From da89bca2c57d90e1524e741e61ce168fe1bfbdf7 Mon Sep 17 00:00:00 2001 From: admin Date: Fri, 24 Nov 2023 01:02:05 +0000 Subject: [PATCH] Jenkins update build 173. --- automated_tool_installation_log.tsv | 43 +++ staging.gvl.org.au/annotation.yml | 79 +++--- staging.gvl.org.au/assembly.yml | 195 +++++++------- staging.gvl.org.au/bacterial_typing.yml | 6 +- staging.gvl.org.au/bed.yml | 14 +- staging.gvl.org.au/blast.yml | 10 +- staging.gvl.org.au/chemicaltoolbox.yml | 54 ++-- staging.gvl.org.au/chip_seq.yml | 6 +- staging.gvl.org.au/collection_operations.yml | 2 +- staging.gvl.org.au/convert_formats.yml | 34 +-- staging.gvl.org.au/deeptools.yml | 122 ++++----- staging.gvl.org.au/dna_metabarcoding.yml | 14 +- staging.gvl.org.au/emboss.yml | 4 +- staging.gvl.org.au/epigenetics.yml | 2 +- staging.gvl.org.au/fastafastq.yml | 92 +++---- staging.gvl.org.au/fastq_quality_control.yml | 20 +- staging.gvl.org.au/gemini_tools.yml | 26 +- staging.gvl.org.au/genome_editing.yml | 6 +- staging.gvl.org.au/get_data.yml | 31 +-- staging.gvl.org.au/graphdisplay_data.yml | 62 ++--- staging.gvl.org.au/hca_single_cell.yml | 4 +- staging.gvl.org.au/hicexplorer.yml | 14 +- staging.gvl.org.au/imaging.yml | 56 ++-- staging.gvl.org.au/ivar.yml | 72 +++--- .../join_subtract_and_group.yml | 8 +- staging.gvl.org.au/machine_learning.yml | 46 ++-- staging.gvl.org.au/mapping.yml | 44 ++-- staging.gvl.org.au/metagenomic_analysis.yml | 102 ++++---- staging.gvl.org.au/mothur.yml | 4 +- staging.gvl.org.au/multiple_alignments.yml | 52 ++-- staging.gvl.org.au/nanopore.yml | 36 +-- staging.gvl.org.au/none.yml | 40 +-- staging.gvl.org.au/phylogenetics.yml | 87 ++++--- staging.gvl.org.au/picard.yml | 8 +- staging.gvl.org.au/proteomic_ai.yml | 12 +- staging.gvl.org.au/proteomics.yml | 142 +++++----- staging.gvl.org.au/rad_seq.yml | 68 ++--- staging.gvl.org.au/rna_seq.yml | 156 +++++------ staging.gvl.org.au/rseqc.yml | 2 +- staging.gvl.org.au/sambam.yml | 82 +++--- staging.gvl.org.au/send_data.yml | 6 +- staging.gvl.org.au/single_cell.yml | 54 ++-- staging.gvl.org.au/statistics.yml | 30 +-- staging.gvl.org.au/text_manipulation.yml | 30 +-- staging.gvl.org.au/variant_calling.yml | 28 +- staging.gvl.org.au/vcfbcf.yml | 244 +++++++++--------- usegalaxy.org.au/annotation.yml | 85 +++--- usegalaxy.org.au/assembly.yml | 197 +++++++------- usegalaxy.org.au/bacterial_typing.yml | 8 +- usegalaxy.org.au/bb_tools.yml | 2 +- usegalaxy.org.au/bed.yml | 12 +- usegalaxy.org.au/blast.yml | 14 +- usegalaxy.org.au/chemicaltoolbox.yml | 56 ++-- usegalaxy.org.au/chip_seq.yml | 12 +- usegalaxy.org.au/collection_operations.yml | 6 +- usegalaxy.org.au/convert_formats.yml | 34 +-- usegalaxy.org.au/deeptools.yml | 106 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 8 +- usegalaxy.org.au/epigenetics.yml | 4 +- usegalaxy.org.au/fastafastq.yml | 86 +++--- usegalaxy.org.au/fastq_quality_control.yml | 34 +-- usegalaxy.org.au/filter_and_sort.yml | 2 +- usegalaxy.org.au/gemini_tools.yml | 20 +- usegalaxy.org.au/genome_editing.yml | 4 +- usegalaxy.org.au/get_data.yml | 33 +-- usegalaxy.org.au/graphdisplay_data.yml | 60 ++--- usegalaxy.org.au/hca_single_cell.yml | 4 +- usegalaxy.org.au/hicexplorer.yml | 12 +- usegalaxy.org.au/imaging.yml | 52 ++-- usegalaxy.org.au/ivar.yml | 60 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 8 +- usegalaxy.org.au/machine_learning.yml | 42 +-- usegalaxy.org.au/mapping.yml | 46 ++-- usegalaxy.org.au/metagenomic_analysis.yml | 94 +++---- usegalaxy.org.au/mothur.yml | 4 +- usegalaxy.org.au/multiple_alignments.yml | 44 ++-- usegalaxy.org.au/nanopore.yml | 44 ++-- usegalaxy.org.au/none.yml | 40 +-- usegalaxy.org.au/phylogenetics.yml | 83 +++--- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 10 +- usegalaxy.org.au/proteomics.yml | 140 +++++----- usegalaxy.org.au/rad_seq.yml | 78 +++--- usegalaxy.org.au/rna_seq.yml | 142 +++++----- usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 62 +++-- usegalaxy.org.au/send_data.yml | 2 +- usegalaxy.org.au/single_cell.yml | 49 ++-- usegalaxy.org.au/statistics.yml | 36 +-- usegalaxy.org.au/text_manipulation.yml | 32 +-- usegalaxy.org.au/variant_calling.yml | 32 +-- usegalaxy.org.au/vcfbcf.yml | 244 +++++++++--------- usegalaxy.org.au/viral_tools.yml | 2 +- 93 files changed, 2244 insertions(+), 2162 deletions(-) diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 99c99ec8c..c7d7c150f 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -5981,3 +5981,46 @@ Update 172 16/11/23 23:43:51 scanpy_remove_confounders False Installed iuc 73ab2 Update 172 17/11/23 00:03:25 sklearn_build_pipeline False Installed bgruening 4c4ec859c31a 4c4ec859c31a 18/18 0/0 Statistics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_172/install_log.txt Update 172 17/11/23 02:10:27 sklearn_ensemble False Installed bgruening 060ca94ac049 060ca94ac049 12/12 12/12 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_172/install_log.txt Update 172 17/11/23 02:55:35 sklearn_estimator_attributes False Installed bgruening 30d21a6041f6 30d21a6041f6 8/8 8/8 Statistics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_172/install_log.txt +Update 173 23/11/23 20:22:03 anndata_import False Shed-tools test error iuc 93dd15e13e6a 93dd15e13e6a Staging Testing Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 20:44:40 anndata_inspect False Tests failed iuc 6f0d0c784f09 6f0d0c784f09 Staging Testing 12/16 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 20:54:25 bam_to_sam False Installed devteam a53efedba9e7 a53efedba9e7 3/3 3/3 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 21:33:23 busco False Tests failed iuc 2a5b8b9936bf 2a5b8b9936bf Staging Testing 7/8 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 21:37:21 cat_bins False Tests failed iuc 31853794ace2 31853794ace2 Staging Testing 0/4 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 21:47:06 chipseeker False Tests failed rnateam 8bd92f2404dd 8bd92f2404dd Staging Testing 4/6 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 22:20:38 edger False Tests failed iuc 5bf899c13979 5bf899c13979 Production Testing 13/13 12/13 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 22:22:41 encyclopedia_encyclopedia False Tests failed galaxyp eac99effe86f eac99effe86f Staging Testing 0/1 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 22:24:41 encyclopedia_walnut False Tests failed galaxyp 0d2e93e01e68 0d2e93e01e68 Staging Testing 0/1 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 22:27:45 funannotate_annotate False Tests failed iuc 756376aeb1ae 756376aeb1ae Staging Testing 0/2 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 22:31:20 funannotate_compare False Tests failed iuc e94187d661df e94187d661df Staging Testing 0/3 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 23/11/23 23:33:50 hicexplorer_hicpca False Tests failed bgruening 77919cc3618e 77919cc3618e Production Testing 5/5 1/5 HiCExplorer toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 00:22:19 hifiasm False Installed bgruening 0ee0c3089254 0ee0c3089254 15/15 15/15 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 00:32:29 humann False Tests failed iuc fc6c328c292f fc6c328c292f Staging Testing 3/8 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 00:37:01 humann_rename_table False Tests failed iuc 094ad9c068af 094ad9c068af Staging Testing 2/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 00:51:07 keras_model_config False Installed bgruening 4d81e3e2fb63 4d81e3e2fb63 5/5 5/5 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 01:03:25 merqury False Tests failed iuc 09c589057ee8 09c589057ee8 Staging Testing 3/6 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 02:10:39 ml_visualization_ex False Installed bgruening 8334dc98c48e 8334dc98c48e 8/8 8/8 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 03:02:04 ncbi_blast_plus False Tests failed devteam d999e774072a d999e774072a Staging Testing 42/67 Blast + toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 03:04:09 openms_targetedfileconverter False Tests failed galaxyp 9c70a651a53e 9c70a651a53e Staging Testing 0/20 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 03:06:16 openms_xmlvalidator False Tests failed galaxyp f036e8cf1a55 f036e8cf1a55 Staging Testing 0/1 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 03:16:34 raxml False Installed iuc b1e68bbe4cef b1e68bbe4cef 2/2 0/0 Phylogenetics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 03:35:15 samtools_bedcov False Installed devteam 6856f8a01905 6856f8a01905 7/7 7/7 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 03:38:37 samtools_calmd False Tests failed devteam c89806670ab9 c89806670ab9 Staging Testing 0/2 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 04:28:41 samtools_fastx False Tests failed iuc 66e23b11feae 66e23b11feae Production Testing 18/18 17/18 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 04:37:04 samtools_flagstat False Installed devteam fefd89ab563c fefd89ab563c 3/3 0/0 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 04:44:57 samtools_idxstats False Installed devteam fa5d3e61e429 fa5d3e61e429 2/2 2/2 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 04:54:14 samtools_merge False Installed iuc 65a38e8c8e2a 65a38e8c8e2a 6/6 0/0 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 05:11:04 samtools_mpileup False Installed devteam b61f5d6a7f25 b61f5d6a7f25 6/6 6/6 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 05:19:39 samtools_reheader False Installed devteam d7b4851d1971 d7b4851d1971 2/2 2/2 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 05:28:27 samtools_slice_bam False Installed devteam b5c88b7b153e b5c88b7b153e 3/3 3/3 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 05:56:18 samtools_sort False Installed devteam a577ea614bed a577ea614bed 9/9 9/9 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 06:03:21 samtools_split False Tests failed devteam bd850490c7f1 bd850490c7f1 Production Testing 1/1 0/1 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 06:27:22 samtools_stats False Installed devteam fed4aa48ba09 fed4aa48ba09 13/13 13/13 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 06:59:15 samtools_view False Tests failed iuc 6be888be75f9 6be888be75f9 Staging Testing 29/31 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 07:32:42 scanpy_cluster_reduce_dimension False Tests failed iuc 6acb08931836 6acb08931836 Production Testing 12/12 0/12 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 07:43:10 scanpy_filter False Tests failed iuc a03ff8633507 a03ff8633507 Staging Testing 7/8 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 08:10:28 scanpy_inspect False Installed iuc 3081ff5c84a3 3081ff5c84a3 12/12 12/12 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 08:16:06 scanpy_normalize False Tests failed iuc 94c19fb1281c 94c19fb1281c Staging Testing 2/4 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 10:07:42 scanpy_plot False Installed iuc 9b0cdb8cf6be 9b0cdb8cf6be 34/34 0/0 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 10:18:19 scanpy_remove_confounders False Installed iuc 458e8f43a775 458e8f43a775 2/2 0/0 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 10:34:48 snpeff False Installed iuc 9473cd297a76 9473cd297a76 5/5 5/5 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt +Update 173 24/11/23 11:01:46 sra_tools False Installed iuc e407b9da183a e407b9da183a 20/20 0/0 Get Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_173/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 85b2b2857..b9a394ef7 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - - 78c75f134c16 - c2ef298da409 - 4efdca267d51 - 6e9aea89e388 + - 3f3e247c053d + - 78c75f134c16 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,15 +36,15 @@ tools: - name: annotatemyids owner: iuc revisions: - - 3e1f6f6d557e - - cd2480f35935 - - 133f36c29579 + - 1aae04680c4b - b5d8e5475247 - - 44018dd6b447 - 4f2967b27e67 - - 1aae04680c4b - - f29602ae449e - fe3ca740a485 + - 44018dd6b447 + - 3e1f6f6d557e + - 133f36c29579 + - cd2480f35935 + - f29602ae449e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -57,17 +57,17 @@ tools: - name: augustus_training owner: bgruening revisions: - - 7be22100e5e1 - - dc027fa56d55 - 6519ebe25019 + - dc027fa56d55 + - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - - ca6d970d931c - 28433faa6e42 + - ca6d970d931c + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -79,9 +79,9 @@ tools: - name: barrnap owner: iuc revisions: + - 8fd427007e93 - fe48aa4ccd5e - 7355bbf5e05f - - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: chipseeker @@ -99,8 +99,8 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 63662ae295d6 - 9d1fbff733cf + - 63662ae295d6 - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -119,49 +119,49 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 14f588312c56 - b6b5cd37f2a2 - 9f2455341fac - 582fd74dc2a1 - - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 989f7c061f35 - a230ea445788 - - 0ffe5be70caf + - 989f7c061f35 - 30fb23d4c31c + - 0ffe5be70caf - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 5a5ae61da69c - 563a19373357 - - 30f08d74024f + - 5a5ae61da69c - 494f0bb4a993 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - 7abc5f6dd595 - - 1bc5a03faf2e - - f31125bb85ea - 2bba2ff070d9 + - f31125bb85ea - d6c7106b7b2e + - 1bc5a03faf2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 52af33194019 - - 520e30695ec3 - b3cf4684e9c7 + - 52af33194019 - 54961e026fe4 - d3af38b9c7e1 + - 520e30695ec3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -173,9 +173,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 79261884facd - 07d7991bf205 + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -187,9 +187,9 @@ tools: - name: goseq owner: iuc revisions: + - 43798b4caee0 - 8b3e3657034e - ef2ad746b589 - - 43798b4caee0 - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -216,8 +216,8 @@ tools: owner: bgruening revisions: - c55643c3d813 - - 74810db257cc - 98cafcbd2578 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -242,16 +242,16 @@ tools: - name: maker owner: iuc revisions: - - d46d803ca6cc - - 3c1a01127868 - 370c210d9541 + - 3c1a01127868 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -277,8 +277,8 @@ tools: revisions: - bf68eb663bc3 - d643e3b03500 - - eaee459f3d69 - a17498c603ec + - eaee459f3d69 - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -311,21 +311,22 @@ tools: - name: snpeff owner: iuc revisions: - - 5a29ab10dba6 - 68693743661e - - 5c7b70713fb5 - 8f92c2b26e6d + - 5c7b70713fb5 - 268d162b9c49 - cfcf33df7fc0 + - 5a29ab10dba6 - 5b80f544c67f + - 9473cd297a76 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - 09d6806c609e - - 5fab4f81391d - 2b3e65a4252f + - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -337,8 +338,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -350,15 +351,15 @@ tools: - name: tbprofiler owner: iuc revisions: - - 809dfc93d593 + - 2c68b0c38785 + - e1a9d6fd258d + - 37213cf56392 - 037a11682176 - 200c378d85f3 - - e1a9d6fd258d - - ba6f87115e13 - 45083d070fb8 - ac8250086ac3 - - 2c68b0c38785 - - 37213cf56392 + - ba6f87115e13 + - 809dfc93d593 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 3635cd6b5..80b365099 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,42 +2,42 @@ tools: - name: abyss owner: iuc revisions: - - 0e93176640ac - - 553bfe8bd0b5 + - a929ce596a34 - 890b794c997d - fa5259cc561b - - a929ce596a34 - - 841084c5fc46 - 7547fcab5d19 + - 0e93176640ac + - 841084c5fc46 - 8f1b150a2487 + - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - b2860df42e16 - - 94fe43e75ddc - - b9e31c5c01c7 - - 21e491ad532a - ddddce450736 + - 21e491ad532a + - b9e31c5c01c7 + - 94fe43e75ddc - 067592b6b312 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 - 5258e18bbe23 - - 3371c5bdc17a - - a7f16f24e9a1 - 22286dab5aa1 + - faee8629b460 + - a7f16f24e9a1 + - 3371c5bdc17a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,29 +49,29 @@ tools: - name: busco owner: iuc revisions: - - 1e62c28ba91d + - f18f0b887c31 + - 94170eee0ad8 - e824f5d958d0 - - 41030a6c03b7 + - 2dd755c1c6ff + - 0d243f458b53 + - e4bd1e99bacf - cf13a1e03e5b - - 4048d82f0c88 - - 602fb8e63aa7 - 1440ae06552f + - 46ae58b1d792 + - 4048d82f0c88 - 5ecdeca79a0d - - e4bd1e99bacf - - f18f0b887c31 - bb935709506a - - 2dd755c1c6ff - - 94170eee0ad8 - - 46ae58b1d792 - - 0d243f458b53 + - 1e62c28ba91d + - 41030a6c03b7 + - 602fb8e63aa7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 5732f959936a - c5b7390290b1 - 86f150c8019d - - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -83,20 +83,20 @@ tools: - name: flye owner: bgruening revisions: + - 276f5d8712d5 + - 3ee0ef312022 - 1ce9b1d72ec3 - 8d4f03b5fe9d - e27815e82dd4 - - 276f5d8712d5 - - 3ee0ef312022 - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - 01210c4e9144 - b2f674562a18 - 3169a38c2656 - - 01210c4e9144 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle @@ -111,9 +111,9 @@ tools: owner: bgruening revisions: - 690c2caa367e + - 3fba9c77550a - 5127a713de83 - 3ef480892a9f - - 3fba9c77550a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -126,19 +126,20 @@ tools: owner: bgruening revisions: - 9ef6920c3089 - - 71740308d412 - - 41cea2aa2dce - - 3f7be05a1597 - - f3c89da3af16 - da9d8bf98802 + - 5f625c63b8bc + - 0ee0c3089254 + - f3c89da3af16 - 2061fb3b81b4 + - 3f7be05a1597 - ec9e21e9c71b - - 5bec28269d95 - - 045c7c3d8e59 - - 60024a528cbd - 6505bd37670d + - 71740308d412 - 366a11d316a7 - - 5f625c63b8bc + - 045c7c3d8e59 + - 41cea2aa2dce + - 60024a528cbd + - 5bec28269d95 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -157,36 +158,36 @@ tools: owner: iuc revisions: - 7518ee87b53d - - de387b2b2803 - 14ddfc8ffb93 + - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 39edec572bae - - f8113c25bc6b - 9d79beb19ac3 + - f8113c25bc6b + - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: + - 29dabd8db6f2 - 51c2360aa807 - eadfd71dde37 - - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - 606b09cc9860 + - 2ecf5a570907 - f338e9942b27 + - 3ca2d2a9068c - eb7a370f6588 - fd128c111ab0 - e731ea24e48d - - 2ecf5a570907 - - 606b09cc9860 - - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -198,11 +199,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8b6d0d85252b - - a7b889b90140 + - 73a3846701e1 - 8dee0218ac7d + - 8b6d0d85252b - 80d1250bd5fd - - 73a3846701e1 + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -215,8 +216,8 @@ tools: owner: iuc revisions: - 15200570e926 - - 7c2f5268d01c - 64a1c751d99b + - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -228,12 +229,12 @@ tools: - name: pretext_map owner: iuc revisions: - - 02831bf9e95f + - d256a51a656b - dfb8a4497339 + - bbe19ef04a74 + - 02831bf9e95f - 8fef980d48b5 - 2b16ba799da9 - - bbe19ef04a74 - - d256a51a656b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups @@ -248,53 +249,53 @@ tools: owner: iuc revisions: - 675488238c96 - - 342a1d1fed7b + - 59db8ea8c845 - ebb0dcdb621a + - 72472698a2df - 875d0f36d66f - - 59db8ea8c845 + - 342a1d1fed7b - 6fcbee531de6 - - 3061c8b029e5 - 7594365c546b - - 72472698a2df + - 