf554 - 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toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - 89254095cbf6 - - 8b814eafce2c - 4bb198c0bd3e + - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - f9ed7e074900 + - 05ec9fb05ed1 - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - d31426ef20f6 - 6e8cc5ed2a9b - 18826fb8e5db + - d31426ef20f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -530,36 +530,36 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - 3d8d4ada5405 - - decc397c3b7e - - 6b01678ec2fc - 5ae104d0da6e + - 6b01678ec2fc + - decc397c3b7e + - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - 539a3a4dcc9e - e039cc5c7aed - - d6aca689dd48 - - dd173849c3d8 - 5182338d5e7c + - dd173849c3d8 + - d6aca689dd48 + - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - - 8a45fd5a608a - d426affe977c + - 8a45fd5a608a + - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 9c70a651a53e - - 43b9ed22e8ce - dd71e020e2aa + - 43b9ed22e8ce + - 9c70a651a53e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter @@ -573,25 +573,25 @@ tools: - name: openms_xmlvalidator owner: galaxyp revisions: + - 78c080d36945 - ad2ba3a95a02 - f036e8cf1a55 - - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: + - fb52e95a370c - c8b225c69a7f - 5c2a97a234d6 - 7f6a1f27553e - - fb52e95a370c 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 @@ -611,13 +611,13 @@ tools: owner: galaxyp revisions: - 3634c90301af - - 1beff3ddce58 - - a72c48001f7c + - 3ec27b4cee7c - da885ca16cb2 + - 1beff3ddce58 - 943a34df6047 - - 7fdd9119cc4f + - a72c48001f7c - 07ff622ec007 - - 3ec27b4cee7c + - 7fdd9119cc4f 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: - - 1a5690a5eedc - 12692567c7f9 - - a371252a2cf6 + - 1a5690a5eedc - 265c35540faa + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.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/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index ba1413ffa..18a3837d6 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,109 +2,109 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 110a346daf36 - - 2f1d464ebfd2 - - cd5f98911089 + - e345aadf914f - 42201b90e3f4 - 289b7d6b69a4 - - e345aadf914f + - 2f1d464ebfd2 + - 110a346daf36 + - cd5f98911089 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b - - 42d9087b4789 - - 8501601a118d - - 0cd2df8af811 - fcce77c09289 - c207119ba5f6 + - 8501601a118d + - 0cd2df8af811 + - 0345dbaaa79b + - 42d9087b4789 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - 89eb29319bf4 + - 04db7fd6b238 - 421c33b8bf17 - 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 - - 1d839ead7ad3 - fa51dc5e8386 - - 7b72fde3d27e + - 1d839ead7ad3 + - eb784fa07f80 - 7370bb65bad4 + - 7b72fde3d27e - f6e91108b7b1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - c9b77ced9a78 - 1544278c272e - - 8a55d29c8fcf - a3e86cd9cac7 - 3d70c2996730 + - 8a55d29c8fcf - d30e36c48c93 + - c9b77ced9a78 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - a5969aa9347e - e2db212d64ad - - 7b881f5f5ad5 - 887cf585cafc - - b242deb58952 + - a5969aa9347e - 564c33e5c3e3 + - 7b881f5f5ad5 + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - bd5ff77e2036 + - 9a171f9a450b - b4bab607eb05 - - e897c74a48bb + - bd5ff77e2036 - 8cff84759bf6 - - 9a171f9a450b + - e897c74a48bb 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 + - 6dafad990086 + - 5e10f396979e + - 887e0991eb24 - adc7a7610d4f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - c287418eb288 + - 43e3eeb2e0ec + - 97575d01f06b - c5d7050e4ad7 - 4e280b27a831 + - c287418eb288 - 17d39bf0a63a - - 97575d01f06b - - 43e3eeb2e0ec tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: + - 