3061c8b029e5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - - 39bed8de8017 - - a199cd7ac344 - d865b62f501c - - aa39b19ca11e - 78c533842eeb + - a199cd7ac344 + - cd06929b224b + - aa39b19ca11e + - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - 2b2a352488fa - - f8564b2d7f63 - f11b994b7eb2 - - 3edba9afc9bc - 33b7d8481a76 + - 2b2a352488fa + - 3edba9afc9bc + - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - 1d06c8b38e77 - e122f9101584 + - 378e55aeeb25 + - 1d06c8b38e77 - ef69617ecb42 - 53c2bc8c2ae3 - - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: + - ab5b7f6b7198 - ba7b0f11e470 - f77f7a7f3b83 - - ab5b7f6b7198 - 9a22227bb6d0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -309,78 +310,78 @@ tools: revisions: - 865119fcb694 - d9f6a00b6db7 - - ad80238462c1 - f698c7604b3b - - 196a599ec43d - ee17a294d3a3 - 83ead2be47b2 + - 196a599ec43d + - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - 24e471d13fe9 - - 5e0825476fb7 - 5a0ddb4dc3a4 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 7490b213baa9 - 1bb12736175c + - 7490b213baa9 + - 051fd2db8a27 - 904bf932cf78 - 1fc82fe7ebef - - 051fd2db8a27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - d6e617c4e338 - - 808b3a0a6716 - ad8b536d1caa - 34305b013402 - fee85957cebe + - d6e617c4e338 + - 808b3a0a6716 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 21da31ed41a1 - - b8002c3f7141 - e5a3b75a271f - 8d4b90bf9caf + - 21da31ed41a1 + - b8002c3f7141 - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - f1532cb33c75 - - 86f66ab58e14 - 328aa71f0f3c - - 9de69775f512 + - 86f66ab58e14 - 2a10645aeadd + - f1532cb33c75 + - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - e41dcb0e913b - 85fb02c43042 - - 340bc17f49cf - 6aad515a5270 + - 340bc17f49cf - 1708851f8804 + - e41dcb0e913b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - d5fb354f745d + - 249f6a28c751 - d159735a6a9f - b65a43f70b99 - - 249f6a28c751 - - d5fb354f745d - b3490b036c5a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -388,20 +389,20 @@ tools: owner: nml revisions: - 9006e5836729 - - dd7ad84f3943 - - 33368fec3b70 + - 7897763d14ec - d2d1df21dfb9 + - dd7ad84f3943 - b7829778729f - - 7897763d14ec + - 33368fec3b70 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: + - ced385aa976d - 189e837009c9 - 505a9833ab5d - 6f4c8ad6ea01 - - ced385aa976d - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -409,38 +410,38 @@ tools: owner: iuc revisions: - 9ded6109434a - - 356afed970b4 - d40ed4eb0c0e - - 19bdfd1e6fe3 - e59bee4565b3 + - 356afed970b4 + - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - b23249f81bc4 - 80a17897564d + - 4688ae3b49b5 - 6dd935e4984b - - b23249f81bc4 - ebd801e712bc - - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 59bd28f6265d - - cb1e3db43020 - 937ea677d437 - - b5e35a2ca4f3 - b64696992ee9 + - b5e35a2ca4f3 + - cb1e3db43020 + - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6015aa0303f2 - cb4768eeca3b - 2628f6790eda + - 6015aa0303f2 - 05bd7504fdb2 - 383bb5ad32e2 tool_panel_section_label: Assembly @@ -448,30 +449,30 @@ tools: - name: unicycler owner: iuc revisions: - - 0a3a602cd1e3 - - d10bdad2fd17 - - 9e3e80cc4ad4 - 6e26c9afd301 - e92675014ac9 + - 9e3e80cc4ad4 + - 0a3a602cd1e3 + - d10bdad2fd17 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f + - 5da9a0e2fb2d - 8d09f8be269e - 920677cd220f - - 5da9a0e2fb2d + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 82398ba86ba7 - 4a53b89fa703 + - 0e2b4e3f9ca1 - 37d88f41c810 + - 82398ba86ba7 - d81360ea69d8 - - 0e2b4e3f9ca1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 77342bd18..8c803c9b1 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,8 +2,8 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - 4768f7f8e93f + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -15,17 +15,17 @@ tools: - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - 1f5641a52664 - ded48b36f3b7 - 31812e7a1315 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 17fcac7ddf54 - 24a7a95867b0 + - 17fcac7ddf54 - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing 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 df5667096..be47613bd 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - b28e0cfa7ba1 - - a8eabd2838f6 - - 589e7e57fd6d + - 07e8b80f278c - ce3c7f062223 + - dde39ba9c031 - a1a923cd89e8 - - 0a5c785ac6db + - b28e0cfa7ba1 - 87ee588b3d45 - - a68aa6c1204a - - dde39ba9c031 - e19bebe96cd2 - - 07e8b80f278c + - 0a5c785ac6db + - a68aa6c1204a + - 589e7e57fd6d + - a8eabd2838f6 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 bb9a4ad6e..6c354c15b 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - 62c9df8382c2 - e8ac2b53f262 - 54f751e413f4 - f921014aba5a + - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,12 +23,12 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 6f386c5dc4fb - - acf4e47b734c - - 2889433c7ae1 - e25d3acf6e68 - a52d2d93e595 - 5edc472ec434 + - acf4e47b734c + - 6f386c5dc4fb + - 2889433c7ae1 - 0e3cf9594bb7 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu @@ -41,8 +41,8 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index b5fc15fc1..a11a175d5 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 6ca543ec1bf8 - - c8cdde00b105 + - f4230f116196 + - 095ad4d096d1 - da6bd1975a71 - 710301bc46fa - - 095ad4d096d1 - - f4230f116196 - 27ee142314a9 + - c8cdde00b105 + - 6ca543ec1bf8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -100,71 +100,71 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - bfb65cb551d8 - - 88076940fa94 + - 3b8a9d5ced85 - 0fac8e2afc13 + - 88076940fa94 + - bfb65cb551d8 - 79cfd9ead848 - - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - d532b7e5f64b - - f5d979cb4b54 - eb6564a60136 + - 55918daa5651 + - f5d979cb4b54 - 715cd0e87781 - b46d4b4d995c - - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - d2f955aea23a - - fdf2cc80adb5 - - f26afd1b7104 - 97872d87ba80 - 5579659312e6 + - fdf2cc80adb5 + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - - d1d0efda35c0 - 319a28774da9 + - d1d0efda35c0 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: + - 2c349b027a01 - 070e3ecc3fda - - cac1886249a2 - 4da9ee404eab - - 2c349b027a01 + - cac1886249a2 - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - c0c9a5024177 - - f197e34c33a9 - da8753545526 - - 73008ef1f487 + - c0c9a5024177 + - 525ca7c8065f - 807aa4c9293d - - 2e219a2d9327 + - 73008ef1f487 - d1f803b5943c - - 525ca7c8065f + - f197e34c33a9 + - 2e219a2d9327 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 7568ae18908a - - 2c8ed1b52bf7 - 61094e01eff9 + - 2c8ed1b52bf7 + - 7568ae18908a - c4fbab8e03c5 - 27ea4e1a3f95 - 1809414a9454 @@ -173,10 +173,10 @@ tools: - name: md_converter owner: chemteam revisions: - - d7ec25187599 - - ccfbd956a2d3 - - 730ef07b90ae - 79e8ab8f1e81 + - 730ef07b90ae + - ccfbd956a2d3 + - d7ec25187599 - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -196,9 +196,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - e6011617c748 - 1400d1977e7b - b59c91adeac1 - - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction @@ -228,10 +228,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 85fad59f8168 - 9b48456a96fe - bf99565cec1f - d4c67ced6abc - - 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 b8ca6a381..e25416782 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - c97a786e8fb5 - fa56d93f7980 - 163688bb8f73 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -31,9 +31,9 @@ tools: revisions: - 640d3af5d833 - 424aefbd7777 - - 86e2413cf3f8 - f5d67c722d67 - 495a4173006f + - 86e2413cf3f8 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -52,9 +52,9 @@ tools: - name: sicer owner: devteam revisions: + - 5c2cc3b58c7d - 74c9214cc8e6 - 4a14714649b4 - - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index f353d59e2..c26062214 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -10,9 +10,9 @@ tools: owner: nml revisions: - 33151a38533a + - 830961c48e42 - 90981f86000f - 25136a2b0cfe - - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index a07a1a80b..e40857671 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -8,37 +8,37 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - dad9da48a09a - - 6ef0b5664c69 + - 367b1ed91207 - a3b86937ead6 - - 5e1240a87bcb - 4a6ee918c13a - - 367b1ed91207 + - dad9da48a09a + - e3cbd2287f63 - 0b3c3ad92827 - f3a19509108a - - e3cbd2287f63 + - 6ef0b5664c69 + - 5e1240a87bcb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - a4db66553a61 - - 72ed72122deb - - e525f9ffb9ac - - 584008e574b2 - 33c99804a32f - bd46669113b9 + - a4db66553a61 - 54ccb7e1f49a + - 72ed72122deb + - e177a8ea0bf1 + - e525f9ffb9ac - 501c21cce614 + - 584008e574b2 - 1b5fc03380d4 - - e177a8ea0bf1 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 @@ -50,8 +50,8 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta @@ -78,8 +78,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -91,8 +91,8 @@ tools: - name: gffread owner: devteam revisions: - - 154d00cbbf2d - 4dea02886337 + - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -110,8 +110,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - f5c632894818 - 8190f6083c0d + - f5c632894818 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -131,11 +131,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 19e45916daf9 - 92ac8e086317 - 26c6706bfb07 - - 63769c4217a7 - b9b385097f13 + - 63769c4217a7 + - 19e45916daf9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index c8262a7fb..43c4c2f3c 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,25 +2,25 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 29451af70c52 - - c929a006727f - - de72ba3ed6f2 - - a1ca9bccc7f2 - 268e91e540ee - - e821645ef8fc - 5f6d123679f4 + - de72ba3ed6f2 + - e821645ef8fc + - c929a006727f + - a1ca9bccc7f2 + - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e143b4c3987 - - 0e49b109abc2 - bb1e4f63e0e6 - - 2d2cf5c1ea8a - - 5d11599b8a7d - - 7a7fd0f5f15d + - 0e143b4c3987 - 12af64f93288 + - 7a7fd0f5f15d + - 5d11599b8a7d + - 2d2cf5c1ea8a + - 0e49b109abc2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize @@ -28,106 +28,106 @@ tools: revisions: - c06951d10364 - 7c1beb6d6eca - - 81b1e3e1fc6c - dc059492a995 - 195e98217334 - 1d848bc4585f + - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - 26e7304d6737 + - 71aa86af6762 - a67ac707496a - 07418a30ed01 + - 3d211717a775 - 93eb012d9eed - bfff7454b59a - - 71aa86af6762 - - 3d211717a775 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - dd0b7398bb96 - - 26983857c91a - - 2bc10a9ca58b - 56d5b797ce84 - - b8858746dc1f - 29fcfd36e90a + - 26983857c91a - 5be24eba848d + - dd0b7398bb96 + - 2bc10a9ca58b + - b8858746dc1f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - c3e012dfe21f + - 7ef978dc1b8a - 72bfafe3330b + - ee3a1b0f45f1 + - e6d0bff01239 - 7e6bcd2e5128 - - 7ef978dc1b8a - 9384cd033f30 - - e6d0bff01239 - - ee3a1b0f45f1 + - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - 9470f29702f8 + - 514fa53b5efb - fb9cf9c97ec4 - fd1275e01605 - - a60c359ec43c + - 9470f29702f8 - b73e213add0c - - 167788df3b46 - - 514fa53b5efb - d9a637e83828 + - 167788df3b46 + - a60c359ec43c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: + - a02cfa31e9cb + - 5bffaa8354a1 - e479c7ca5570 - - 2c37ce318bc3 + - 86febdcc4283 - ca0616bb2cdf - - 5bffaa8354a1 + - 2c37ce318bc3 - c34d11ea4ba6 - - a02cfa31e9cb - - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 78f405266706 - 01fb6a7654e6 - - 192ef85c0b0b - 2d466b530754 - - 004aea905d4d - - 78f405266706 - - 1fcb7adc39b8 - 69a8621ca2f0 + - 192ef85c0b0b + - 1fcb7adc39b8 + - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 137c4beed34b - - 9ecba5e225a6 + - d9ce4897dbb2 - 3c9f0c486cca + - db940c262830 + - 137c4beed34b - d580d6acd1df + - 9ecba5e225a6 - 2f9e4843f480 - - db940c262830 - 459cfa861f0b - - d9ce4897dbb2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - 2c66e43f1c86 - - bd7db9e2f2cb - - fd408d755394 - f264afa9fa6f + - fd408d755394 - fbe773640707 + - bd7db9e2f2cb - bad3ca889618 - 32e451def88c tool_panel_section_label: DeepTools @@ -135,72 +135,72 @@ tools: - name: deeptools_plot_coverage owner: bgruening revisions: - - 3b9d990a0a0e - - 7e361d147872 + - 9368fbc49c8b - 56bce3c82278 + - 7e361d147872 + - 3b9d990a0a0e - 231994413f89 - 7fda5607e777 - 4e12ea27f788 - - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 94ca68515826 - d9114ef1c8a5 - - b1779366c8e9 - - 4431f39ede55 - e65d16fb2724 + - 94ca68515826 + - 4431f39ede55 - c03c3384cd81 - ce4ce3316f74 + - b1779366c8e9 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 4ed32329e0ed - - 2da482e408b8 - - d57251071381 - 23f7c5f1fdaf - 793665fff0f8 - - b88ebb3672a1 + - d57251071381 - f8fc4e5aff9d + - b88ebb3672a1 + - 2da482e408b8 + - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - ba6efa77fb79 - - 25d830337d31 - - 010e58e9d822 + - e4c7985d4585 - a4dfb122e52b - a7849312d328 - 512155688d98 - - e4c7985d4585 + - ba6efa77fb79 + - 010e58e9d822 + - 25d830337d31 - c60570fa602f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 00d869ea03a1 - - aa200e4f3939 - - 69264da0ce77 - - 4d678170d29b - - 443d9a9d6d11 - 38e3f226248b - c899e0ccff8c + - 4d678170d29b + - 69264da0ce77 + - aa200e4f3939 + - 443d9a9d6d11 + - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - 6662b1a8d326 - - aac8444d6681 - - d806504e96d9 + - 10301d137111 - c361b12d207a + - d806504e96d9 - a2d70c4fd406 - - 10301d137111 + - aac8444d6681 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 71acc956f..04d7c3bb5 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -2,8 +2,8 @@ tools: - name: obi_annotate owner: iuc revisions: - - 3021b9f5809f - f82cefbbcea5 + - 3021b9f5809f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean @@ -23,29 +23,29 @@ tools: - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - fe7ec8a3d35e + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 83fbdf93d51e - 94f412098ac8 + - 83fbdf93d51e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 3bf57dadf7cd + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort owner: iuc revisions: - - 12b9e285ca1c - e614dcabd870 + - 12b9e285ca1c tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat @@ -58,14 +58,14 @@ tools: - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 5f7003111e32 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - ec215ed98831 + - 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 3c40a1102..2bdbfb936 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - 832c20329690 - dba489bfcd62 - - 63dd26468588 + - 832c20329690 - ce385837c160 + - 63dd26468588 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 f21e9b48f..ba15ac0a2 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -3,9 +3,9 @@ tools: owner: iuc revisions: - 62f5fab76dfb - - 6da3972210ee - d82648ad25a3 - 29bdbc353f20 + - 6da3972210ee tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index bd34252c0..8166c9d5d 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,22 +8,22 @@ tools: - name: cutadapt owner: lparsons revisions: - - c5e2e5902201 - - 4e5056fefd88 - - 48f587c13075 - - 660cffd8d92a + - 135b80fb1ac2 + - c4b82dce8335 + - 44e2cc14f75b - 8665bcc8b847 - - e4691e1589d3 - 288f97432497 - - 5915ea1ec9b1 - - 135b80fb1ac2 + - e4691e1589d3 + - 49370cb85f0f - 8c0175e03cee - - de6cebe3c043 + - 48f587c13075 - c053d4cad713 - - c4b82dce8335 + - de6cebe3c043 + - c5e2e5902201 + - 4e5056fefd88 - 093678460093 - - 49370cb85f0f - - 44e2cc14f75b + - 660cffd8d92a + - 5915ea1ec9b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -35,9 +35,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: - - f666895cbebd - 9db07fd39f85 - 8889eb864cef + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -49,8 +49,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - de2db1bdfbf8 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -90,16 +90,16 @@ tools: - 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: - - f773e98b26cf - ec0b5076173a - f81d4362b6c1 + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -111,10 +111,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - cd0874854f51 - 9c620a950d3a - - 0dbb995c7d35 - 56022eb50bbd + - cd0874854f51 + - 0dbb995c7d35 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -127,8 +127,8 @@ tools: owner: iuc revisions: - dbf9c561ef29 - - 65b93b623c77 - 1d8fe9bc4cb0 + - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -140,8 +140,8 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -154,8 +154,8 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 47e5dbc3e790 - 8611b80a14d6 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -168,8 +168,8 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -182,23 +182,23 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 2ccb8dcabddc - 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 + - 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 - 249c8393f2d4 + - e39cc71d3ed6 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -211,8 +211,8 @@ 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 @@ -231,8 +231,8 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - 33794bdb7fe0 - b63b2bfb3ea3 + - 33794bdb7fe0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -245,8 +245,8 @@ tools: owner: devteam revisions: - 529bccd5e4a1 - - 567d5b3c52b1 - d5e9e83cd3d8 + - 567d5b3c52b1 - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -259,9 +259,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - - 0b7ec11b3c7c - 8abdedf55101 + - 0b7ec11b3c7c + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -288,9 +288,9 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 - - 421f0af4ee95 - 07497255281e + - 421f0af4ee95 + - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -302,10 +302,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - f984bb114520 - 3599f5451ee2 - - b29d37ca9e41 + - f984bb114520 - 02f8a17a4ebd + - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -317,10 +317,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: + - e246088b6e34 - 177f0621c266 - 6027ef51ef91 - 0c2907307ba4 - - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -332,10 +332,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 73194cdd4f57 - - 547e8d00f11c - - 377ac2829eac - 61b4cedc8934 + - 377ac2829eac + - 547e8d00f11c + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -391,15 +391,15 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - bf04bd405d5b - 71f649c23021 + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -411,11 +411,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - e654095ab143 - - 8250ea3a1501 - - b557acca0b56 - 24013bf85a6f + - b557acca0b56 - a535cf1e5da4 + - 8250ea3a1501 + - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -433,12 +433,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 7accf7407811 - f3759eec3018 - 9fa7803d1c51 - - 828dba98cdb4 - - 6a675c3aa610 - 27ac32a22ad2 + - 6a675c3aa610 + - 828dba98cdb4 + - 7accf7407811 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 61c980e5d..be4fb1d0b 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 7b4468117008 - 64e9a6afdd0c - e41385662e5e - ce9cd02d5b88 + - 7b4468117008 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,13 +18,13 @@ tools: - name: fastqc owner: devteam revisions: + - 9da02be9c6cc - e7b2202befea - - 3d0c7bdf12f5 - 2b0c9d9fc6ca + - 3d0c7bdf12f5 - f2e8552cf1d0 - - 5ec9f6bceaee - - 9da02be9c6cc - ff9530579d1f + - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -54,29 +54,29 @@ tools: owner: iuc revisions: - 1f296803dfa3 - - a72af9de6bf5 - 8880fb74ef56 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - bf675f34b056 + - f7985e0479b9 - 9a913cdee30e - - 5e33b465d8d5 + - 3d93dd18d9f8 - 1c2db0054039 - - f7985e0479b9 + - 75c93c70d094 + - 5e33b465d8d5 - b2f1f75d49c4 - abfd8a6544d7 - - 3d93dd18d9f8 - - 75c93c70d094 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - 949f01671246 - cd7e644cae1d + - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control 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 5b7929d8a..d83a05b0c 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 @@ -17,8 +17,8 @@ tools: owner: iuc revisions: - 0c8f7322f8fc - - f2f3bc622a16 - 8f53b238a360 + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -52,15 +52,15 @@ tools: - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -86,16 +86,16 @@ tools: - name: gemini_load owner: iuc revisions: + - 45296e47d565 - b2c25142267e - cf61daf064fe - - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors @@ -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: + - da74170c55c7 - 840fb4850be3 - 666f60a9331a - - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,35 +137,35 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - e4e2128460e3 - ef9991a4a9a7 + - e4e2128460e3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 2b81e95ea..f729cfa4c 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,22 +2,22 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f 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 a43a8174a..fd2e90966 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,48 +2,49 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - c1b437242fee - 983bf725dfc2 - - e9df53a75f3c - b39347891609 + - e9df53a75f3c + - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: + - 1c58de56d587 - 28587613264f - e063168e0a81 - - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - 6591f049cf7e - - 4df8de2d0e48 - - e08a7ad4378b - - 7068f48d0ef9 + - 4317d3cb6cba + - 83c7d564b128 + - f5ea3ce9b9b0 - c441583adae5 + - 653e89d73fc4 + - 1790dcf3c32d - 734abc7ac21d - - 5e6237d58b0c - - f5ea3ce9b9b0 + - 7068f48d0ef9 + - e407b9da183a + - aad3885b3216 - 6ea73833cf67 - - 83c7d564b128 - - 1790dcf3c32d - 9a776b080193 + - 5e6237d58b0c - 69ebb7f46e45 - - aad3885b3216 - - 4317d3cb6cba - - 653e89d73fc4 + - e08a7ad4378b + - 4df8de2d0e48 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 7863f1abcdda - 9aaa46d45472 - - 34758ab8aaa4 - 75b3b3d0adbf + - 7863f1abcdda + - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index a829eec80..d045683fd 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: - - 7f13dc906cb9 - - 290a11559985 - - c4bde687c846 - 4b519282a05b + - fd59d783248a + - c4bde687c846 - ae9994cf526f - 740057a5126d - - fd59d783248a - - df7356989ac1 - a64dc31ab7f2 + - 7f13dc906cb9 + - df7356989ac1 + - 290a11559985 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,18 +34,18 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - f95284aa2946 + - 7cf5b1d072b5 - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - - 3b37b1b1c3a7 - '566197475670' + - 53460afd5115 - ca7cb0eaad62 + - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap @@ -53,20 +53,20 @@ tools: revisions: - d3a9e32672ec - 3d059e9c2fba - - 391a4cc45fea - da4c086cff5b + - 391a4cc45fea - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 5fe1dc76176e - - 299307abd804 - - d0fc8b746d57 + - e3a675da7fd0 - 3b12bf9b4b87 + - 5fe1dc76176e - 1acf88921176 - - e3a675da7fd0 + - d0fc8b746d57 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -78,8 +78,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - cf1df6b2220a - 5d6f8f0bef7c + - cf1df6b2220a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -92,24 +92,24 @@ tools: - name: histogram owner: devteam revisions: - - cdb9e89e2970 - 6f134426c2b0 + - cdb9e89e2970 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse owner: iuc revisions: + - ca2def38369c - 2bb2e07a7a21 - 4542035c1075 - - a6e57ff585c0 - - 667e17248bfe - fd5dbf0f732e - - 836d1aa3e89a - 112eb40ba6cf - - ca2def38369c - - 1cfc579079a6 + - a6e57ff585c0 + - 836d1aa3e89a - 17359b808b01 - 6cd09d7b5f37 + - 667e17248bfe + - 1cfc579079a6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -127,9 +127,9 @@ tools: - name: pathview owner: iuc revisions: - - fe154a7af404 - 03c13085aecc - f1691de443a7 + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -141,15 +141,15 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - 62e3a4e8c54c + - 85da91bbdbfb 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 @@ -174,22 +174,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 59fd173ac850 - 326a3db8d9d1 - - a1abfa420d9d - - 2824d77cd8f8 - - 7dd841a32245 - - 4ac4e7083b7e - 360df4999907 - 14e7c35f3d00 + - 7dd841a32245 + - 4ac4e7083b7e + - a1abfa420d9d + - 59fd173ac850 + - 2824d77cd8f8 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 73b8cb5bddcd - - 44608d0193ed - 83c573f2e73c + - 44608d0193ed + - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 @@ -201,7 +201,7 @@ 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 1cb6532ff..82e8916e7 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -173,8 +173,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - 767a675b5254 + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 47f8e32fd..50ef57b8a 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -11,35 +11,35 @@ tools: - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 5746d61f0a91 + - 78fb5e286609 - d404277cc87a - ec4b948dc6f0 - - 78fb5e286609 + - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - 9e357a8b2ec3 - - 4d511437b1e5 - - 977dc15add20 - 03dd3c16ae4e + - 977dc15add20 + - 4d511437b1e5 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 3b5b54ed6392 - - 0ba4f56a3613 - 41dbf4d162a2 + - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 + - b63363075c2e - 7babd8a46fe0 + - 9939786dd9c9 - 5308ca68ef3d - - b63363075c2e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index c2d254ebf..701739a5f 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,16 +2,16 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 3df9f0a4bf34 - - 81f0cbca04a7 - 0c777d708acc + - 81f0cbca04a7 + - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - 0a53256b48c6 + - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features @@ -31,8 +31,8 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - dba87c4b32d3 + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert @@ -40,31 +40,31 @@ tools: revisions: - f3360fbeda64 - 10eed33aa9b2 - - b07f4839ca77 - 85edbb7a436b + - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - - 664232d2a3f7 - 5bf8eb50b280 + - 664232d2a3f7 - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - eb6c08714244 - 0e4dccaafef5 - e917a2424690 + - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -85,16 +85,16 @@ tools: - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - - df3ad3ba5c6f - cdf8e3c57dae + - df3ad3ba5c6f + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - 2484086dee41 + - 5d28ac336861 - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -109,97 +109,97 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f8fa0f6718a3 - - d0178bdcd00e - f24c370e5ea4 + - d0178bdcd00e + - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - ad271f78a87a - 3245681b2f6d - 31d195bedf6d - - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - 993faa34333b - - 87d4d92d7487 - b6eec6087271 + - 87d4d92d7487 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - c09dcda1143f - ff1a86a87364 + - c09dcda1143f - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - 667a513e67e4 - 3a05117669cf + - 667a513e67e4 - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - ac5bea85a391 - 2564f461de62 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - a32c3f810ade - - 91e03287f285 - 20dbb1f7ec7b + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - 8536b1ae0254 - - 5499dc6f8ac1 - b64af54c5c09 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - e972e07c7845 - - 6f4715b8540a - d3890df07463 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: + - 407925835dd9 - e52c75a28c4b - 980aed9e8fd5 - - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: + - 79e10d12d90a - d85f11570109 - acf3aa487283 - - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - 80b200ae516b - b76841ee5560 + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -211,17 +211,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 8083a87d2fdf - 3a3033222f61 - 48102a685037 + - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - 4ecf93628f97 - - 27edbb90ab2b - 33f4fa1413fb + - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -233,8 +233,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info @@ -247,7 +247,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 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 7acf83510..24c137634 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - e4ee04da1c19 + - 78bbd17d0703 - d6e72da3ec35 - - 1069f6db0a0e - - 17f911830a8c - - e319b5b65879 + - a38934e303b9 - 3e4f434a69c6 - - 78bbd17d0703 + - 17f911830a8c - f362150bef41 - - a38934e303b9 + - e319b5b65879 + - 1069f6db0a0e + - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 1ef5b6e3e09d - - c88553ec696e + - 8f8df367470d - 9537184d421f + - 7fe36019c073 - 2b95d5c04908 - - 72ddd32392cd - - 0135f1d487a0 - f91cfb73d369 - - 7fe36019c073 - - 8f8df367470d + - 0135f1d487a0 + - 72ddd32392cd + - 1ef5b6e3e09d + - c88553ec696e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - fafb3d685fa9 - - ad0dc9f4c9e2 - 2cf4a1cafc16 + - fafb3d685fa9 - d7e79eb3bcb3 + - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - 8d36959b000d - - 28a6f1908fcc - - 43aac8d29685 - - 3d18f8c3c0f6 - - 94df24c6bc00 - - 8c05afb547fa - 9eaadf03e0df + - 43aac8d29685 - 7f1cfa4c0e32 - - ee2beb764a7b - - 69797fa273c3 + - 6a1515bb0687 + - 28a6f1908fcc - bd2a7d1316b9 + - 8c05afb547fa + - 69797fa273c3 + - ee2beb764a7b + - 94df24c6bc00 - ee29337f905c - - 6a1515bb0687 + - 3d18f8c3c0f6 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5d6ed46cc101 - - 364f4ffec275 - - 8858fa037a15 + - 5671e1d3d5ee - db536ad45f28 - - 0893a1dbb807 + - 8858fa037a15 - cb903c9dc33d - - 9f978da6528a - d37ede8589b2 - bcaa0d571ce2 - - c092052ed673 + - 9f978da6528a + - 364f4ffec275 + - 5d6ed46cc101 + - 0893a1dbb807 - e3bb03cf207a - - 5671e1d3d5ee + - c092052ed673 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 12d66d0d05ac - - 230b05597996 - - 49236b03e4fd - f95f403841ad + - c5c9f02b6167 + - 230b05597996 - 584beffa972b + - 12d66d0d05ac + - 045d6d00f606 + - 3b6a16d82c1b - 38b91a3190cd - - c5c9f02b6167 - - ed28dd32141c + - 49236b03e4fd - e1a015876aa9 - - 3b6a16d82c1b - - 045d6d00f606 + - ed28dd32141c 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 d913cf89e..a8ad17f96 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 17e3b698dd52 + - 0f1724dd59d2 - f198773344e4 - b8a457820315 - - 0f1724dd59d2 + - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 374cb875d38a - 22c2a1ac7ae3 - - ac092723240d + - 374cb875d38a - ba0c40780ecf - a513e3fbb4c5 + - ac092723240d 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 03ff6199f..9e18b744c 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,56 +2,58 @@ tools: - name: keras_model_builder owner: bgruening revisions: + - 772e0e89fc68 - 522137aaa9c4 - 66d7efc06000 - - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 8a794e6d3388 + - 4d81e3e2fb63 - f22a9297440f + - 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 - - f1b9a42d6809 - 2af1346e68c9 + - f1b9a42d6809 + - b6ef6d0cb6b7 - 818f9b69d8a0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 947c2eacccb8 - c80db5d6fd8c - - 1588f9076e32 + - 8334dc98c48e - 05143043ca13 + - 947c2eacccb8 + - 1588f9076e32 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 9991c4ddde14 - 29e4122c90de + - 9991c4ddde14 - 83228baae3c5 - - 1552b8cb4a94 - 25b46af53232 + - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: + - 060ca94ac049 + - 53616c8b0865 - 841a6cc5fc58 - - f3dfa4bdf87e - a07ab242b0b5 - 1a53edc4b438 - - 060ca94ac049 - - 53616c8b0865 + - f3dfa4bdf87e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear @@ -59,8 +61,8 @@ tools: revisions: - 2fc89dcd41c8 - 40f4447733b2 - - 91c4e3331208 - dc4b5fd604a6 + - 91c4e3331208 - d4808d5b83da - 927586a18553 tool_panel_section_label: Machine Learning @@ -68,31 +70,31 @@ tools: - name: sklearn_searchcv owner: bgruening revisions: - - e5a5ad882f1f - - 25ab6b4e376e - - c6ae57f774c6 + - 7626ea9c2e1b - 36e8d6d5d01b + - 25ab6b4e376e + - e5a5ad882f1f - 301e07345c93 - - 7626ea9c2e1b + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - b7c3e9a3b954 - - 0630258dcf35 - - 80852884053f - f9639b488779 - - 02d2be90dedb + - 80852884053f + - 0630258dcf35 - 4ed102b922cb + - 02d2be90dedb + - b7c3e9a3b954 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - ec69cbe34b73 - - 61634a87efc7 - 14180f9c831e + - 61634a87efc7 + - ec69cbe34b73 - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 8cf720e1d..f2e5f67f2 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - 17062a0decb7 - - cd659e8cc5fa - - 03e9b2fbc005 - - 937aa69e715f + - 749c918495f7 - f6877ad76b00 + - 937aa69e715f - 3ba8d4563129 + - 03e9b2fbc005 - a6d65b0c67af + - cd659e8cc5fa + - 17062a0decb7 - 017aba02828d - - 749c918495f7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -22,16 +22,16 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - e188dc7a68e6 - 3fe632431b68 - 64f11cf59c6e + - e188dc7a68e6 - dfd8b7f78c37 - 53646aaaafef tool_panel_section_label: Mapping @@ -45,43 +45,43 @@ tools: - name: lastz owner: devteam revisions: + - 60afcc2c1d05 + - 2ff111fac1d7 + - 37b497aa133f - 3e1ea2facca6 - e7f19d6a9af8 - - 37b497aa133f - - 2ff111fac1d7 - - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 6b1e195506a3 - - c0c2d0941de8 - - f54f5baedfdd - - 11a0d50a54e6 + - 09b53c1d4ab1 - 3f4d6399997b + - 6b1e195506a3 - 8c6cd2650d1f - - b3eab4b67562 - be1d967337e4 + - b3eab4b67562 + - 11a0d50a54e6 + - f54f5baedfdd - 037c6e54df11 - 53c0b7a1a0c3 - - 09b53c1d4ab1 - 77b2770508f6 + - c0c2d0941de8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 13022c3d3076 - - 5ef7ec16b04f + - 9ee34ba73ebf + - 79b885ce78d7 + - ec9cbd6b9a49 - e403d27e8f24 - 178bdbdb6d24 - - 79b885ce78d7 - - b8f5f6e87f5c + - 5ef7ec16b04f - 00fbfac99d39 + - b8f5f6e87f5c - 1cd2511a396e - - ec9cbd6b9a49 - - 9ee34ba73ebf + - 13022c3d3076 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 8f9481d46..6c8a6c2b7 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -2,8 +2,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -34,90 +34,90 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 63f86089423e - - 7c2100246a2f - - 5b5a7af9fbb4 - 76d3d2b10738 + - 5b5a7af9fbb4 + - 7c2100246a2f + - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: + - 1c35dadbe76f - 18a502a9d287 - - 84fd33a60b35 - 96336c6a2bb7 - - 1c35dadbe76f + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - addaf9d22850 - 34e55239e68b - - f732237754fc - a9f4a217dcd6 + - addaf9d22850 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - 0776d824d896 - - 04c15826a0b8 - - 8c202e741d68 - 75403243703a + - 8c202e741d68 + - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 8470de786d47 - - 43c99742158b - - e96bbb9e24ea - 1c9b3bcd4261 + - e96bbb9e24ea + - 43c99742158b + - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 306a40d4bb8f - - 84743da21318 - 5c865a382933 + - 306a40d4bb8f - 1d75bd0595e2 + - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - ac72310b038a - 78faebd0879c - 555ccac8a4c5 + - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - - d60df8727f59 - 7b8cb2b02978 - a58e4a43f49c + - d60df8727f59 + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e - - 7136e9ab70db - 7f3b59dee073 + - 04144473e59e - 1bc3657cd694 + - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - d943081510da - - 0a1224c4b781 - 9058d8943303 + - 0a1224c4b781 - 19299bb1c6af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -132,8 +132,8 @@ tools: owner: iuc revisions: - dbf1798c0dcc - - c4db8c4de66f - 6501b5b33988 + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -147,8 +147,8 @@ tools: owner: iuc revisions: - 654548ae1357 - - 6d364c65c946 - 6c84982ee6f7 + - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -160,24 +160,24 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - e66ab198ec15 - bd7a9c6efb10 - 6aad8ca3918b + - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - b084117133af - d77397f09da1 - c6676a890f50 + - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - 7f208f1eb64f + - 9704f1a3b32d - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -190,10 +190,10 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - e88b731dad59 - c409a495841f - 31c6d107e7a5 - 79706f10d680 + - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table @@ -201,46 +201,46 @@ tools: revisions: - 71ea608ddfa3 - d24841f5c3d2 - - 714d5a28cc5c - 172920f67a84 + - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 12fb63b5f63f - - a293a742194f - 4137b492233e - - a4d7148ccee4 - d7e9a3c41657 + - a293a742194f + - a4d7148ccee4 + - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - cf87759761eb + - e2c71b852aba - 75bedfb2078b + - 64bc7acc22a9 - 97f7bb0851e7 - - e2c71b852aba - 6fcb8ac37a3e - - 64bc7acc22a9 + - cf87759761eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - 5e5a999ffaa9 - - c82508e76ad1 - - 2d35528d2141 - 4033827c76b8 - 080ea153677c + - c82508e76ad1 + - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 6b7622dda516 - 95bf7479d53c + - 6b7622dda516 - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -335,8 +335,8 @@ tools: - name: kraken_report owner: devteam revisions: - - 1902d3de4a4f - 6c09bed3444f + - 1902d3de4a4f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -348,8 +348,8 @@ tools: - name: kraken owner: devteam revisions: - - aec58624706f - 8ba2174315aa + - aec58624706f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -361,8 +361,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 88d274322340 - 2deaada69b14 + - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: mash_sketch @@ -386,19 +386,19 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - e073891b2afc + - 4fd3b5d8706b - 0270541aaf46 + - e073891b2afc - 27250f92a01a - - 4fd3b5d8706b - 2cff76cf35c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - 708abf08a626 - eb50e7eca3dc - 76bc4efa1aeb - - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -464,19 +464,19 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: + - a92a632c4d9b - 2131d7dca455 - - a16313517e55 - 1a6cdf55390f - ff8f55893e7d - 6dee4abadccb - - a92a632c4d9b + - a16313517e55 - b89b0765695d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -549,8 +549,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 9168545e09df + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -599,13 +599,13 @@ tools: - name: staramr owner: nml revisions: + - 4d83eccf5f81 - 2fd4d4c9c5c2 - 3b22de20bd4b - - 141afacabcfa - - 4d83eccf5f81 - aeaa20b96ef2 - - 4b9a8031ab74 + - 141afacabcfa - be818ae858e4 + - 4b9a8031ab74 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -636,7 +636,7 @@ tools: owner: iuc revisions: - 576963db5f1b - - b3c7199d8786 - 9495df9dd6ef + - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 2274dc82a..429d251d3 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index bc5544932..2932b9035 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 9baa871cb1d1 - - 80f03df2e2ce + - 2263989660f5 - 9422c5a87ee2 + - 9baa871cb1d1 - 9eeb13a92d79 - - 48c13389050d - - bdfbaf0c10aa - - 94b8c6013083 - - cd07731e4434 - a74dbfee5a86 - 8b67dd48fec1 - 6ae5a7b5a0a2 - - 2263989660f5 + - 94b8c6013083 + - bdfbaf0c10aa + - 80f03df2e2ce + - 48c13389050d + - cd07731e4434 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 5abf2c2249aa - - d7ce0ec78e51 - - d390fe1567dc - - be78f13134e2 - - c18157c68134 - - f14193ec1f50 - - aaa0d6a8b808 - f0af8936ed41 - - '764845535798' - bc3831dd65c1 - - 3ff17bad4006 - - 4a60927aaca5 - fc2e49f91e52 + - '764845535798' + - 3ff17bad4006 + - d390fe1567dc - 2e093badc689 + - 4a60927aaca5 + - f14193ec1f50 + - be78f13134e2 + - 5abf2c2249aa + - d7ce0ec78e51 + - c18157c68134 + - aaa0d6a8b808 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -64,19 +64,19 @@ tools: - name: mafft owner: rnateam revisions: - - c5908940967d - - f0d493f8f84f - - 15974dd17515 - - a65296ffb4a0 - - f1a5908ea2cb - 6f28e90db932 + - f1a5908ea2cb + - a65296ffb4a0 + - 15974dd17515 + - f0d493f8f84f + - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -89,15 +89,15 @@ tools: - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 48823c9635a4 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer @@ -110,7 +110,7 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 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 abcef7228..51b710e15 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,35 +8,35 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - a7228a7ea146 - - cb34f00cc10f - - 72b5e9dda577 - fc8804320156 - - 0e9e7fcdd543 - 79e9a869f40e + - 72b5e9dda577 + - 0e9e7fcdd543 + - a7228a7ea146 + - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - 18505fe2bdb1 - - db25ec99c3ea - - fa11aa8103b2 - d6cddc06aeae + - fa11aa8103b2 + - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - cc36773a3681 - - 19f3b583a9b3 - - 0f5f4a208660 - 2bf63b38ee9b - edf6d4003fad + - 222669c4afb6 - ec699520444c - eb746fa6f514 - 43815fa60f3a - - 222669c4afb6 + - 19f3b583a9b3 + - cc36773a3681 + - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -55,10 +55,10 @@ tools: - name: nanoplot owner: iuc revisions: + - a3c4fe6f49ab + - edbb6c5028f5 - 645159bcee2d - 0f1c34698076 - - edbb6c5028f5 - - a3c4fe6f49ab tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -71,15 +71,15 @@ tools: - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - be95355fef8d + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - 449e9aeded2d + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants @@ -92,16 +92,16 @@ tools: - name: porechop owner: iuc revisions: + - 93d623d9979c - 5f76b20953e5 - 543cbeef3949 - - 93d623d9979c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - 28d7819c312f + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -146,8 +146,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -177,8 +177,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - ca22d8497db5 - 64a83664b814 + - ca22d8497db5 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 0d27b4d0f..7fc3079c3 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -14,15 +14,15 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 4e85a3a5dbd1 - 71186bb66ca2 + - 4e85a3a5dbd1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 58341ad4fb42 - 96d2000977ab + - 58341ad4fb42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -52,8 +52,8 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - d74850cf4e42 - adfd6bf710bd + - d74850cf4e42 - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -74,9 +74,9 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 2f27f3b86827 - - edacc4bcd3cb - ed1518ce2237 + - edacc4bcd3cb + - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -101,9 +101,9 @@ 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 @@ -130,8 +130,8 @@ tools: - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -143,17 +143,17 @@ 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 - - 5bcf0e24f42c - 172815da3d41 + - 27a6a256cd23 - b4b2b284230a + - 5bcf0e24f42c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -179,15 +179,15 @@ tools: owner: iuc revisions: - 19bbd19b74b3 - - 87febc68b45b - fea85c467896 + - 87febc68b45b 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 @@ -211,9 +211,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 9c43baa60906 - 4ba60cb14cb0 - 5fe20c915fa6 + - 9c43baa60906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -225,25 +225,25 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 0db22932bc39 - 9d09724f2bf1 + - 0db22932bc39 - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - ed7a967cb11b + - 6e24e79d3d69 - df30a2f1db55 - 29c738066906 - - 6e24e79d3d69 + - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - 1865e693d8b2 - 3e4d45aca422 + - 1865e693d8b2 - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -263,9 +263,9 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: + - 64deddb6a8ec - d63c1442407f - c520a52b5174 - - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder @@ -1017,8 +1017,8 @@ 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: rdock_rbcavity @@ -1032,8 +1032,8 @@ tools: owner: bgruening revisions: - e4b7d1507a75 - - a22969b08177 - c362398df83b + - a22969b08177 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 08819f37e..e1ddb1060 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -33,87 +33,87 @@ tools: - name: hyphy_absrel owner: iuc revisions: + - d033ffc1c161 + - 81e66674859e + - f04a1264e2a2 + - 5a7c56a5cc08 + - b89cac5156ec + - '841557158611' - a6619171428e + - d7c7ef3353fe - 8834daeb9892 - - d033ffc1c161 - - f73435dc282b - c78f3d7dd1db - - 107d3ba7024a - - b89cac5156ec + - f73435dc282b - 3f59ebfbfe3d - 6a457678efcb - - d7c7ef3353fe - - '841557158611' - 26de3a7b1cb9 - - 81e66674859e - - cce7b18495e4 - - f04a1264e2a2 - 3b8b5bde0bd9 - - 5a7c56a5cc08 + - 107d3ba7024a + - cce7b18495e4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 7a2092844346 - - 6223845127ea - - 02b8758214b0 - - df47d4845b62 + - 6283babe736e - aa8cc71438cf + - b0af57c1a968 + - 4755f52427c4 + - 6a726db04d4b + - 6223845127ea - 5b777002c2de + - 88c4aa435ded + - df47d4845b62 + - e75442c7f4da - 3b96e92e8ec3 - - 6a726db04d4b + - 7a2092844346 + - a185b079b095 - 5fcd1ece3a6e - - 88c4aa435ded + - 02b8758214b0 - 659517798cc4 - - b0af57c1a968 - - 6283babe736e - - 4755f52427c4 - - a185b079b095 - - e75442c7f4da tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - b8476e82ac20 - f97743d52b87 - d1c340a5664b - - 9b892d7f82cc - 524d31add34a + - 9b892d7f82cc + - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 128ba8da994f - - feb40665d7cd - daddf188c13f + - 128ba8da994f - 9e10ba792be2 + - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - ca0d8cf80567 - - 3a43c3982401 + - 2fa9d4f1b48f + - 437e28791761 - 36912871ccdc + - b6abccb1f25b + - ca0d8cf80567 + - 83a69484cb87 - 03ed9524dcd1 - - 7bb8726be37c - - abf6dbe8c9d7 - b7e297c2ede6 - - 14ae456b8cc5 - - 9d61d3fa046c - - 2f1019071464 - - 5f8727ff21e7 - - b6abccb1f25b - - 437e28791761 - - 42a174224817 + - abf6dbe8c9d7 - ca337cce3888 + - 5f8727ff21e7 - 81804a978fc0 - - 2fa9d4f1b48f - - 83a69484cb87 + - 2f1019071464 + - 14ae456b8cc5 + - 7bb8726be37c - a2099fb98cdb + - 3a43c3982401 + - 9d61d3fa046c + - 42a174224817 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -126,21 +126,22 @@ tools: - name: raxml owner: iuc revisions: - - 29ff6a849eac - ea30d3089354 - - ba29b5e2a4be - a4b71be30c3c + - 29ff6a849eac - 73a469f7dc96 + - ba29b5e2a4be + - b1e68bbe4cef tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - dbe2b2204555 - - 91887494eb97 - 809e42326fc2 + - 15ac71df11a0 - f1ccc8a6eb05 - e88a7de55d6e - - 15ac71df11a0 + - dbe2b2204555 + - 91887494eb97 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 b14c18c79..0302bfaf8 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - f9242e01365a - - f6ced08779c4 - - 881d7645d1bf - 1aac2a13842a + - f9242e01365a - a1f0b3f4b781 - - 7d34178f2812 + - 881d7645d1bf + - f6ced08779c4 - b502c227b5e6 + - 7d34178f2812 - fc288950c3b7 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 0edf49c49..45be1cf81 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,14 +2,14 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - e4a053d67e24 - - 5b85006245f3 + - 7fbec959cf2b + - a58f7eb0df2c - d00e15139065 - - 3bd420ec162d + - 5b85006245f3 + - e4a053d67e24 - eb085b3dbaf8 - - a58f7eb0df2c - - c0e71cb2bd1b - - 7fbec959cf2b - ca90d17ff51b + - 3bd420ec162d + - c0e71cb2bd1b 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 4fc1aa09e..9ba9a055b 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,48 +2,48 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - ece627528a78 - - 277dc652246e - f28ad96b76dc - - b18329a8ac14 - 0a18ac48ac53 + - b18329a8ac14 - b574b84afc4d + - 277dc652246e + - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - bf06d196e23d - - b41107d8fe89 - - e988563cc6e5 - e215f71d7983 - 525f201b86c1 + - b41107d8fe89 + - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 - - bb6397b94018 - 4fbffddde8cd + - bb6397b94018 + - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - a8157342d9a3 - - f23d67e28cc8 - b8c79e70516d + - f23d67e28cc8 + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 25b83cbd596a - - 59e85306eae5 - a95a82eb4d50 - a69865da6f80 + - 25b83cbd596a + - 59e85306eae5 - 80600735685d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -51,25 +51,25 @@ tools: owner: galaxyp revisions: - e0669b1854b1 - - ed9ed1e6cca2 - - f1897eb07081 - 798da6bdff3d + - f1897eb07081 - 611d80c0e29d + - ed9ed1e6cca2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: + - 74b61bf5bc4b - 5a35e3a8d013 - a7fb9b395ddf - - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - cc430977c8ff - 82f6c2f4332d + - cc430977c8ff - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -77,10 +77,10 @@ tools: owner: galaxyp revisions: - 10566783d718 - - c5aa9fca18c6 - 043f9c91f686 - - d2483487e077 - 1693b2126f30 + - c5aa9fca18c6 + - d2483487e077 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -98,8 +98,8 @@ tools: - name: diann owner: galaxyp revisions: - - ae4dc0c041f9 - 9fa3dbf06f17 + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -111,23 +111,23 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d0ea7589e95f - d263296cd73e + - d0ea7589e95f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - 4081e4faa4ab + - 1c5cbf8f79ce - 0fa397f4f40b 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 @@ -154,8 +154,8 @@ tools: - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -168,70 +168,70 @@ tools: - name: maxquant owner: galaxyp revisions: - - 37d669de2828 - - 1f39c833f65f - 97a7f34fcb6a - - 7f432d87c82c - - 4d17fcdeb8ff + - 8934bc76bb52 + - 1f39c833f65f - 837224ad1694 + - e42225f8a659 - f522c08e900c + - 37d669de2828 + - 4d17fcdeb8ff - 2133b0be850a - - 8934bc76bb52 - - e42225f8a659 + - 7f432d87c82c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: + - 85b8866f06d7 + - 0ed07016d668 - '860429737408' - a72ac2c7cc5b - - 0ed07016d668 - - 85b8866f06d7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 1974224d63c2 - 352b37c66d97 - 4187b6df1a40 + - 1974224d63c2 - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - a1daafbf5233 - - 99450519d727 - 4f359549383c - deaf035bbe9f + - a1daafbf5233 + - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c1343e3389ca - 40ca115438d2 - - c7745841de24 + - c1343e3389ca - e79958768a2c + - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: + - da986f83631b - d46d64e7964d - d2eac53666f0 - b648e45fd3cf - - da986f83631b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - eb811f3018ea + - 9bf325045235 - 1199751329b0 - 944b43462104 - - 9bf325045235 + - eb811f3018ea tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -249,10 +249,10 @@ tools: - name: msstats owner: galaxyp revisions: - - b7034eff0db1 - 8212e342e482 - 28434abe6c5c - 593839e1f2c3 + - b7034eff0db1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -265,9 +265,9 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 01dbaf6a57e0 - 8960fb791701 - 4e77b8f12cd3 + - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -280,10 +280,10 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - c9eff69a7c62 - - 9cdf15d3cfc8 - f7fef900f5b2 + - c9eff69a7c62 - 518b1730cf2a + - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex @@ -298,40 +298,40 @@ tools: owner: galaxyp revisions: - 658494a2cb00 - - 890025d6e426 - 41859bbdc16e + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - 9b7977080f6d - 5ad0b5bf1deb + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 05d5e1ddc985 - - d6878d27f051 - 0bb5056cb775 + - d6878d27f051 + - 05d5e1ddc985 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - febd569ad26f - 52ba9695e752 - 5ad830edc021 + - febd569ad26f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 92352a475eed - - 39e8fde08881 - 27cba4c5fc42 + - 39e8fde08881 + - 92352a475eed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector @@ -345,66 +345,66 @@ tools: - name: openms_idconflictresolver owner: galaxyp revisions: - - 3720e349ba2a - c28f13cab67a - 8a04ed1c1d1b + - 3720e349ba2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c427a8628cbe + - 382cde407f81 - ca799a7246e7 + - c427a8628cbe - c55dddc5844a - - 382cde407f81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: + - 8ddb7bab1138 - b5d0905419da - 39caaa778d2e - - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 18f93351f8b6 - 8d4db262964c - - f817513840a9 - 1c5f31b8d632 + - f817513840a9 + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a - 5d9f175dff81 - 111c3a00136d + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - be74a8cd7d66 - - 0e52c85f3b15 - 476b5e296979 + - 0e52c85f3b15 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - e133b5c8878f - 9866e1170611 + - e133b5c8878f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - 2b2a7551a857 - a407b6790342 - c18d8efa4474 + - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver @@ -417,16 +417,16 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - ee860980edc6 - 8098330f6d91 + - ee860980edc6 - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - a2a6e9551046 - 0ced5bc9f4dd + - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator @@ -439,15 +439,15 @@ tools: - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - 1bf940c18d93 - e8f64a7dc470 + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - f861ec9fbe59 - 9f505cd4428f + - f861ec9fbe59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -489,17 +489,17 @@ tools: owner: galaxyp revisions: - 5ae104d0da6e - - decc397c3b7e - 3d8d4ada5405 + - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - 5182338d5e7c - e039cc5c7aed - 539a3a4dcc9e - dd173849c3d8 - - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -531,9 +531,9 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: + - c8b225c69a7f - fb52e95a370c - 7f6a1f27553e - - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -555,12 +555,12 @@ tools: revisions: - 1beff3ddce58 - 3ec27b4cee7c - - a72c48001f7c - da885ca16cb2 + - 07ff622ec007 - 943a34df6047 - - 3634c90301af - 7fdd9119cc4f - - 07ff622ec007 + - a72c48001f7c + - 3634c90301af tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -614,10 +614,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 265c35540faa - - 12692567c7f9 - a371252a2cf6 - 1a5690a5eedc + - 12692567c7f9 + - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index 477c2cf3a..9a708220a 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 110a346daf36 + - e345aadf914f + - 2f1d464ebfd2 - cd5f98911089 - 289b7d6b69a4 - 42201b90e3f4 - - 2f1d464ebfd2 - - e345aadf914f - - 110a346daf36 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: - - 0345dbaaa79b - - 0cd2df8af811 + - 8501601a118d + - c207119ba5f6 - 42d9087b4789 - fcce77c09289 - - c207119ba5f6 - - 8501601a118d + - 0cd2df8af811 + - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - 33486216eec0 - ad5ab22ffe24 - - 421c33b8bf17 - - 405a212b32ab - - 04db7fd6b238 - 89eb29319bf4 + - 33486216eec0 + - 04db7fd6b238 + - 405a212b32ab + - 421c33b8bf17 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,9 +53,9 @@ tools: - name: stacks2_gstacks owner: iuc revisions: + - 1d839ead7ad3 - eb784fa07f80 - f6e91108b7b1 - - 1d839ead7ad3 - fa51dc5e8386 - 7b72fde3d27e - 7370bb65bad4 @@ -71,11 +71,11 @@ tools: owner: iuc revisions: - c9b77ced9a78 - - 3d70c2996730 - a3e86cd9cac7 - - 1544278c272e - 8a55d29c8fcf - d30e36c48c93 + - 1544278c272e + - 3d70c2996730 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: - - 7b881f5f5ad5 - - e2db212d64ad - - b242deb58952 - 887cf585cafc + - b242deb58952 - a5969aa9347e - 564c33e5c3e3 + - e2db212d64ad + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - - 8cff84759bf6 - b4bab607eb05 - - 9a171f9a450b - bd5ff77e2036 + - 9a171f9a450b + - e897c74a48bb + - 8cff84759bf6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 6dafad990086 - 887e0991eb24 - 5e10f396979e - - 33f0793edf93 - - adc7a7610d4f - 4f65e343ecdf + - 6dafad990086 + - adc7a7610d4f + - 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: - - c287418eb288 + - 97575d01f06b - 4e280b27a831 + - c5d7050e4ad7 - 43e3eeb2e0ec - - 97575d01f06b - 17d39bf0a63a - - c5d7050e4ad7 + - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,11 +154,11 @@ tools: - name: stacks2_sstacks owner: iuc revisions: + - d9bf483266a1 - 09b8edb56d80 - 9586f08634c0 - a819ec3b362d - 0b8c84a7fdb5 - - d9bf483266a1 - cd034465d4a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,11 +171,11 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - 69842dd5aa48 - - a9c34a289493 - bf0e43ab0416 - - a4b4bd84f69e - 95351dd0fd3f + - a4b4bd84f69e + - 69842dd5aa48 + - a9c34a289493 - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -188,11 +188,11 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - d033e1ccb386 - - bb0475c884ff + - cfb504394ae1 - 912f904a6e1e - 8a35a3bc6752 - - cfb504394ae1 + - bb0475c884ff + - d033e1ccb386 - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -235,8 +235,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - d504d945a655 - d1fad35bdb4a + - d504d945a655 - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index aedeb99de..bc20f4ea8 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,24 +2,24 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - 2d4e3aff9dc7 - cf01dd6c6b1f - 31f8063eedea - - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - 703a2cb3fb38 + - 125d20cb23d7 - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - 01ccd366690d + - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -56,8 +56,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - e66b9b5b8580 + - f648e5180e40 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -70,8 +70,8 @@ tools: - name: cuffmerge owner: devteam revisions: - - 86285ddd4512 - cf747d1bd79a + - 86285ddd4512 - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -84,8 +84,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 9a854107dbb2 - 6cbfede05833 + - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -109,10 +109,10 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - - e3b16fd7dd08 - 3b36efd62b3e - 8f0181aacb7a + - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -124,12 +124,12 @@ tools: - name: deseq2 owner: iuc revisions: - - 24a09ca67621 - - cd9874cb9019 - 6a3a025714d3 + - 24a09ca67621 - 9a882d108833 - d027d1f4984e - 8fe98f7094de + - cd9874cb9019 - 0696db066a5b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -143,9 +143,9 @@ tools: owner: iuc revisions: - 62adf13b86ea - - 2872c633f07e - - b47c006d90c5 - df929f257179 + - b47c006d90c5 + - 2872c633f07e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -157,16 +157,16 @@ tools: - name: edger owner: iuc revisions: - - 555659de7321 - - 0cb907a2a810 - - 070900306913 - - 3d89af8a44f0 - - f2843df56434 - - 6e53e565fc6a - 9bdff28ae1b1 + - 6e53e565fc6a + - 555659de7321 - a8305cf0c951 - - df0c8d0a5992 - 334ce9b1bac5 + - f2843df56434 + - 3d89af8a44f0 + - 0cb907a2a810 + - df0c8d0a5992 + - 070900306913 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -197,17 +197,17 @@ tools: - name: featurecounts owner: iuc revisions: + - 38b6d12edc68 + - a56fbe2d6ba7 - ea04b737afa0 + - af814359d244 - a37612abf7f9 - f3a5f075498f - - a56fbe2d6ba7 + - e6a2a912677a - f9d49f5cb597 + - 90d16db017d7 - 6f66ae7c5f7a - - e6a2a912677a - 7db9d3ea71c9 - - 90d16db017d7 - - af814359d244 - - 38b6d12edc68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -251,13 +251,13 @@ tools: - name: hisat2 owner: iuc revisions: + - 6c19daec423d + - 26371a1df031 + - 3fb01a8c902d - d4b55e2beb12 - f4af63aaf57a - - 26371a1df031 - - a86e80d3c09c - 6ab42baa56e9 - - 6c19daec423d - - 3fb01a8c902d + - a86e80d3c09c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -294,11 +294,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - ce5d418183c5 - 01247aaf0a10 - - 87c11c05d238 - 1c75aa5de15e + - 87c11c05d238 - 5ae5c312d718 + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -310,10 +310,10 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 10c98fab6c5a - c971db6f0fe5 - - 40985510cd98 + - 10c98fab6c5a - 4f9c4e6566e5 + - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -325,13 +325,13 @@ tools: - name: limma_voom owner: iuc revisions: - - 32511f586472 - 97e06a4c7c75 - - 0921444c832d - e827f9aae031 - - 58c35179ebf0 - - d6f5fa4ee473 + - 32511f586472 - 708348a17fa1 + - d6f5fa4ee473 + - 0921444c832d + - 58c35179ebf0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -392,18 +392,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - 4df95e2d7f61 - - e132e7d02a3e - - 3ea5a2a63fa2 + - c7c55b694974 + - 5ec75f5dae3c + - c772497b2c32 + - 99b17b74a8cd - b9e04854e2bb - 0a563fd2f22e - - c772497b2c32 + - 980d2a2e1180 + - 4df95e2d7f61 + - 3ea5a2a63fa2 - 7ed2edc1337f - - c7c55b694974 - 4074fc1940e2 - - 980d2a2e1180 - - 99b17b74a8cd - - 5ec75f5dae3c + - e132e7d02a3e - 79de45b5069b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -428,13 +428,13 @@ tools: - name: salmon owner: bgruening revisions: - - 15cd64d7c58b - - e3d32471da11 - - ebab418107f5 + - 49121db48873 - 53e9709776a0 - - 2c0ca397d302 - cc05793bb896 - - 49121db48873 + - ebab418107f5 + - 2c0ca397d302 + - 15cd64d7c58b + - e3d32471da11 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -447,21 +447,21 @@ tools: owner: iuc revisions: - fab6ff46e019 - - c0fd285eb553 - - 56242ff81c84 - 8c28affc7c48 + - 56242ff81c84 + - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 914cfcba0ec8 - - dd4df992d93d + - ae618321f34a - 258d696dbd7e - - 76d290331481 - 1ebd14235b92 - cef79931dda5 - - ae618321f34a + - dd4df992d93d + - 76d290331481 + - 914cfcba0ec8 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -491,10 +491,10 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 - c6334cb383ff - 0db979fead3a - ffd1300599a1 + - d0d4cef4f967 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -506,10 +506,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - 74217fbfba4d - - d6a479fd4281 - bcc5f03f1900 + - 74217fbfba4d - ba3720d7e68b + - d6a479fd4281 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -521,10 +521,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 + - 56162e446004 - c2b82a94493e - 2fb4ee002432 - - 56162e446004 + - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -536,9 +536,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: + - 9ff3765e7172 - 3f4094b6a565 - fab23c3b5258 - - 9ff3765e7172 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -550,10 +550,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: + - 34a018cbee9c + - be3f26533209 - 4687ecf0eb2d - 870ac06dff8e - - be3f26533209 - - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -565,11 +565,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 65e7dea767ea - 33406f5a445c - 5192f657f305 - - 05ab8d5e04a2 + - 65e7dea767ea - c5fbddcac63a + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -581,10 +581,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - e406ac71165d - a35cba31d904 - 6f0fb35b799c + - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -596,10 +596,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 - - 7c7fbf13aadd - 37a1129c89d2 + - 964b7efe2639 - c2c039e421af + - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -612,9 +612,9 @@ tools: owner: iuc revisions: - 1d689e4e1caf + - 047c22569787 - eafea3083352 - 24e94d84adc9 - - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -626,9 +626,9 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: + - 9871104ea630 - 3a4ac03d1266 - 1812dbc5bb7b - - 9871104ea630 - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -641,15 +641,15 @@ tools: - name: trinity owner: iuc revisions: - - 9fa24d5aac68 - - 8f1c3df4dd49 - d2bc35f3d1c5 - - db1f362cca3e - - cee61b3fcf78 - - c9cfec002f71 - - 32b86cd8eb50 - 48636f857c4b - d84caa5a98ad + - c9cfec002f71 + - db1f362cca3e + - 32b86cd8eb50 + - 8f1c3df4dd49 + - cee61b3fcf78 + - 9fa24d5aac68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -661,10 +661,10 @@ tools: - name: trinotate owner: iuc revisions: - - 6fd16fad465d - - 2b093007fab9 - 9e61bc67866f - 4383070d29ed + - 6fd16fad465d + - 2b093007fab9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index ad071beec..b41c54fe8 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 - 080fd5739bb4 - 1a052c827e88 + - 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 652fb2b20..d9d4e0e8f 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -3,13 +3,14 @@ tools: owner: devteam revisions: - 88eedb4abea0 + - a53efedba9e7 - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc + - a53efedba9e7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -54,9 +55,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 19ece8afbaab - 5f8e69cc4c6e - e7fd6754d093 + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -81,15 +82,15 @@ 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: - - 9bd1568619cd - cf1ffd88f895 + - 9bd1568619cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -108,30 +109,31 @@ tools: owner: devteam revisions: - 56c31114ad4a - - 649a225999a5 - dc6ff68ea5e8 + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - - 12749212f61b + - 6856f8a01905 - 46c6639921f1 + - 12749212f61b + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 46c6639921f1 + - 6856f8a01905 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 06dc50b7b711 - - 92ec40abcdcf - 33208952b99d + - 92ec40abcdcf + - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -158,53 +160,57 @@ tools: owner: devteam revisions: - cc61ade70eb8 - - fe34990e5ce7 - 22970df7a40e - db17d5321bad + - fefd89ab563c + - fe34990e5ce7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - fe34990e5ce7 + - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: + - 88b8c2916784 - 811fc2d75ad4 - - 7a6034296ae9 - 7def34e6cf4d - - 88b8c2916784 + - 7a6034296ae9 + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 7def34e6cf4d + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 740ce0a18f0d - - b40e2d865d52 - 36677f429310 + - 65a38e8c8e2a + - b40e2d865d52 + - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 583abf29fc8e - - 329deb17a9f7 + - b61f5d6a7f25 - 9da0311ab1dd - fa7ad9b89f4a + - 583abf29fc8e + - 329deb17a9f7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 9da0311ab1dd + - b61f5d6a7f25 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -224,14 +230,15 @@ tools: owner: devteam revisions: - db000c6007a0 - - bb8cfc6f6e0c - 30388d878f81 + - d7b4851d1971 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c + - d7b4851d1971 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -243,37 +250,39 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - a4a10c7924d1 - 344fc91e1bfd + - b5c88b7b153e + - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd + - b5c88b7b153e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - cab3f8d35989 - 6c2c1836728b + - a577ea614bed - e613c1ad4c4c + - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b + - a577ea614bed tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - 5d9ae78f34d3 - - b7f7826ef1cd - bcedabb53ddf - 135c85f4cfaf + - b7f7826ef1cd + - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -285,29 +294,30 @@ tools: - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f - 1cc79f49b8d5 - - 145f6d74ff5e + - 3a0efe14891f - 5a08c09b9311 - 24c5d43cb545 + - fed4aa48ba09 + - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f + - fed4aa48ba09 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - 350bbc5c2ffd - - 0dbf49c414ae - - bf328cec6a42 - - c370440f901e - 5826298f6a73 - - b01db2684fa5 + - c370440f901e - b72793637686 + - b01db2684fa5 + - 0dbf49c414ae + - bf328cec6a42 + - 350bbc5c2ffd 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 ee8ba7005..4f708f2d3 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,11 +2,11 @@ tools: - name: ena_upload owner: iuc revisions: - - 4aab5ae907b6 + - a62c4a11a67d - 59bb6d34fca6 + - 4aab5ae907b6 - 6f6537780379 - - a62c4a11a67d - - d147d6455873 - 480d9e9d156b + - d147d6455873 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 a8d708c82..3a1e69f41 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -5,6 +5,7 @@ tools: - fb9e030ffae4 - 00712416fdaa - 55e35e9203cf + - 93dd15e13e6a - 32e547223c9e - cfc3f5a57dc6 tool_panel_section_label: Single-cell @@ -12,17 +13,17 @@ tools: - name: anndata_import owner: iuc revisions: - - fb9e030ffae4 + - 93dd15e13e6a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: + - 038e32885fec - b9fac48532eb - - ee98d611afc6 - 688357ad5e61 - - 038e32885fec - 39e945f0b2c1 + - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -34,12 +35,12 @@ tools: - name: anndata_manipulate owner: iuc revisions: + - 43cb7b5a6fe7 - 3d748954434b - b85871dd69f9 + - ed4996a16f7f - d4af736e7b83 - 9bd945a03d7b - - 43cb7b5a6fe7 - - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -72,8 +73,8 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -86,8 +87,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -100,8 +101,8 @@ tools: owner: iuc revisions: - 7e014059a88d - - f911a64454fb - 0bff0ee0683a + - f911a64454fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -119,9 +120,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: + - 37a47c4fd84d - f3eb2291da05 - 2b0d3e2f402a - - 37a47c4fd84d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -147,8 +148,8 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - 2af7c5086a96 - 44b935f2271b + - 2af7c5086a96 - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -162,8 +163,8 @@ tools: owner: iuc revisions: - 77b91b9bdf52 - - b2df381a6004 - aaa5da8e73a9 + - b2df381a6004 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -175,9 +176,9 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 3c86f71498bc - - b409c2486353 - a97abb8cd15b + - b409c2486353 + - 3c86f71498bc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -189,24 +190,25 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - c5d3684f7c4c - - 6c145a6868cc - 5e9171dc8244 - cc0deb593fc8 + - 6c145a6868cc + - 3081ff5c84a3 + - c5d3684f7c4c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - c5d3684f7c4c + - 3081ff5c84a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - a407e7f8bdc1 - ab55fe8030b6 - 3bcd5445cd7a + - a407e7f8bdc1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -219,29 +221,31 @@ tools: owner: iuc revisions: - dbbe1ea8ecb1 - - 6adf98e782f3 + - 9b0cdb8cf6be - aa0c474463c2 + - 6adf98e782f3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - aa0c474463c2 + - 9b0cdb8cf6be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: + - bf2017df9837 - f2f6c703da06 - - 73ab2ac53d06 - 215733a383f2 - - bf2017df9837 + - 73ab2ac53d06 + - 458e8f43a775 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 73ab2ac53d06 + - 458e8f43a775 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -261,9 +265,9 @@ tools: - name: scater_filter owner: iuc revisions: - - 652923ce664f - - b7ea9f09c02f - 7a365ec81b52 + - b7ea9f09c02f + - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -275,9 +279,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - 81e5bdff4853 - ef4c80837bc5 + - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index b4956b3e8..6166659f5 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 - - 562f3c677828 - 419027d822d6 - 4c07ddedc198 + - 562f3c677828 + - 2f3c6f2dcf39 - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -63,15 +63,15 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 6c29c7e347e8 - cb1c59d69557 + - 6c29c7e347e8 - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,41 +120,41 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - aef56d0e7a61 - 4c4ec859c31a - - 840f29aad145 - 9c3e1d3235c8 - b1eda492f063 + - 840f29aad145 - 7442b94d6a1e - - aef56d0e7a61 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: + - d0352e8b4c10 + - 375bbd555f4a - 9fda0b82f419 - 07843f917990 - 30d21a6041f6 - - d0352e8b4c10 - - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 2c58b83c9bad - - 4cc980df6265 - 8b1b2b91f8d0 - - cd02bf168d23 + - 4cc980df6265 + - 2c58b83c9bad - 7ae443e6217d + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - bb9fc9d46ea4 - - ad7e0b4291ee - - 1dd433d2c92c - 7dd3fb35904f + - 1dd433d2c92c + - ad7e0b4291ee + - bb9fc9d46ea4 - e10e776f2109 - 4bbaf77573ef tool_panel_section_label: Statistics diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index 989bf0f36..4c86b190c 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -8,8 +8,8 @@ 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 @@ -28,14 +28,14 @@ tools: - name: column_maker owner: devteam revisions: - - 6e8d94597139 - 02026300aa45 - - 6595517c2dd8 + - be25c075ed54 - 464b9305180e - 9cd341095afd - - 13b6f0007d9e + - 6595517c2dd8 - 626658afe4cb - - be25c075ed54 + - 13b6f0007d9e + - 6e8d94597139 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -100,20 +100,20 @@ tools: owner: devteam revisions: - dd40b1e9eebe - - f2aac0c5c60d - ae7843d06f8f + - f2aac0c5c60d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - 2e8f945f7285 - - 3a6b78c39dca - 623f3eb7aa48 - - 33d61c89fb8d - 83069b38aa85 - - 1ea4e668bf73 + - 33d61c89fb8d + - 3a6b78c39dca - cf34c344508d + - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace @@ -134,26 +134,26 @@ tools: owner: iuc revisions: - b722161a845a - - f768f6183386 - bce29ec10b78 + - f768f6183386 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: - - 74a8bef53a00 - - ddf54b12c295 - - f46f0e4f75c4 - 9ff72e942410 - - 0a8c6b61f0f4 - d698c222f354 - a6f147a050a2 + - 0a8c6b61f0f4 + - 74a8bef53a00 + - f46f0e4f75c4 + - ddf54b12c295 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 80d8b63bc..78fbabe2c 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -2,8 +2,8 @@ tools: - name: breseq owner: iuc revisions: - - 82fb5e3bb93e - 0d18a3ba2d1c + - 82fb5e3bb93e - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -16,32 +16,32 @@ tools: - name: freebayes owner: devteam revisions: + - a5937157062f + - 04fa42777df9 - 57def2d7c093 - ef2c525bd8cd - 156b60c1530f - - a5937157062f - - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 435b157bed6d - 791f73caa0c8 - 09d6e4693887 - e61c9ac190ad - - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 074d44697036 + - 4805fe3d8fda - 3b4b2121842f + - 074d44697036 - e1461b5c52a0 - - 03627f24605f - 65432c3abf6c - - 4805fe3d8fda - dfadc322b065 + - 03627f24605f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter @@ -56,17 +56,17 @@ tools: owner: iuc revisions: - 426d707dfc47 + - 971e07ca4456 - c27549b9aa1f - f4473557ffc7 - - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - dbd9f2db9ed8 - - aa35ee7f3ab2 - cdaab621d454 + - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -84,11 +84,11 @@ tools: - name: snippy owner: iuc revisions: - - c9a8ef2aa380 - - 9bccc8404a3c - d220115f882b + - c9a8ef2aa380 - 5bbf9eada9c2 - fa016f1eea1a + - 9bccc8404a3c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -130,19 +130,19 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - ee4a90760848 - 40f0591deda0 - 3b1e7c170b10 - 32f14a2723ec - e7aff4a85df5 + - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 02d81b994ef5 - - adc0645b945c - 4934c0ac6197 + - adc0645b945c + - 02d81b994ef5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_somatic diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index bc183f6a2..7ac057ac7 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,13 +2,13 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - e075b1be5abb - - 3f62d4939d54 + - 6a88248893c4 - 8a2e296c07ef + - ebe5fc018e72 + - 3f62d4939d54 + - e075b1be5abb - b7ea370b8f5d - 265fe0f9ea64 - - ebe5fc018e72 - - 6a88248893c4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -20,13 +20,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - c37b684e7f4e - - 22637b1a55bf - 21687e35f066 + - 22637b1a55bf + - c37b684e7f4e - b03984136ce4 - - 544cb432072b - - f0d44631365f - 0fba2c15b40d + - f0d44631365f + - 544cb432072b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -38,14 +38,14 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 6d35a3780bfd + - 3a7084316a6e - 8408bffd5616 + - 6d35a3780bfd + - 0238f68ad641 - 01d6b7d6365e + - 8ca3647c90fd - bf1f4994f104 - 8627b2b383b4 - - 0238f68ad641 - - 3a7084316a6e - - 8ca3647c90fd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -58,13 +58,13 @@ tools: owner: iuc revisions: - 9b5abbf50d23 - - 6b6c992d3a14 - - 62ca6da715bf + - 08296952d12f - 81426b3cf18b - - f430a1ec7ee4 - - d144af39073a - 03e0645395d2 - - 08296952d12f + - d144af39073a + - 62ca6da715bf + - 6b6c992d3a14 + - f430a1ec7ee4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -77,12 +77,12 @@ tools: owner: iuc revisions: - d37e313a41be - - d3081540d175 - 1829900b5dcd - - 95c6f3f4c77f - e522022137f6 - - 2363ef414c9b - 147de996e34f + - d3081540d175 + - 