0b8c84a7fdb5 - a819ec3b362d + - 9586f08634c0 - d9bf483266a1 - - 0b8c84a7fdb5 - cd034465d4a4 - - 9586f08634c0 - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -112,22 +112,22 @@ tools: owner: iuc revisions: - 95351dd0fd3f - - bf0e43ab0416 - - 2645575d1bf2 - - 69842dd5aa48 - a4b4bd84f69e - a9c34a289493 + - bf0e43ab0416 + - 69842dd5aa48 + - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - 8a35a3bc6752 - - d033e1ccb386 - - cfb504394ae1 - - 912f904a6e1e - d1fda11e602f + - cfb504394ae1 - bb0475c884ff + - 912f904a6e1e + - d033e1ccb386 + - 8a35a3bc6752 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: - - d504d945a655 - 95286af4139b - d1fad35bdb4a + - d504d945a655 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: - - 563af4497055 - 96de7538bf0c + - 563af4497055 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 dcbaea176..25c5bd71a 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,27 +2,27 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - 2d4e3aff9dc7 - 31f8063eedea - - 7acb00fc980a - cf01dd6c6b1f - - 2d4e3aff9dc7 + - 7acb00fc980a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - - 7a5a2d28c539 - 125d20cb23d7 + - 703a2cb3fb38 - 32e542c2a773 + - 7a5a2d28c539 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - - 45c2ec061cf9 - 01ccd366690d + - 45c2ec061cf9 + - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -89,35 +89,35 @@ 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: cufflinks owner: devteam revisions: - - d080005cffe1 - 6926716bbfb5 - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - 6a6717a5f421 - - 04adc9db1581 - 86285ddd4512 - - 22cf48ad7b16 - cf747d1bd79a + - 6a6717a5f421 + - 22cf48ad7b16 + - 04adc9db1581 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 28b94cfbfdb9 - 6cbfede05833 - 9a854107dbb2 + - 28b94cfbfdb9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -142,49 +142,49 @@ tools: - name: describe_samples owner: iuc revisions: - - 3b36efd62b3e - 0693ccd171c4 - 8f0181aacb7a - e3b16fd7dd08 + - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: + - 9a882d108833 + - 0696db066a5b + - 6a3a025714d3 - d027d1f4984e - - cd9874cb9019 - 8fe98f7094de - - 6a3a025714d3 - - 0696db066a5b - 24a09ca67621 - - 9a882d108833 + - cd9874cb9019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 9a7c5b6d8f1e - 2872c633f07e - - df929f257179 + - 9a7c5b6d8f1e - 62adf13b86ea + - df929f257179 - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 9bdff28ae1b1 - - 3d89af8a44f0 + - 6e53e565fc6a + - 5bf899c13979 - 0cb907a2a810 + - 555659de7321 - a8305cf0c951 - - f2843df56434 - - 5bf899c13979 - 334ce9b1bac5 - - df0c8d0a5992 - - 070900306913 - - 555659de7321 - ae2aad0a6d50 - - 6e53e565fc6a + - 070900306913 + - f2843df56434 + - 9bdff28ae1b1 + - df0c8d0a5992 + - 3d89af8a44f0 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: - - af814359d244 - 90d16db017d7 - - 6f66ae7c5f7a - - a56fbe2d6ba7 - - 1b851f87fbe0 - - 7db9d3ea71c9 - f9d49f5cb597 - - f3a5f075498f + - a56fbe2d6ba7 - 38b6d12edc68 + - 1b851f87fbe0 + - 6f66ae7c5f7a - ea04b737afa0 - - e6a2a912677a + - f3a5f075498f - a37612abf7f9 + - af814359d244 + - e6a2a912677a + - 7db9d3ea71c9 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: - - 0f710191a66d - - 3c97c841a443 - 3c5e024a18cf + - 3c97c841a443 + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -252,20 +252,20 @@ tools: - name: hisat2 owner: iuc revisions: - - f4af63aaf57a - - 6ab42baa56e9 - - a86e80d3c09c + - 26371a1df031 - d4b55e2beb12 - 3fb01a8c902d - 6c19daec423d - - 26371a1df031 + - f4af63aaf57a + - a86e80d3c09c + - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - 4418229c501e + - 916cb26bd9d3 - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -278,33 +278,33 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 1c75aa5de15e - 87c11c05d238 - - 5ae5c312d718 - 01247aaf0a10 - ce5d418183c5 + - 5ae5c312d718 + - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 10c98fab6c5a - - 40985510cd98 - c971db6f0fe5 + - 10c98fab6c5a - 4f9c4e6566e5 + - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 0921444c832d - - 97e06a4c7c75 - - 32511f586472 - 119b069fc845 - - 58c35179ebf0 + - 708348a17fa1 + - 0921444c832d - d6f5fa4ee473 - e827f9aae031 - - 708348a17fa1 + - 32511f586472 + - 97e06a4c7c75 + - 58c35179ebf0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -360,21 +360,21 @@ tools: - name: rgrnastar owner: iuc revisions: + - 4074fc1940e2 - b0f2be869d6d - - 4df95e2d7f61 - - c7c55b694974 - - 4014de1b6daf - - e132e7d02a3e + - 980d2a2e1180 + - b9e04854e2bb - 3ea5a2a63fa2 - - 79de45b5069b - - 5ec75f5dae3c - - 4074fc1940e2 - c772497b2c32 - - b9e04854e2bb - - 0a563fd2f22e - - 980d2a2e1180 - - 7ed2edc1337f + - e132e7d02a3e + - 5ec75f5dae3c + - 4df95e2d7f61 - 99b17b74a8cd + - c7c55b694974 + - 7ed2edc1337f + - 0a563fd2f22e + - 79de45b5069b + - 4014de1b6daf 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: - - cc05793bb896 + - f4d5237a84f6 - 49121db48873 - - 2c0ca397d302 - - 15cd64d7c58b - 53e9709776a0 - ebab418107f5 - e3d32471da11 - - f4d5237a84f6 + - cc05793bb896 + - 15cd64d7c58b + - 2c0ca397d302 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - 56242ff81c84 - fab6ff46e019 - c0fd285eb553 + - 56242ff81c84 - 8c28affc7c48 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cbf488da3b2c + - dd4df992d93d - 258d696dbd7e - - 76d290331481 - - ae618321f34a + - 914cfcba0ec8 + - cbf488da3b2c - cef79931dda5 + - ae618321f34a + - 76d290331481 - 1ebd14235b92 - - 914cfcba0ec8 - - dd4df992d93d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -445,63 +445,63 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 - - c6334cb383ff - ffd1300599a1 + - c6334cb383ff + - d0d4cef4f967 - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - ba3720d7e68b - d6a479fd4281 - 74217fbfba4d + - ba3720d7e68b - 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 + - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - 9ff3765e7172 - fab23c3b5258 + - 9ff3765e7172 - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 4687ecf0eb2d - 870ac06dff8e - - be3f26533209 - 34a018cbee9c + - be3f26533209 + - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 65e7dea767ea - 5192f657f305 - - c5fbddcac63a - 33406f5a445c + - c5fbddcac63a - 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: - - 6f0fb35b799c - - a35cba31d904 - 1fdb25a8384d + - a35cba31d904 + - 6f0fb35b799c - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -509,8 +509,8 @@ tools: owner: iuc revisions: - 37a1129c89d2 - - c2c039e421af - 964b7efe2639 + - c2c039e421af - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -519,17 +519,17 @@ tools: revisions: - 047c22569787 - 24e94d84adc9 - - eafea3083352 - 1d689e4e1caf + - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: + - 1812dbc5bb7b - 3a4ac03d1266 - - 04bb8bb7c198 - 9871104ea630 - - 1812dbc5bb7b + - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -547,15 +547,15 @@ tools: - name: trinity owner: iuc revisions: - - d2bc35f3d1c5 - - c9cfec002f71 + - 48636f857c4b + - 32b86cd8eb50 - 9fa24d5aac68 + - d84caa5a98ad - 8f1c3df4dd49 + - d2bc35f3d1c5 - cee61b3fcf78 - - d84caa5a98ad - - 48636f857c4b + - c9cfec002f71 - db1f362cca3e - - 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 6715dd810..ee524b79e 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: + - 080fd5739bb4 - 27e16a30667a - 1a052c827e88 - - 080fd5739bb4 - 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 e4fe1406f..11c6e49ed 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,18 +2,18 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 88eedb4abea0 - 3c661e57a88f - 10184eaa85fc + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - 1dfd95ee241e - - 108db6635177 - 993b19f20c76 - cb20f99fd45b + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -25,15 +25,15 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 75d5afa09972 - 5325e44297b9 + - 75d5afa09972 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag owner: iuc revisions: - - e9b9c489aacc - e30af4e78cd3 + - e9b9c489aacc 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: - - 30a201c9c310 - e7fd6754d093 - 5f8e69cc4c6e + - 30a201c9c310 - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - 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: sam2interval @@ -103,15 +103,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - 890d97772e2a - a3b4ad6858ff + - 890d97772e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - cf1ffd88f895 - 0e60e2dd20af + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -123,26 +123,26 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 56c31114ad4a - 649a225999a5 + - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - 46c6639921f1 - - 6856f8a01905 - 9149ad20699a + - 6856f8a01905 - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 26b4f9f98aca - - 92ec40abcdcf - 33208952b99d + - 92ec40abcdcf - 06dc50b7b711 + - 26b4f9f98aca tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,26 +160,26 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 66e23b11feae - - b906586a6596 - - 720217c23995 - b3d99709fe1a + - 720217c23995 - a8d69aee190e + - 66e23b11feae + - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate owner: iuc revisions: - - d2df79922531 - e5ece8fa99de + - d2df79922531 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: + - cc61ade70eb8 - fe34990e5ce7 - 22970df7a40e - - cc61ade70eb8 - db17d5321bad - fefd89ab563c tool_panel_section_label: SAM/BAM @@ -187,10 +187,10 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 - - 88b8c2916784 - - 7a6034296ae9 - fa5d3e61e429 + - 7a6034296ae9 + - 88b8c2916784 + - 811fc2d75ad4 - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -204,21 +204,21 @@ tools: - name: samtools_merge owner: iuc revisions: - - 65a38e8c8e2a - cae2794d2deb - - 740ce0a18f0d - - 36677f429310 - b40e2d865d52 + - 65a38e8c8e2a + - 36677f429310 + - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: + - 583abf29fc8e - 9da0311ab1dd - - 8da515fbc1bf - 329deb17a9f7 - b61f5d6a7f25 - - 583abf29fc8e + - 8da515fbc1bf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -231,10 +231,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - db000c6007a0 - - bb8cfc6f6e0c - 30388d878f81 + - db000c6007a0 - 85e38b31e8b3 + - bb8cfc6f6e0c 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 + - b8beef827165 - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - cab3f8d35989 - - d54a4df48867 - e613c1ad4c4c + - cab3f8d35989 - 6c2c1836728b + - d54a4df48867 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd - 5d9ae78f34d3 - - 135c85f4cfaf - bcedabb53ddf - bd850490c7f1 + - 135c85f4cfaf - 818030fa6bbf + - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 5a08c09b9311 - 1cc79f49b8d5 - - 24c5d43cb545 - - 3a0efe14891f - 145f6d74ff5e + - 24c5d43cb545 - 541082d03bef + - 3a0efe14891f + - 5a08c09b9311 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: + - 6be888be75f9 + - bf328cec6a42 - 5826298f6a73 - - b01db2684fa5 + - 2dce91e11ca7 - c370440f901e - - 0dbf49c414ae - 32dc5f781059 - - bf328cec6a42 - - b72793637686 - - 6be888be75f9 - - 2dce91e11ca7 - 350bbc5c2ffd + - b01db2684fa5 + - b72793637686 + - 0dbf49c414ae 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 ffca37932..32e52de63 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: + - ea5e944f447d + - d147d6455873 - 5cb6146337d8 - 4aab5ae907b6 - - 6f6537780379 - - a62c4a11a67d - - d147d6455873 - - ea5e944f447d - 480d9e9d156b + - 6f6537780379 - 59bb6d34fca6 + - a62c4a11a67d 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 55ec55afe..38e972f19 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,100 +8,100 @@ tools: - name: alevin owner: bgruening revisions: + - ecb9ea6269ee + - f2000bc73102 - e4c01dcece8b - e32b215b7c04 - - ecb9ea6269ee - b0fe3e482cb7 - - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - c0b037b12765 - 707023fa62fe - e1c3c2f2a834 - 7a6655aa6eb2 + - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: + - 00712416fdaa + - 55e35e9203cf - cfc3f5a57dc6 - - 93dd15e13e6a - fb9e030ffae4 - - 6f143dfe902a + - 93dd15e13e6a - 32e547223c9e - - 00712416fdaa - - 55e35e9203cf + - 6f143dfe902a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - b9fac48532eb - - ee98d611afc6 - 14c576ea6148 - 6f0d0c784f09 - 39e945f0b2c1 - - 038e32885fec + - b9fac48532eb - 688357ad5e61 + - ee98d611afc6 + - 038e32885fec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b - - 3d748954434b + - c4209ea387d4 + - d4af736e7b83 - b85871dd69f9 - - ed4996a16f7f + - 3d748954434b + - 9bd945a03d7b - 43cb7b5a6fe7 - - d4af736e7b83 - - c4209ea387d4 + - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - a4774b7b2e85 - - fe75d2414dc0 - 2e8022f1923c + - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - 769d815e4b0d - - 4fff5a293013 - - 0e70b2dfe4be - 02b1fe7aed76 + - 0e70b2dfe4be + - 4fff5a293013 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - a90f8efe08b4 - - 344c2af50552 - 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: - - c32347702e12 + - b13d3e4c48e1 - 5b7c81b35b89 - 050cf43887d3 - - b13d3e4c48e1 + - c32347702e12 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: + - ae969fdb8442 + - 239193b96d72 - 02fc39c8610d - 1d77986f9ddc - - 239193b96d72 - - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -138,9 +138,9 @@ tools: owner: iuc revisions: - cfe1e6c28d95 - - 8855361fcfc5 - - cdf4443d5625 - a9caad671439 + - cdf4443d5625 + - 8855361fcfc5 - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,137 +171,137 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 952abbc4b1de - - fb7068d30ec9 - 01c37e54e86e + - fb7068d30ec9 + - 952abbc4b1de tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 57aeaf6b237d - 9d42a6133690 - f1c35f3f310d + - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: + - 23b8d6b8960c - 163fd744e235 - cab616fe7e64 - - 23b8d6b8960c 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: - a63e9713c39d - - b892fa1fcaec - 9ea228a9afc8 + - b892fa1fcaec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 45a386d18509 - - 640e0e45518a - f8320df1866b + - 640e0e45518a + - 45a386d18509 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 - 40fee49bc6c3 + - f881c94fb3b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - e06265d204f6 - - 2dccb6bb0add - 782bdcb775fb + - 2dccb6bb0add 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: + - 8a11d70b6cd8 - fe3aa71590d5 - c72fa6cb8817 - - 8a11d70b6cd8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - e03780179ee5 - 4f9305d3bb34 - 3ee5332bf57c + - e03780179ee5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - - 3a6a5381db36 - a315574104c6 + - 3a6a5381db36 + - 4401ed529d2c 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 owner: bgruening revisions: - - 30d7390bc918 - - ea19190ce5e0 - 62b720dceb56 + - ea19190ce5e0 + - 30d7390bc918 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - cd40ca76865a - - 2b4d6a8dab36 - 2786a931cad2 + - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - 0410b6aada45 - - bf9379529c3e - ffc33339cd3e + - bf9379529c3e + - 0410b6aada45 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad @@ -315,16 +315,16 @@ tools: - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 6c5097f6d41e - - 972dcccb5bbc - f1b3902f8baf + - 972dcccb5bbc + - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - bb8849fca57c - 409396ea5cf0 + - bb8849fca57c - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -332,32 +332,32 @@ tools: owner: bgruening revisions: - e4f8fceab96a - - 51e40e9b6c3c - b0f33533181d + - 51e40e9b6c3c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: + - 55b013e59018 - c261b6b05ee3 - 32173084d53f - - 55b013e59018 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - b6b8c8672756 - - b376ef118807 - 4b194e675916 + - b376ef118807 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - 910c6a1c3a27 - - ed900cd4a0a9 - 1511a8ebe906 + - ed900cd4a0a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize @@ -379,24 +379,24 @@ tools: - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: + - 11f39d7f6c64 - 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 + - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - - e285920f8585 - 58de3c7c8e89 + - e285920f8585 - 8d203e74869b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -404,16 +404,16 @@ tools: owner: bgruening revisions: - 21d859ad4502 - - ea8fb5e899e8 - 5cbd7a902a8d + - ea8fb5e899e8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - f81750434d70 - - 36dfa2825a59 - 1d6af10874d5 + - 36dfa2825a59 + - f81750434d70 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -432,27 +432,27 @@ tools: owner: bgruening revisions: - 1de2276f633f - - f36828ebdc54 - 27fe5cd1729c + - f36828ebdc54 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 1d201e8378b3 - - cef9fb4ece1c - 11a3385e03b5 + - cef9fb4ece1c + - 1d201e8378b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: + - 7784821452ac - db575b4c8b22 - - e98619de2776 - eeab712b0b99 - - 4b0adaa31c95 - - 7784821452ac - 59be31ac9dc3 + - e98619de2776 + - 4b0adaa31c95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -464,16 +464,16 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 2cfd0db49bbc - 48f0fb3061b1 + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 8cd2ecfa2e61 - 56371b5a2da9 + - 8cd2ecfa2e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -498,46 +498,46 @@ tools: - name: raceid_clustering owner: iuc revisions: - - a4b734cd253b - 49776718ae90 - - c4f39bf4a068 - 7e014059a88d + - c4f39bf4a068 - f911a64454fb + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: + - 8b917923f7d4 - 43c146e25a43 - 7608d5faee41 - d45f092caf24 - - 8b917923f7d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: - c7ddb719554d - - 2b0d3e2f402a - 37a47c4fd84d + - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory owner: iuc revisions: - - 6e90c8adf84f - df8e4e54d367 + - 6e90c8adf84f - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 - 44b935f2271b - e93b008c637a - - 2bfd55b87af3 - 72979cac22b2 + - 2bfd55b87af3 + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -555,111 +555,111 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 77b91b9bdf52 - 4d8f983cd751 - - aaa5da8e73a9 + - cb43c5d3acd3 - 8983e7a04ba7 + - aaa5da8e73a9 + - 77b91b9bdf52 + - 38db3fef7aad - 6f83f8fd381f - 6acb08931836 - - cb43c5d3acd3 - b2df381a6004 - - 38db3fef7aad - f9353ee6a0d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - d636ce5cde16 + - 3c86f71498bc + - a97abb8cd15b + - fc0321c000a3 - 64388be6d510 - 72a6bebab2a5 - - b409c2486353 - - 8cb783c81905 - - a97abb8cd15b - - a03ff8633507 - - 3c86f71498bc - 277313130da5 - - fc0321c000a3 + - a03ff8633507 + - d636ce5cde16 + - 8cb783c81905 + - b409c2486353 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: + - c0a80a16560f + - d86cb2ce311b - f54f0f0598ad + - 5c3ebe2adc77 - 6c145a6868cc - - 18262103fa61 - - c5d3684f7c4c - 3081ff5c84a3 - - 5e9171dc8244 + - c5d3684f7c4c + - 18262103fa61 - 6bd82ed14acd - - c0a80a16560f - - 5c3ebe2adc77 - - d86cb2ce311b + - 5e9171dc8244 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 56c0d4acef02 - - d844935c906c - - ab55fe8030b6 - - 7b9fafe32c86 + - 4bda4412b8c2 - a407e7f8bdc1 + - 9f354c7c8c92 + - c9cb76cf8d6c - 146ae5d70b47 + - d844935c906c + - 7b9fafe32c86 - 94c19fb1281c + - ab55fe8030b6 - 3bcd5445cd7a - - c9cb76cf8d6c - - 4bda4412b8c2 - - 9f354c7c8c92 + - 56c0d4acef02 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: + - 40812a65a78b + - f7446fd8d5e7 + - 95777145cb92 - 0185bd174ea0 - - 1072ce66b426 - 9b0cdb8cf6be - 62acdd96d4a0 - - 40812a65a78b - - 95777145cb92 - - 6adf98e782f3 - 7647e5cd1b8b - - f7446fd8d5e7 - - dbbe1ea8ecb1 - - 6f5349dd5c49 + - 6adf98e782f3 - aa0c474463c2 + - 1072ce66b426 + - 6f5349dd5c49 + - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: + - c65fce500915 - c5541bfb8feb + - fe8f16c594ec - 9fb627495ec2 - - bf2017df9837 - - 215733a383f2 + - 458e8f43a775 - f2f6c703da06 - - c65fce500915 - - fe8f16c594ec - d18e7a6e5cd4 - - 458e8f43a775 - a39040ae0a38 - 73ab2ac53d06 + - bf2017df9837 + - 215733a383f2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: + - 8f333f90d8d6 - fd808de478b1 - b834074a9aff - - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: + - b7ea9f09c02f - 7a365ec81b52 - 652923ce664f - - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -671,9 +671,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - ef4c80837bc5 - 81e5bdff4853 - 2e41b35b5bdd + - ef4c80837bc5 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: - - 46fc6751d746 - - c99ba278dfa9 - 9e5c0bb18d08 + - c99ba278dfa9 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -916,8 +916,8 @@ tools: - name: sinto_fragments owner: iuc revisions: - - 6f66f523a9b7 - 29e6bfb2cf49 + - 6f66f523a9b7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image @@ -936,22 +936,22 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 64fa083411f1 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - fecf9664c885 - 05bd4db20227 + - fecf9664c885 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - c5c94e01a1b5 + - cec3e76eaf05 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 feeadf51d..18c1d1305 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,11 +32,11 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 - - 746e8e4bf929 - - 419027d822d6 - 4c07ddedc198 - 562f3c677828 + - 419027d822d6 + - 2f3c6f2dcf39 + - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,8 +49,8 @@ tools: - 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 @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - cb1c59d69557 - 6c29c7e347e8 - 7a15159140d1 + - cb1c59d69557 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: - - 9c3e1d3235c8 - - 840f29aad145 - - aef56d0e7a61 + - b1eda492f063 - 4c4ec859c31a + - 840f29aad145 - 7442b94d6a1e - - b1eda492f063 + - 9c3e1d3235c8 + - aef56d0e7a61 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 375bbd555f4a - 30d21a6041f6 - - 07843f917990 - - 9fda0b82f419 - d0352e8b4c10 + - 9fda0b82f419 + - 375bbd555f4a + - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - 8b1b2b91f8d0 - 7ae443e6217d - 4cc980df6265 - - 8b1b2b91f8d0 - - 2c58b83c9bad - cd02bf168d23 + - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - 4bbaf77573ef - - ad7e0b4291ee - - 7dd3fb35904f - 1dd433d2c92c - bb9fc9d46ea4 + - ad7e0b4291ee - e10e776f2109 + - 7dd3fb35904f 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 1a3aaf4b2..f5da5abf5 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -27,21 +27,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - f18f67056946 - 6c6d26ff01ff + - f18f67056946 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 6595517c2dd8 - - 02026300aa45 - - 9cd341095afd - - aff5135563c6 + - 464b9305180e - 6e8d94597139 - be25c075ed54 + - 9cd341095afd - 13b6f0007d9e - - 464b9305180e + - 6595517c2dd8 + - 02026300aa45 + - aff5135563c6 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: + - 34d29339abab + - 557ec8d7087d - 9cc411a62277 - 37cde8134c6a - - 34d29339abab - 90f657745fea - - 557ec8d7087d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -113,14 +113,14 @@ tools: - name: query_tabular owner: iuc revisions: - - 83069b38aa85 + - 623f3eb7aa48 - cf4397560712 - - 2e8f945f7285 - - 3a6b78c39dca - - 1ea4e668bf73 - 33d61c89fb8d + - 1ea4e668bf73 + - 2e8f945f7285 + - 83069b38aa85 - cf34c344508d - - 623f3eb7aa48 + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace @@ -142,28 +142,28 @@ tools: revisions: - f768f6183386 - bce29ec10b78 - - c4d18aa4ec4a - b722161a845a + - c4d18aa4ec4a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 3bf5661c0280 - 60ff16842fcd + - 3bf5661c0280 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: + - f46f0e4f75c4 - 9ff72e942410 + - 74a8bef53a00 - 86755160afbf - - fbf99087e067 + - d698c222f354 - 12615d397df7 - ddf54b12c295 - - f46f0e4f75c4 - - 74a8bef53a00 + - fbf99087e067 - a6f147a050a2 - - 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 403f24a31..01033f076 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -28,27 +28,27 @@ tools: - name: cutesv owner: iuc revisions: - - c0f8fe52948e - - 23d7e75d850e - cb441f258c37 + - 23d7e75d850e + - c0f8fe52948e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: - 04fa42777df9 + - 156b60c1530f + - 3e954e7125bf - 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: - - 791f73caa0c8 - 435b157bed6d + - 791f73caa0c8 - e61c9ac190ad - 09d6e4693887 tool_panel_section_label: Variant Calling @@ -56,12 +56,12 @@ tools: - name: lofreq_call owner: iuc revisions: - - 03627f24605f - - dfadc322b065 - - 4805fe3d8fda - 3b4b2121842f - 65432c3abf6c - 074d44697036 + - dfadc322b065 + - 03627f24605f + - 4805fe3d8fda - e1461b5c52a0 - b11e8e9c23bf tool_panel_section_label: Variant Calling @@ -69,9 +69,9 @@ tools: - name: lofreq_filter owner: iuc revisions: - - 7dfca164d2e3 - - 9cb929f21cfa - 701d134358ad + - 9cb929f21cfa + - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual @@ -79,8 +79,8 @@ tools: revisions: - f4473557ffc7 - 971e07ca4456 - - 426d707dfc47 - c27549b9aa1f + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi @@ -108,9 +108,9 @@ tools: - name: snippy owner: iuc revisions: - - fa016f1eea1a - - 5bbf9eada9c2 - d220115f882b + - 5bbf9eada9c2 + - fa016f1eea1a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -146,21 +146,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 40f0591deda0 - - 3b1e7c170b10 - 32f14a2723ec - - e7aff4a85df5 - ee4a90760848 + - e7aff4a85df5 + - 40f0591deda0 + - 3b1e7c170b10 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - adc0645b945c + - 9793bc5d741b - 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 b48b84001..f4a3417b3 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ 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