2363ef414c9b + - 95c6f3f4c77f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -94,12 +94,12 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 92c0aff8b53e + - cacc9970727a - 1137ce8efc1e - 348cd212dbad - - 9b29129fb491 - - cacc9970727a - 09f37afb3621 + - 9b29129fb491 + - 92c0aff8b53e - b14ff40958cb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -113,11 +113,11 @@ tools: owner: iuc revisions: - 55c0e906c14c - - 4935320a59a8 - - 1f2183a23823 - de68c11034f6 - 367ba501b6eb + - 1f2183a23823 - ecc9192912b8 + - 4935320a59a8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -129,12 +129,12 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 039ea3f1dea9 - - ae68ceb4cca3 - f01b2c9506b9 - - 64a8f7dae3ad - - 6c790a091c7c + - ae68ceb4cca3 + - 039ea3f1dea9 - 7cbf3c66d4ad + - 6c790a091c7c + - 64a8f7dae3ad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -146,13 +146,13 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 963a3635b2e1 - - cdb7b4927742 - e7452697afd9 - - 277719af4dd7 - 656a916779fe - - 6ea7170a016d - 33bd9301568c + - 277719af4dd7 + - 963a3635b2e1 + - cdb7b4927742 + - 6ea7170a016d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -164,11 +164,11 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 501bfb078342 - a1213a0b7b66 + - 501bfb078342 + - 3eac729e66c9 - 5a321fab1fe4 - a29a2f40b665 - - 3eac729e66c9 - b7f0f59baa7e - 26d97cdd5410 tool_panel_section_label: VCF/BCF @@ -182,14 +182,14 @@ tools: - name: bcftools_isec owner: iuc revisions: - - c803c34361e0 - - 768d04526638 - - 709dd8291b83 - d7d1663559e9 - - 5f27e814a119 - - 63aabc920911 - 81e4014fa809 + - 709dd8291b83 + - 63aabc920911 - 97d19c008d15 + - c803c34361e0 + - 5f27e814a119 + - 768d04526638 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -201,13 +201,13 @@ tools: - name: bcftools_merge owner: iuc revisions: + - b931e65638b8 + - 86296490704e + - b1eba148b35b - 7ba36babba2d - 85ee7e6c4204 - - 86296490704e - af163c712539 - - b931e65638b8 - 2215287d5cc9 - - b1eba148b35b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -219,15 +219,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 03191140c66a + - ce9396ddcb2b - 5660b21a0dbd - 31ea13dfe5e6 - - cf06b44624c7 + - 4e1d23e5c691 + - 9c711df3258d - f506df85c652 + - 03191140c66a + - cf06b44624c7 - 37757ffb4c5f - - 9c711df3258d - - 4e1d23e5c691 - - ce9396ddcb2b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -239,11 +239,11 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 6deb4d549bc9 - - a404f786a94c - - 021693fdadaa - ebb2e12a6de1 + - 6deb4d549bc9 - 19905c025d2a + - 021693fdadaa + - a404f786a94c - 48291658fdf6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -256,13 +256,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 71c78e0eea52 - f7879f1e77f9 - - 69d8b7567281 - - 5ad5d4243987 - c450406f722b - 97e8145d7e30 + - 5ad5d4243987 - be6b217710af + - 69d8b7567281 + - 71c78e0eea52 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -274,13 +274,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 79f7a1acc2cd - - 0fe007201caf + - 89720ec3d58e - cc7f9a4e186b - - 52f9e4a660e3 - - 2514e684f8a3 - d31a2e310a52 - - 89720ec3d58e + - 0fe007201caf + - 2514e684f8a3 + - 52f9e4a660e3 + - 79f7a1acc2cd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -292,12 +292,12 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: + - 80e6e399ccd0 - 1411bef27a75 - 230e424bde67 + - 75ddd081f608 - 99f4a81a47be - - 80e6e399ccd0 - 0a62420cb9cd - - 75ddd081f608 - 026a989b7cee tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -310,13 +310,13 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - bca7ce81688f - - 444e6a756c35 - - 5acfca5a76af - 5808f77b2bb6 - - c01be0ab9806 - e493702b19eb + - bca7ce81688f + - 444e6a756c35 - ba20340426fe + - c01be0ab9806 + - 5acfca5a76af tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -328,12 +328,12 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - 12152af85697 - - 157ffcdd3fa7 - - 7fe09ad6a939 - 68fec03a63b7 + - 12152af85697 - d52b8947b269 - f2482aa4862e + - 7fe09ad6a939 + - 157ffcdd3fa7 - 4d236c696844 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -347,11 +347,11 @@ tools: owner: iuc revisions: - 8dbce095986c - - 29ba253e2e05 - - 0e5d11004815 - 6f8e223f78f3 - - 27e2611639a9 + - 0e5d11004815 - cbe39e530cbf + - 29ba253e2e05 + - 27e2611639a9 - 8f2fc0ab30fb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -364,13 +364,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 9708e3086f32 - - 88bb477f45f7 - - a8630d4fbaf8 - - 3ff5654b4e7d + - af36eb5418fe - a367a15c6de5 - e0a856def0b0 - - af36eb5418fe + - a8630d4fbaf8 + - 3ff5654b4e7d + - 88bb477f45f7 + - 9708e3086f32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -382,13 +382,13 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 96d0145c041a - - 4ed46189d6c6 - 03e30f06f15f - - 6ce175385dd9 - 31c096c6b156 - - 5c9729d54721 + - 4ed46189d6c6 - 2f4eef1f0d22 + - 96d0145c041a + - 6ce175385dd9 + - 5c9729d54721 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -400,13 +400,13 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - a1aad8b559c6 - - 09f5e45a8212 - - 11af7fce71cf - - 46eb13bc2c73 - - 262bba5b90ef - 40daf124be88 + - 11af7fce71cf - 2c4941386820 + - 262bba5b90ef + - 09f5e45a8212 + - 46eb13bc2c73 + - a1aad8b559c6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -418,14 +418,14 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 6cbb9c47795c - - 0594ea1417c8 - - 743cd1472aeb - - 12038f59c0f4 - f272b8ba0983 + - 12038f59c0f4 + - 882b2e649602 + - 743cd1472aeb - 8cb121b6a1d2 + - 6cbb9c47795c - 4b796b58938b - - 882b2e649602 + - 0594ea1417c8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -437,13 +437,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - 18cf9de1cf73 - - cced6715f926 + - adee7e8b746f - eccb508bb678 - 238f78e38a8b - - adee7e8b746f - dba06328556a - 8c3ff4ef1190 + - 18cf9de1cf73 + - cced6715f926 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -455,13 +455,13 @@ tools: - name: bcftools_query owner: iuc revisions: - - a850902cac64 - - c9935c9e8a24 - - 3ce32adc55b2 - e53501abf992 - e0ad88dec40d - - 9f36041495a3 + - a850902cac64 - f64e7ca2efd2 + - 3ce32adc55b2 + - c9935c9e8a24 + - 9f36041495a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -473,13 +473,13 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - fd3539749127 - - d43eb39b989e - - b7be725976b6 - d68c43202172 - 4db0695a6fc7 - - 8057cf55fa41 + - fd3539749127 - 79489d5685dd + - b7be725976b6 + - d43eb39b989e + - 8057cf55fa41 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -492,11 +492,11 @@ tools: owner: iuc revisions: - 58091e1be01b - - 1ccf0e7fb4f6 + - bdc67eeb0bc9 + - 78cd8b69da4c - 5296d26b0373 - b0d39ef600a7 - - 78cd8b69da4c - - bdc67eeb0bc9 + - 1ccf0e7fb4f6 - 6a636d58dfc2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -509,13 +509,13 @@ tools: - name: bcftools_stats owner: iuc revisions: + - e8af591435d1 - '388983871932' - - baa8823f8073 - b641062a2587 - - e8af591435d1 + - 4d3ce9dc1525 - b17394940c7a - a2f8dc22d7c0 - - 4d3ce9dc1525 + - baa8823f8073 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -527,13 +527,13 @@ tools: - name: bcftools_view owner: iuc revisions: - - 59fa8742285e - - e6b5cbbf449b - - 38d75661c235 - abc3ced31cd1 + - 3ca3de4e5291 - 3a233c8eb814 + - 59fa8742285e - d1f8f55f564d - - 3ca3de4e5291 + - 38d75661c235 + - e6b5cbbf449b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -545,15 +545,15 @@ tools: - name: vcf2tsv owner: devteam revisions: - - e92b3c0f9224 - 285060661b45 + - e92b3c0f9224 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo owner: devteam revisions: - - 6ea73d6151ec - afc0ba768690 + - 6ea73d6151ec tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives @@ -566,8 +566,8 @@ tools: - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -580,8 +580,8 @@ tools: - name: vcfbedintersect owner: devteam revisions: - - 9edfe5145ba8 - aea8e90ad788 + - 9edfe5145ba8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -594,8 +594,8 @@ 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 @@ -615,23 +615,23 @@ tools: - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - eae7c08ebb6f - - fa24bf0598f4 - 6b935ab36d7b + - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -651,8 +651,8 @@ tools: - name: vcfgenotypes owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -665,8 +665,8 @@ tools: - name: vcfleftalign owner: devteam revisions: - - 29f9b782727e - d2406f98a782 + - 29f9b782727e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers @@ -724,7 +724,7 @@ 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 2061832a3..cc7318fe7 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: + - 4efdca267d51 + - c2ef298da409 - 6e9aea89e388 - 3f3e247c053d - - 4efdca267d51 - 78c75f134c16 - - c2ef298da409 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,37 +36,37 @@ tools: - name: annotatemyids owner: iuc revisions: - - fe3ca740a485 - - 1aae04680c4b - - 3e1f6f6d557e - - b5d8e5475247 + - 4f2967b27e67 + - 133f36c29579 - f29602ae449e - 44018dd6b447 + - 1aae04680c4b + - b5d8e5475247 - cd2480f35935 - - 4f2967b27e67 - - 133f36c29579 + - 3e1f6f6d557e + - fe3ca740a485 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: - - 6519ebe25019 - dc027fa56d55 - 7be22100e5e1 + - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - ca6d970d931c + - 09855551d713 - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -79,8 +79,8 @@ tools: - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - fe48aa4ccd5e + - 7355bbf5e05f - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -105,9 +105,9 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - 63662ae295d6 - 9d1fbff733cf + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -125,18 +125,18 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - b6b5cd37f2a2 - - 9f2455341fac - 582fd74dc2a1 - 14f588312c56 + - 9f2455341fac + - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - a230ea445788 - 989f7c061f35 - 73428a792541 - - a230ea445788 - 30fb23d4c31c - 0ffe5be70caf tool_panel_section_label: Annotation @@ -145,29 +145,29 @@ tools: owner: iuc revisions: - 494f0bb4a993 - - 5a5ae61da69c - - 563a19373357 - 30f08d74024f + - 563a19373357 + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f31125bb85ea - - d6c7106b7b2e - - 1bc5a03faf2e - 2bba2ff070d9 + - d6c7106b7b2e + - f31125bb85ea - 7abc5f6dd595 + - 1bc5a03faf2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - 520e30695ec3 - - d3af38b9c7e1 - - b3cf4684e9c7 - 52af33194019 - 54961e026fe4 + - d3af38b9c7e1 + - b3cf4684e9c7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -179,9 +179,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 79261884facd - 07d7991bf205 + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -193,10 +193,10 @@ tools: - name: goseq owner: iuc revisions: + - 8b3e3657034e + - 43798b4caee0 - ef2ad746b589 - 602de62d995b - - 43798b4caee0 - - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -214,16 +214,16 @@ 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: - - 98cafcbd2578 - - c55643c3d813 - 74810db257cc + - c55643c3d813 + - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -241,8 +241,8 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker @@ -256,8 +256,8 @@ tools: - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -296,15 +296,15 @@ 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: snap_training @@ -316,13 +316,14 @@ tools: - name: snpeff owner: iuc revisions: - - 8f92c2b26e6d - - cfcf33df7fc0 - - 5a29ab10dba6 - 5c7b70713fb5 - - 268d162b9c49 - - 5b80f544c67f + - 9473cd297a76 - 68693743661e + - 5a29ab10dba6 + - 5b80f544c67f + - cfcf33df7fc0 + - 268d162b9c49 + - 8f92c2b26e6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -349,15 +350,15 @@ tools: - name: tbprofiler owner: iuc revisions: - - ba6f87115e13 - - 45083d070fb8 - 037a11682176 - 2c68b0c38785 + - 37213cf56392 - ac8250086ac3 - - 200c378d85f3 + - ba6f87115e13 - e1a9d6fd258d + - 45083d070fb8 - 809dfc93d593 - - 37213cf56392 + - 200c378d85f3 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 486476edb..832b6796c 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,42 +2,42 @@ tools: - name: abyss owner: iuc revisions: - - 8f1b150a2487 - fa5259cc561b - - 0e93176640ac - 890b794c997d - - 553bfe8bd0b5 - 841084c5fc46 - - a929ce596a34 - 7547fcab5d19 + - 553bfe8bd0b5 + - a929ce596a34 + - 8f1b150a2487 + - 0e93176640ac tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 067592b6b312 - - 94fe43e75ddc - b9e31c5c01c7 - - b2860df42e16 - 21e491ad532a - ddddce450736 + - 94fe43e75ddc + - 067592b6b312 + - b2860df42e16 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 321347bd0494 - 25ca5d73aedf + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - 3371c5bdc17a + - a7f16f24e9a1 - faee8629b460 - 5258e18bbe23 - 22286dab5aa1 - - a7f16f24e9a1 + - 3371c5bdc17a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,28 +49,28 @@ tools: - name: busco owner: iuc revisions: - - bb935709506a - - 46ae58b1d792 - - 2dd755c1c6ff - - 4048d82f0c88 - - e824f5d958d0 - - cf13a1e03e5b - - 41030a6c03b7 - - 0d243f458b53 + - 602fb8e63aa7 - 1440ae06552f - e4bd1e99bacf - 5ecdeca79a0d + - 46ae58b1d792 + - 2dd755c1c6ff + - 41030a6c03b7 - 94170eee0ad8 - - 602fb8e63aa7 + - bb935709506a + - cf13a1e03e5b + - 4048d82f0c88 + - 0d243f458b53 + - e824f5d958d0 - 1e62c28ba91d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - c5b7390290b1 - 86f150c8019d - 5732f959936a - - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -82,11 +82,11 @@ tools: - name: flye owner: bgruening revisions: - - 8d4f03b5fe9d + - cb8dfd28c16f + - 276f5d8712d5 - 3ee0ef312022 - 1ce9b1d72ec3 - - 276f5d8712d5 - - cb8dfd28c16f + - 8d4f03b5fe9d - e27815e82dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -109,10 +109,10 @@ tools: - name: gfastats owner: bgruening revisions: - - 3fba9c77550a - 690c2caa367e - 5127a713de83 - 3ef480892a9f + - 3fba9c77550a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -124,20 +124,21 @@ tools: - name: hifiasm owner: bgruening revisions: - - 366a11d316a7 - - 045c7c3d8e59 - - 3f7be05a1597 - - 60024a528cbd - - f3c89da3af16 + - 5f625c63b8bc + - 0ee0c3089254 + - 5bec28269d95 + - 6505bd37670d + - 9ef6920c3089 - ec9e21e9c71b + - 60024a528cbd - da9d8bf98802 - 2061fb3b81b4 - - 6505bd37670d - - 41cea2aa2dce - - 5bec28269d95 - - 9ef6920c3089 - 71740308d412 - - 5f625c63b8bc + - 045c7c3d8e59 + - 41cea2aa2dce + - 366a11d316a7 + - f3c89da3af16 + - 3f7be05a1597 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -155,37 +156,37 @@ tools: - name: megahit owner: iuc revisions: + - 14ddfc8ffb93 - de387b2b2803 - 7518ee87b53d - - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 9d79beb19ac3 - 39edec572bae - f8113c25bc6b + - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - - 29dabd8db6f2 - eadfd71dde37 + - 29dabd8db6f2 + - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - f338e9942b27 - e731ea24e48d - 606b09cc9860 - eb7a370f6588 - - 2ecf5a570907 - 3ca2d2a9068c - fd128c111ab0 + - f338e9942b27 + - 2ecf5a570907 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -197,11 +198,11 @@ tools: - name: miniasm owner: iuc revisions: - - 80d1250bd5fd + - 73a3846701e1 - 8dee0218ac7d - 8b6d0d85252b - a7b889b90140 - - 73a3846701e1 + - 80d1250bd5fd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -213,9 +214,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - 15200570e926 - 64a1c751d99b + - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -227,73 +228,73 @@ tools: - name: pretext_map owner: iuc revisions: - - 2b16ba799da9 - 02831bf9e95f - - d256a51a656b - - dfb8a4497339 - bbe19ef04a74 - 8fef980d48b5 + - 2b16ba799da9 + - dfb8a4497339 + - d256a51a656b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: + - e9bd16ba5ebd - a315c25dc813 - 76d4cbefff85 - - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 342a1d1fed7b - - 3061c8b029e5 - 59db8ea8c845 + - 7594365c546b + - 3061c8b029e5 + - 342a1d1fed7b - 875d0f36d66f + - ebb0dcdb621a - 6fcbee531de6 - 72472698a2df - - 7594365c546b - - ebb0dcdb621a - 675488238c96 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 78c533842eeb - - aa39b19ca11e - - d865b62f501c - a199cd7ac344 + - d865b62f501c - 39bed8de8017 + - aa39b19ca11e + - 78c533842eeb - cd06929b224b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - 2b2a352488fa - - f8564b2d7f63 - - 33b7d8481a76 - f11b994b7eb2 + - 33b7d8481a76 + - 2b2a352488fa - 3edba9afc9bc + - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - 378e55aeeb25 + - 53c2bc8c2ae3 + - ef69617ecb42 - 1d06c8b38e77 - e122f9101584 - - ef69617ecb42 - - 53c2bc8c2ae3 - - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - ba7b0f11e470 - ab5b7f6b7198 - 9a22227bb6d0 + - ba7b0f11e470 - f77f7a7f3b83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -306,169 +307,169 @@ tools: - name: shovill owner: iuc revisions: - - 83ead2be47b2 - - 196a599ec43d - - f698c7604b3b - - ee17a294d3a3 - 865119fcb694 - ad80238462c1 + - f698c7604b3b + - 83ead2be47b2 - d9f6a00b6db7 + - ee17a294d3a3 + - 196a599ec43d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5a0ddb4dc3a4 - - 24e471d13fe9 - 5e0825476fb7 + - 24e471d13fe9 + - 5a0ddb4dc3a4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 1fc82fe7ebef - - 7490b213baa9 - 051fd2db8a27 - - 1bb12736175c - 904bf932cf78 + - 7490b213baa9 + - 1fc82fe7ebef + - 1bb12736175c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - fee85957cebe + - 34305b013402 - ad8b536d1caa - d6e617c4e338 - 808b3a0a6716 - - 34305b013402 - - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - e5a3b75a271f - - 6b5a5842531e - 8d4b90bf9caf - 21da31ed41a1 - b8002c3f7141 + - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 86f66ab58e14 + - 9de69775f512 - 2a10645aeadd - f1532cb33c75 + - 86f66ab58e14 - 328aa71f0f3c - - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 6aad515a5270 - - 85fb02c43042 - 1708851f8804 + - 85fb02c43042 - e41dcb0e913b - 340bc17f49cf + - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - 249f6a28c751 - - b3490b036c5a - d5fb354f745d + - b3490b036c5a - b65a43f70b99 - d159735a6a9f + - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 7897763d14ec - - d2d1df21dfb9 - dd7ad84f3943 + - d2d1df21dfb9 + - 33368fec3b70 - b7829778729f + - 7897763d14ec - 9006e5836729 - - 33368fec3b70 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 8f631679571f - - 505a9833ab5d - - 6f4c8ad6ea01 - ced385aa976d - 189e837009c9 + - 505a9833ab5d + - 8f631679571f + - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - - 19bdfd1e6fe3 + - 356afed970b4 - e59bee4565b3 + - 19bdfd1e6fe3 - 9ded6109434a - - 356afed970b4 + - d40ed4eb0c0e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - ebd801e712bc - 80a17897564d + - ebd801e712bc + - 6dd935e4984b - 4688ae3b49b5 - b23249f81bc4 - - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - 937ea677d437 - - b5e35a2ca4f3 - 59bd28f6265d - cb1e3db43020 - b64696992ee9 + - b5e35a2ca4f3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - 383bb5ad32e2 + - 2628f6790eda - 6015aa0303f2 - - 05bd7504fdb2 - cb4768eeca3b - - 2628f6790eda - - 383bb5ad32e2 + - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 9e3e80cc4ad4 - d10bdad2fd17 - e92675014ac9 - 6e26c9afd301 - 0a3a602cd1e3 + - 9e3e80cc4ad4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f + - 5da9a0e2fb2d - 8d09f8be269e - 920677cd220f - - 5da9a0e2fb2d + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 4a53b89fa703 - 37d88f41c810 - 82398ba86ba7 + - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index 9f04a6e96..d6774a7e7 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,24 +2,24 @@ tools: - name: integron_finder owner: iuc revisions: - - 4768f7f8e93f - 1ae00120dd24 + - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: + - 8e8dc9a1e3e5 + - 31812e7a1315 - ded48b36f3b7 - 1f5641a52664 - - 31812e7a1315 - - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - 5c8ff92e38a9 - - 17fcac7ddf54 - 24a7a95867b0 + - 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 26700f340..35dcfef42 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 204a131e47db - a9c9d768b751 + - 204a131e47db - 159b04e36791 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index 91c7283a8..a07762222 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: + - a1a923cd89e8 - 589e7e57fd6d - dde39ba9c031 - - a1a923cd89e8 - - ce3c7f062223 - - 07e8b80f278c - - e19bebe96cd2 - - 87ee588b3d45 - b28e0cfa7ba1 - 0a5c785ac6db - - a8eabd2838f6 + - e19bebe96cd2 - a68aa6c1204a + - 87ee588b3d45 + - ce3c7f062223 + - a8eabd2838f6 + - 07e8b80f278c 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 2b3cff117..0826d183b 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,28 +8,28 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 - 54f751e413f4 - - 62c9df8382c2 - f921014aba5a + - e8ac2b53f262 + - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - a52d2d93e595 - 2889433c7ae1 - - 5edc472ec434 - - 6f386c5dc4fb - - 0e3cf9594bb7 - e25d3acf6e68 + - 0e3cf9594bb7 - acf4e47b734c + - 5edc472ec434 + - a52d2d93e595 + - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 7900c7ebb..55ed95b86 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - da6bd1975a71 - - c8cdde00b105 - - 095ad4d096d1 - 6ca543ec1bf8 + - da6bd1975a71 + - f4230f116196 - 710301bc46fa - 27ee142314a9 - - f4230f116196 + - c8cdde00b105 + - 095ad4d096d1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -74,15 +74,15 @@ 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: enumerate_charges owner: bgruening revisions: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -101,31 +101,31 @@ tools: owner: chemteam revisions: - 0fac8e2afc13 + - 88076940fa94 - 3b8a9d5ced85 - bfb65cb551d8 - 79cfd9ead848 - - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 55918daa5651 - - 715cd0e87781 - - eb6564a60136 - b46d4b4d995c + - 715cd0e87781 - f5d979cb4b54 + - eb6564a60136 - d532b7e5f64b + - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a - f26afd1b7104 - 5579659312e6 - - fdf2cc80adb5 - dae135dfd519 + - d2f955aea23a + - fdf2cc80adb5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files @@ -139,52 +139,52 @@ tools: - name: gmx_setup owner: chemteam revisions: + - 4da9ee404eab + - 2c349b027a01 + - 070e3ecc3fda - cac1886249a2 - ed736e6eee39 - - 070e3ecc3fda - - 2c349b027a01 - - 4da9ee404eab tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - d1f803b5943c - - 807aa4c9293d - - 2e219a2d9327 - - 525ca7c8065f - c0c9a5024177 - - f197e34c33a9 + - 525ca7c8065f - da8753545526 - 73008ef1f487 + - 2e219a2d9327 + - 807aa4c9293d + - f197e34c33a9 + - d1f803b5943c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 27ea4e1a3f95 - 1809414a9454 - - c4fbab8e03c5 - 61094e01eff9 - 7568ae18908a + - c4fbab8e03c5 - 2c8ed1b52bf7 + - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - d7ec25187599 - - ba83f0923369 - - 730ef07b90ae - 79e8ab8f1e81 + - ba83f0923369 - ccfbd956a2d3 + - 730ef07b90ae tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: natural_product_likeness @@ -196,8 +196,8 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - e6011617c748 + - b59c91adeac1 - e2c36f62e22f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -228,10 +228,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - bf99565cec1f - - 9b48456a96fe - d4c67ced6abc + - 85fad59f8168 + - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index b8c013c88..b137f292c 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - fa56d93f7980 - c97a786e8fb5 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -16,31 +16,31 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: + - 86e2413cf3f8 + - 495a4173006f - 640d3af5d833 - 424aefbd7777 - - 495a4173006f - - 86e2413cf3f8 - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - 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 96ef6bf8d..dd6abd6b8 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: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 830961c48e42 - - 33151a38533a - 25136a2b0cfe + - 33151a38533a - 90981f86000f + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 99edf823b..3374fac49 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -8,29 +8,29 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 6ef0b5664c69 - - f3a19509108a - - 0b3c3ad92827 - dad9da48a09a - 5e1240a87bcb - - e3cbd2287f63 + - 367b1ed91207 + - 6ef0b5664c69 + - f3a19509108a - 4a6ee918c13a + - e3cbd2287f63 - a3b86937ead6 - - 367b1ed91207 + - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - a4db66553a61 + - e177a8ea0bf1 + - 584008e574b2 - 72ed72122deb + - a4db66553a61 + - 33c99804a32f - e525f9ffb9ac - 1b5fc03380d4 - - 54ccb7e1f49a - - 33c99804a32f - - e177a8ea0bf1 - 501c21cce614 - - 584008e574b2 + - 54ccb7e1f49a - bd46669113b9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -56,16 +56,16 @@ tools: - name: fastq_to_fasta owner: devteam revisions: + - 77b41c89d856 - 186b8d913e6c - 8979c288aefb - - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa @@ -84,8 +84,8 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - 154d00cbbf2d + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -103,8 +103,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - 8190f6083c0d - f5c632894818 + - 8190f6083c0d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -116,18 +116,18 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 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: + - 19e45916daf9 - b9b385097f13 + - 63769c4217a7 - 92ac8e086317 - - 19e45916daf9 - 26c6706bfb07 - - 63769c4217a7 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 ec9a52e4e..9b2d00538 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -3,59 +3,59 @@ tools: owner: bgruening revisions: - de72ba3ed6f2 - - e821645ef8fc - c929a006727f - - 29451af70c52 - - a1ca9bccc7f2 - 5f6d123679f4 + - a1ca9bccc7f2 - 268e91e540ee + - e821645ef8fc + - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 5d11599b8a7d - - 7a7fd0f5f15d - - 12af64f93288 - bb1e4f63e0e6 - 0e143b4c3987 - - 0e49b109abc2 - 2d2cf5c1ea8a + - 7a7fd0f5f15d + - 12af64f93288 + - 0e49b109abc2 + - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - dc059492a995 - - 1d848bc4585f - - 81b1e3e1fc6c - c06951d10364 + - 1d848bc4585f + - dc059492a995 - 7c1beb6d6eca - 195e98217334 + - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 07418a30ed01 - - 71aa86af6762 - - 93eb012d9eed - 3d211717a775 + - 93eb012d9eed - bfff7454b59a - a67ac707496a - 26e7304d6737 + - 07418a30ed01 + - 71aa86af6762 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 2bc10a9ca58b - 26983857c91a - dd0b7398bb96 - 5be24eba848d - - 2bc10a9ca58b + - 56d5b797ce84 - b8858746dc1f - 29fcfd36e90a - - 56d5b797ce84 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations @@ -64,143 +64,143 @@ tools: - c3e012dfe21f - ee3a1b0f45f1 - 72bfafe3330b - - 7ef978dc1b8a - 9384cd033f30 - - e6d0bff01239 - 7e6bcd2e5128 + - e6d0bff01239 + - 7ef978dc1b8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fb9cf9c97ec4 - - 9470f29702f8 - - a60c359ec43c - b73e213add0c + - 514fa53b5efb + - fd1275e01605 + - a60c359ec43c - 167788df3b46 + - 9470f29702f8 + - fb9cf9c97ec4 - d9a637e83828 - - fd1275e01605 - - 514fa53b5efb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - ca0616bb2cdf - - e479c7ca5570 - - c34d11ea4ba6 - 2c37ce318bc3 - - 5bffaa8354a1 - 86febdcc4283 + - e479c7ca5570 + - ca0616bb2cdf - a02cfa31e9cb + - 5bffaa8354a1 + - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 2d466b530754 - 01fb6a7654e6 - - 192ef85c0b0b - 1fcb7adc39b8 - - 2d466b530754 - - 004aea905d4d - 69a8621ca2f0 + - 004aea905d4d + - 192ef85c0b0b - 78f405266706 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 137c4beed34b - 2f9e4843f480 - 3c9f0c486cca - d9ce4897dbb2 - - 137c4beed34b - - db940c262830 - 459cfa861f0b - 9ecba5e225a6 - d580d6acd1df + - db940c262830 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - 32e451def88c - - f264afa9fa6f + - bd7db9e2f2cb - fd408d755394 - 2c66e43f1c86 - - bad3ca889618 - fbe773640707 - - bd7db9e2f2cb + - bad3ca889618 + - f264afa9fa6f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 7e361d147872 - 56bce3c82278 + - 3b9d990a0a0e + - 4e12ea27f788 - 231994413f89 - - 7e361d147872 - 9368fbc49c8b - - 3b9d990a0a0e - 7fda5607e777 - - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: + - 4431f39ede55 + - c03c3384cd81 - 94ca68515826 - e65d16fb2724 - - 4431f39ede55 + - d9114ef1c8a5 - ce4ce3316f74 - b1779366c8e9 - - d9114ef1c8a5 - - c03c3384cd81 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - b88ebb3672a1 - 4ed32329e0ed - 793665fff0f8 - - d57251071381 - 2da482e408b8 - - 23f7c5f1fdaf + - b88ebb3672a1 + - d57251071381 - f8fc4e5aff9d + - 23f7c5f1fdaf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 25d830337d31 - - c60570fa602f - - 010e58e9d822 - e4c7985d4585 + - a7849312d328 - a4dfb122e52b + - 010e58e9d822 - ba6efa77fb79 - 512155688d98 - - a7849312d328 + - c60570fa602f + - 25d830337d31 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 4d678170d29b - 69264da0ce77 - - 38e3f226248b - - c899e0ccff8c - - aa200e4f3939 - 00d869ea03a1 + - aa200e4f3939 - 443d9a9d6d11 + - c899e0ccff8c + - 4d678170d29b + - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - aac8444d6681 - 6662b1a8d326 - a2d70c4fd406 - - aac8444d6681 - c361b12d207a - - 10301d137111 - d806504e96d9 + - 10301d137111 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 3c04ad36d..ab3ab6a94 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 7d16de45c021 - 12baadec7809 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -37,15 +37,15 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 3bf57dadf7cd + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort owner: iuc revisions: - - 12b9e285ca1c - e614dcabd870 + - 12b9e285ca1c tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat @@ -58,8 +58,8 @@ tools: - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 5f7003111e32 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 685df40a5..7f313196d 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - 62f5fab76dfb - - 6da3972210ee - 29bdbc353f20 - d82648ad25a3 + - 6da3972210ee + - 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 5b82ad9e5..b307b92dc 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,22 +8,22 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8665bcc8b847 - - c053d4cad713 - - 44e2cc14f75b - - 093678460093 - - de6cebe3c043 - - 4e5056fefd88 - 288f97432497 - - 8c0175e03cee + - 093678460093 + - c5e2e5902201 + - 44e2cc14f75b - 48f587c13075 - - e4691e1589d3 - 5915ea1ec9b1 + - 8665bcc8b847 + - c4b82dce8335 + - c053d4cad713 + - e4691e1589d3 + - 660cffd8d92a - 135b80fb1ac2 + - de6cebe3c043 - 49370cb85f0f - - 660cffd8d92a - - c5e2e5902201 - - c4b82dce8335 + - 8c0175e03cee + - 4e5056fefd88 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -56,9 +56,9 @@ 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 @@ -79,10 +79,10 @@ tools: - name: fasta_stats owner: iuc revisions: + - cd0874854f51 + - 9c620a950d3a - 56022eb50bbd - 0dbb995c7d35 - - 9c620a950d3a - - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -96,8 +96,8 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -110,8 +110,8 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 47e5dbc3e790 - 8611b80a14d6 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -124,45 +124,45 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 03d57fea6482 - f3936d0632cb + - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - c885369b207b + - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: + - 249c8393f2d4 - e39cc71d3ed6 - 35e38452bb3f - - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: + - 74db4cffab1f - 045f0e1043f7 - 54053ea6c77e - - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -188,62 +188,62 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 567d5b3c52b1 + - 529bccd5e4a1 - d5e9e83cd3d8 - 09070cacefd8 - - 529bccd5e4a1 + - 567d5b3c52b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - 0b7ec11b3c7c - - 4bedca26c133 - 8abdedf55101 + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - bdf1ce174e39 - - cb1e251cac37 - - 90858c306551 - 736b8f6ee456 + - 90858c306551 + - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: + - 07497255281e - 7ce1891db6f5 - 421f0af4ee95 - - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - f984bb114520 + - 3599f5451ee2 - b29d37ca9e41 - 02f8a17a4ebd - - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 0c2907307ba4 - - 177f0621c266 - 6027ef51ef91 - e246088b6e34 + - 0c2907307ba4 + - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - 547e8d00f11c - - 377ac2829eac - 61b4cedc8934 - 73194cdd4f57 + - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -255,8 +255,8 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - b4c6f054210a + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -275,25 +275,25 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - 71f649c23021 - bf04bd405d5b + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f - - a535cf1e5da4 - - b557acca0b56 - 8250ea3a1501 + - b557acca0b56 + - 24013bf85a6f - e654095ab143 + - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -305,11 +305,11 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 7accf7407811 - - 9fa7803d1c51 - - 6a675c3aa610 - - 828dba98cdb4 - f3759eec3018 - 27ac32a22ad2 + - 6a675c3aa610 + - 828dba98cdb4 + - 9fa7803d1c51 + - 7accf7407811 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 f9d21cc37..ed0ee3a64 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,36 +2,36 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c - 7b4468117008 - - ce9cd02d5b88 - e41385662e5e + - 64e9a6afdd0c + - ce9cd02d5b88 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: - - e7b2202befea - - 5ec9f6bceaee - - 2b0c9d9fc6ca - - 9da02be9c6cc + - f2e8552cf1d0 - 3d0c7bdf12f5 + - 2b0c9d9fc6ca + - 5ec9f6bceaee - ff9530579d1f - - f2e8552cf1d0 + - e7b2202befea + - 9da02be9c6cc tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution @@ -45,38 +45,38 @@ tools: - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - cc0fd298cc17 - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 8880fb74ef56 - 1f296803dfa3 + - 8880fb74ef56 - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: + - c1a4b5f3b432 + - 1c2db0054039 + - bf675f34b056 - b2f1f75d49c4 - 5e33b465d8d5 - - 9a913cdee30e - - 3d93dd18d9f8 - - bf675f34b056 - 75c93c70d094 - - 1c2db0054039 - - c1a4b5f3b432 + - 3d93dd18d9f8 + - 9a913cdee30e - abfd8a6544d7 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - 084bbd8ba7b8 - 949f01671246 + - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 7946b577d..5b44a1c25 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.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 diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 24b1e4672..0de725b68 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,23 +9,23 @@ tools: - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate 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 @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,8 +79,8 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load @@ -94,8 +94,8 @@ tools: - 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 @@ -130,8 +130,8 @@ tools: - 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 @@ -151,21 +151,21 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 8627a5283..f729cfa4c 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -16,15 +16,15 @@ 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 diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index a23014611..39c9df7d5 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,48 +2,49 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - e9df53a75f3c - b39347891609 - 983bf725dfc2 - - e9df53a75f3c - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - 1c58de56d587 - - 28587613264f - e063168e0a81 + - 28587613264f + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - f5ea3ce9b9b0 - - 6ea73833cf67 - - 9a776b080193 + - 6591f049cf7e + - 4df8de2d0e48 - 83c7d564b128 + - f5ea3ce9b9b0 - e08a7ad4378b - - aad3885b3216 - - c441583adae5 - - 5e6237d58b0c - - 1790dcf3c32d + - e407b9da183a - 653e89d73fc4 - - 4df8de2d0e48 - 734abc7ac21d - - 69ebb7f46e45 - 7068f48d0ef9 + - aad3885b3216 + - 69ebb7f46e45 + - c441583adae5 + - 1790dcf3c32d + - 5e6237d58b0c - 4317d3cb6cba - - 6591f049cf7e + - 9a776b080193 + - 6ea73833cf67 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - - 9aaa46d45472 - - 34758ab8aaa4 - 7863f1abcdda + - 34758ab8aaa4 + - 9aaa46d45472 + - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index e59ca18a1..4fb1231cb 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - a64dc31ab7f2 - 290a11559985 - - 4b519282a05b - - fd59d783248a - 740057a5126d - 7f13dc906cb9 + - a64dc31ab7f2 - c4bde687c846 - - ae9994cf526f + - 4b519282a05b - df7356989ac1 + - ae9994cf526f + - fd59d783248a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,39 +28,39 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 867ab348287d - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 + - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: - - ca7cb0eaad62 - 3b37b1b1c3a7 - - 53460afd5115 - '566197475670' + - 53460afd5115 + - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b - - 3d059e9c2fba - - 10515715c940 - d3a9e32672ec - 391a4cc45fea + - 10515715c940 + - 3d059e9c2fba + - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 - - e3a675da7fd0 - 5fe1dc76176e - - 299307abd804 + - 1acf88921176 - d0fc8b746d57 - 3b12bf9b4b87 + - e3a675da7fd0 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -72,15 +72,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - cf1df6b2220a + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 8f62f666dcb6 - a490b70e46fc + - 8f62f666dcb6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -93,16 +93,16 @@ tools: owner: iuc revisions: - 667e17248bfe - - ca2def38369c - - 4542035c1075 - - 836d1aa3e89a + - 6cd09d7b5f37 - 17359b808b01 + - 112eb40ba6cf + - 4542035c1075 - a6e57ff585c0 - 1cfc579079a6 + - ca2def38369c + - 836d1aa3e89a - 2bb2e07a7a21 - fd5dbf0f732e - - 112eb40ba6cf - - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -121,8 +121,8 @@ tools: owner: iuc revisions: - f1691de443a7 - - fe154a7af404 - 03c13085aecc + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -134,8 +134,8 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - 62e3a4e8c54c + - 85da91bbdbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -154,8 +154,8 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 - 7c9417381ad5 + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -167,22 +167,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 2824d77cd8f8 - - 14e7c35f3d00 - - 59fd173ac850 - - a1abfa420d9d - 7dd841a32245 + - 14e7c35f3d00 + - 360df4999907 - 326a3db8d9d1 - 4ac4e7083b7e - - 360df4999907 + - 59fd173ac850 + - a1abfa420d9d + - 2824d77cd8f8 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 83c573f2e73c - 73b8cb5bddcd - 44608d0193ed - - 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 5da44f582..240e4b143 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 1c8ce7baf..ba242a43b 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -3,17 +3,17 @@ tools: owner: bgruening revisions: - 29f66c353bcb + - 921a2da49a0c - 9edf8894a22d - ed2cca6b5de4 - - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - d404277cc87a - - 78fb5e286609 - ec4b948dc6f0 + - 78fb5e286609 + - d404277cc87a - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu @@ -21,25 +21,25 @@ tools: owner: bgruening revisions: - 03dd3c16ae4e + - 9e357a8b2ec3 - 977dc15add20 - 4d511437b1e5 - - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - 41dbf4d162a2 - 0ba4f56a3613 + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: + - 7babd8a46fe0 - 9939786dd9c9 - b63363075c2e - 5308ca68ef3d - - 7babd8a46fe0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index d044996a3..a8e320035 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -31,24 +31,24 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - f70b215d155c + - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - 85edbb7a436b + - b07f4839ca77 - 10eed33aa9b2 - f3360fbeda64 - - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 984358e43242 - 6e65fd971e13 + - 984358e43242 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects @@ -62,63 +62,63 @@ tools: - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - - eb6c08714244 - e917a2424690 + - eb6c08714244 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - e7273daa5ae2 - - 6070780813d9 - 670975e92458 + - 6070780813d9 + - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - cdf8e3c57dae + - df3ad3ba5c6f - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - 6a7da2e5f696 - 2484086dee41 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - - 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: - f24c370e5ea4 - - d0178bdcd00e - f8fa0f6718a3 + - d0178bdcd00e 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 @@ -133,73 +133,73 @@ tools: - name: cp_image_math owner: bgruening revisions: - - c09dcda1143f - 6100a22bf4f2 - ff1a86a87364 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - - 667a513e67e4 - 3a05117669cf + - 667a513e67e4 + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - a1a961c46d4b - 2564f461de62 + - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - a32c3f810ade - - 91e03287f285 - 20dbb1f7ec7b + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - 5499dc6f8ac1 - - 8536b1ae0254 - b64af54c5c09 + - 8536b1ae0254 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - 6f4715b8540a - 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 + - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - d85f11570109 - - acf3aa487283 - 79e10d12d90a + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - 80b200ae516b - - 035a58c7f54a - b76841ee5560 + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -212,16 +212,16 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - 8083a87d2fdf + - 48102a685037 - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 4ecf93628f97 - 27edbb90ab2b + - 4ecf93628f97 - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 34733c11a..d957e6ce0 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - a38934e303b9 - e319b5b65879 - - 1069f6db0a0e - - e4ee04da1c19 - - 17f911830a8c - d6e72da3ec35 + - a38934e303b9 + - 17f911830a8c - 3e4f434a69c6 + - e4ee04da1c19 - f362150bef41 - 78bbd17d0703 + - 1069f6db0a0e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - f91cfb73d369 - 2b95d5c04908 - 72ddd32392cd - - 7fe36019c073 - - 0135f1d487a0 - - 1ef5b6e3e09d - - 9537184d421f - 8f8df367470d + - 9537184d421f + - 0135f1d487a0 + - 7fe36019c073 - c88553ec696e + - f91cfb73d369 + - 1ef5b6e3e09d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 - fafb3d685fa9 - - d7e79eb3bcb3 - ad0dc9f4c9e2 + - 2cf4a1cafc16 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 43aac8d29685 - - 9eaadf03e0df - - 69797fa273c3 + - 8c05afb547fa - bd2a7d1316b9 - ee2beb764a7b - ee29337f905c + - 9eaadf03e0df + - 3d18f8c3c0f6 + - 94df24c6bc00 - 7f1cfa4c0e32 - 6a1515bb0687 - - 94df24c6bc00 - - 3d18f8c3c0f6 - - 8c05afb547fa + - 43aac8d29685 - 28a6f1908fcc - 8d36959b000d + - 69797fa273c3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 9f978da6528a - - d37ede8589b2 - 8858fa037a15 + - 5d6ed46cc101 - e3bb03cf207a - - db536ad45f28 - cb903c9dc33d + - 364f4ffec275 + - db536ad45f28 + - d37ede8589b2 + - bcaa0d571ce2 + - 9f978da6528a - 0893a1dbb807 - 5671e1d3d5ee - c092052ed673 - - 364f4ffec275 - - bcaa0d571ce2 - - 5d6ed46cc101 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: + - 045d6d00f606 + - 584beffa972b + - f95f403841ad - 12d66d0d05ac - - 38b91a3190cd + - e1a015876aa9 + - c5c9f02b6167 - 3b6a16d82c1b - - f95f403841ad + - 230b05597996 - 49236b03e4fd - - 045d6d00f606 - - c5c9f02b6167 + - 38b91a3190cd - ed28dd32141c - - e1a015876aa9 - - 230b05597996 - - 584beffa972b 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 ea86a8d8e..a0352d54a 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: - - b8a457820315 - 0f1724dd59d2 - 17e3b698dd52 - f198773344e4 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 374cb875d38a - - 22c2a1ac7ae3 - ac092723240d - - a513e3fbb4c5 + - 22c2a1ac7ae3 - ba0c40780ecf + - a513e3fbb4c5 + - 374cb875d38a 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 f3f6e7ca4..bc5bc78a7 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,8 +2,8 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 522137aaa9c4 - 66d7efc06000 + - 522137aaa9c4 - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -11,17 +11,18 @@ tools: owner: bgruening revisions: - 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: - - f1b9a42d6809 - b6ef6d0cb6b7 - - 818f9b69d8a0 - 2af1346e68c9 - e1317b5502fa + - f1b9a42d6809 + - 818f9b69d8a0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex @@ -29,70 +30,71 @@ tools: revisions: - 05143043ca13 - c80db5d6fd8c - - 947c2eacccb8 - 1588f9076e32 + - 8334dc98c48e + - 947c2eacccb8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: + - 83228baae3c5 - 29e4122c90de - - 25b46af53232 - 9991c4ddde14 + - 25b46af53232 - 1552b8cb4a94 - - 83228baae3c5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: + - f3dfa4bdf87e - 841a6cc5fc58 - - 060ca94ac049 - - a07ab242b0b5 - 53616c8b0865 - 1a53edc4b438 - - f3dfa4bdf87e + - a07ab242b0b5 + - 060ca94ac049 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 91c4e3331208 + - 2fc89dcd41c8 - d4808d5b83da - - dc4b5fd604a6 - 40f4447733b2 - - 2fc89dcd41c8 + - 91c4e3331208 + - dc4b5fd604a6 - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 7626ea9c2e1b + - 301e07345c93 + - 25ab6b4e376e - e5a5ad882f1f - c6ae57f774c6 - 36e8d6d5d01b - - 301e07345c93 - - 25ab6b4e376e + - 7626ea9c2e1b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 - 80852884053f - - b7c3e9a3b954 - - f9639b488779 - - 4ed102b922cb - 02d2be90dedb + - 0630258dcf35 + - 4ed102b922cb + - f9639b488779 + - b7c3e9a3b954 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - caeb57858702 - 14180f9c831e - 61634a87efc7 + - caeb57858702 - ec69cbe34b73 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index b34fcd6ce..e909a8246 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - cd659e8cc5fa - - f6877ad76b00 - - 749c918495f7 - - a6d65b0c67af - 3ba8d4563129 - - 937aa69e715f - 17062a0decb7 - - 03e9b2fbc005 + - a6d65b0c67af + - 937aa69e715f + - 749c918495f7 + - f6877ad76b00 + - cd659e8cc5fa - 017aba02828d + - 03e9b2fbc005 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -22,17 +22,17 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 53646aaaafef - dfd8b7f78c37 - 3fe632431b68 - 64f11cf59c6e + - 53646aaaafef - e188dc7a68e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -45,43 +45,43 @@ tools: - name: lastz owner: devteam revisions: + - 2ff111fac1d7 + - 37b497aa133f - 60afcc2c1d05 - e7f19d6a9af8 - - 37b497aa133f - 3e1ea2facca6 - - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 6b1e195506a3 - - c0c2d0941de8 - - 09b53c1d4ab1 - - 8c6cd2650d1f - - 11a0d50a54e6 - - f54f5baedfdd - - 77b2770508f6 - be1d967337e4 - b3eab4b67562 - 037c6e54df11 + - 8c6cd2650d1f + - 77b2770508f6 - 3f4d6399997b + - f54f5baedfdd + - 6b1e195506a3 + - 09b53c1d4ab1 + - 11a0d50a54e6 + - c0c2d0941de8 - 53c0b7a1a0c3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: + - 1cd2511a396e + - 178bdbdb6d24 + - ec9cbd6b9a49 - b8f5f6e87f5c + - 00fbfac99d39 + - 9ee34ba73ebf - e403d27e8f24 - - 5ef7ec16b04f - - ec9cbd6b9a49 - 13022c3d3076 - - 9ee34ba73ebf - - 1cd2511a396e - - 178bdbdb6d24 - 79b885ce78d7 - - 00fbfac99d39 + - 5ef7ec16b04f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 4bd223fc7..5c4bdbe4c 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,8 +2,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -22,54 +22,54 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 76d3d2b10738 - 63f86089423e - - 5b5a7af9fbb4 - 7c2100246a2f + - 5b5a7af9fbb4 + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - 18a502a9d287 - - 84fd33a60b35 - - 96336c6a2bb7 - 1c35dadbe76f + - 96336c6a2bb7 + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - addaf9d22850 + - 34e55239e68b - a9f4a217dcd6 - f732237754fc - - 34e55239e68b - - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 75403243703a - 0776d824d896 - 04c15826a0b8 - 8c202e741d68 + - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - 8470de786d47 - - e96bbb9e24ea - - 43c99742158b - 1c9b3bcd4261 + - 43c99742158b + - e96bbb9e24ea tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 84743da21318 - - 5c865a382933 - 1d75bd0595e2 + - 5c865a382933 + - 84743da21318 - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -77,36 +77,36 @@ tools: owner: iuc revisions: - 8daf4564ccda - - ac72310b038a - 555ccac8a4c5 + - ac72310b038a - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - 7b8cb2b02978 - a58e4a43f49c - - d60df8727f59 - f947b4bb5107 + - 7b8cb2b02978 + - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 1bc3657cd694 - 7f3b59dee073 - - 04144473e59e - 7136e9ab70db + - 04144473e59e + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 9058d8943303 - 0a1224c4b781 - d943081510da - 19299bb1c6af + - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -119,16 +119,16 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: + - dbf1798c0dcc - 6501b5b33988 - c4db8c4de66f - - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - fa35f1106d3e + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level @@ -148,24 +148,24 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - e66ab198ec15 - bd7a9c6efb10 - 6aad8ca3918b - - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - d77397f09da1 - c6676a890f50 - b084117133af + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 7f208f1eb64f - 9704f1a3b32d + - 7f208f1eb64f - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -180,46 +180,46 @@ tools: revisions: - c409a495841f - 79706f10d680 - - e88b731dad59 - 31c6d107e7a5 + - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: + - 172920f67a84 - d24841f5c3d2 - 714d5a28cc5c - 71ea608ddfa3 - - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - a293a742194f + - 12fb63b5f63f - a4d7148ccee4 - 4137b492233e - - 12fb63b5f63f - d7e9a3c41657 - - a293a742194f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - 6fcb8ac37a3e - 97f7bb0851e7 - - e2c71b852aba - 75bedfb2078b - - 64bc7acc22a9 + - e2c71b852aba - cf87759761eb + - 6fcb8ac37a3e + - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: + - 080ea153677c - c82508e76ad1 - 4033827c76b8 - - 080ea153677c - 2d35528d2141 - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis @@ -297,8 +297,8 @@ tools: - 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 @@ -310,15 +310,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 3d6570bffdb1 - 5bee9adae474 + - 3d6570bffdb1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1902d3de4a4f - 6c09bed3444f + - 1902d3de4a4f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -368,10 +368,10 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 4fd3b5d8706b - - 0270541aaf46 - 27250f92a01a - e073891b2afc + - 4fd3b5d8706b + - 0270541aaf46 - 2cff76cf35c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -379,8 +379,8 @@ tools: owner: iuc revisions: - 708abf08a626 - - 76bc4efa1aeb - eb50e7eca3dc + - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -453,13 +453,13 @@ tools: - name: metaphlan owner: iuc revisions: - - ff8f55893e7d - - 2131d7dca455 - - a16313517e55 - - b89b0765695d - a92a632c4d9b + - b89b0765695d + - ff8f55893e7d - 6dee4abadccb + - a16313517e55 - 1a6cdf55390f + - 2131d7dca455 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -569,20 +569,20 @@ tools: - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 - - 4b9a8031ab74 - - 4d83eccf5f81 - - 3b22de20bd4b - - be818ae858e4 - 141afacabcfa + - 4d83eccf5f81 + - 4b9a8031ab74 - aeaa20b96ef2 + - be818ae858e4 + - 2fd4d4c9c5c2 + - 3b22de20bd4b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - b3c7199d8786 - 576963db5f1b - 9495df9dd6ef + - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index 2bb6093b1..22f68431e 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -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 @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 19d2391ac..b0857c81c 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 6ae5a7b5a0a2 - - 48c13389050d - 9eeb13a92d79 + - 80f03df2e2ce + - bdfbaf0c10aa + - 48c13389050d + - 94b8c6013083 - 9422c5a87ee2 - 2263989660f5 + - a74dbfee5a86 - cd07731e4434 - - 8b67dd48fec1 - - 94b8c6013083 - 9baa871cb1d1 - - bdfbaf0c10aa - - a74dbfee5a86 - - 80f03df2e2ce + - 8b67dd48fec1 + - 6ae5a7b5a0a2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - d7ce0ec78e51 - - f14193ec1f50 - - bc3831dd65c1 - - fc2e49f91e52 + - f0af8936ed41 - d390fe1567dc + - f14193ec1f50 - 4a60927aaca5 - - f0af8936ed41 - - aaa0d6a8b808 + - bc3831dd65c1 - '764845535798' - 2e093badc689 - - 5abf2c2249aa + - be78f13134e2 + - fc2e49f91e52 + - d7ce0ec78e51 - c18157c68134 + - aaa0d6a8b808 - 3ff17bad4006 - - be78f13134e2 + - 5abf2c2249aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -44,8 +44,8 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -64,19 +64,19 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f - 6f28e90db932 - - 15974dd17515 - a65296ffb4a0 - - c5908940967d - f1a5908ea2cb + - 15974dd17515 + - c5908940967d + - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - b3acbb3a6af0 + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -89,15 +89,15 @@ tools: - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 48823c9635a4 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 8a1b7c206..0298982d6 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,42 +2,42 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - fc8804320156 - a7228a7ea146 + - 0e9e7fcdd543 - 79e9a869f40e - - 72b5e9dda577 - cb34f00cc10f - - 0e9e7fcdd543 - - fc8804320156 + - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - fa11aa8103b2 - - 18505fe2bdb1 - d6cddc06aeae + - 18505fe2bdb1 - db25ec99c3ea + - fa11aa8103b2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - 43815fa60f3a - 222669c4afb6 - - 2bf63b38ee9b + - eb746fa6f514 - edf6d4003fad - - 0f5f4a208660 - - 19f3b583a9b3 + - 2bf63b38ee9b - ec699520444c + - 43815fa60f3a - cc36773a3681 - - eb746fa6f514 + - 19f3b583a9b3 + - 0f5f4a208660 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 @@ -49,24 +49,24 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab - 645159bcee2d - - 0f1c34698076 + - a3c4fe6f49ab - edbb6c5028f5 + - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - d219b6d8158a - 85a394edc247 + - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - be95355fef8d + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya @@ -79,23 +79,23 @@ tools: - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - a3afc5f0a96c + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - 93d623d9979c - - 5f76b20953e5 - 543cbeef3949 + - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - 28d7819c312f + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -107,8 +107,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 5a82eb9e1b89 - 47936349f3e9 + - 5a82eb9e1b89 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -120,8 +120,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 338d15b8d6fb + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -133,15 +133,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 4fe6b96aff72 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - 34553d0caa5e - ce8af9373061 + - 34553d0caa5e 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 e71a6fa4c..576553085 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -20,16 +20,16 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - d74850cf4e42 - adfd6bf710bd - 3e73c97f025d + - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - 83da94c0e4a6 + - 1586b111d2a3 - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,9 +42,9 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 19b6a2f0dbe2 - - ed1518ce2237 - 2f27f3b86827 + - ed1518ce2237 + - 19b6a2f0dbe2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -69,30 +69,30 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 48a42ca61006 - 38ccd4589990 - 5711fc06a63e - - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - 81a286e4c5a2 - fcb8bdd124f4 + - 81a286e4c5a2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -118,10 +118,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 172815da3d41 - b4b2b284230a - - 27a6a256cd23 - 52b6a4d98009 + - 172815da3d41 + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -133,8 +133,8 @@ 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 @@ -146,9 +146,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 87febc68b45b - - fea85c467896 - 19bbd19b74b3 + - fea85c467896 + - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -193,33 +193,33 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: + - 9d09724f2bf1 - aec831b54a5b - 0db22932bc39 - - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - 6e24e79d3d69 - - ed7a967cb11b - 29c738066906 + - 6e24e79d3d69 - df30a2f1db55 + - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 1865e693d8b2 - 3e4d45aca422 + - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -231,9 +231,9 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - - 64deddb6a8ec - d63c1442407f + - 64deddb6a8ec + - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index d05b72a10..c0eea4bda 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,114 +33,115 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 107d3ba7024a - cce7b18495e4 + - 26de3a7b1cb9 + - d7c7ef3353fe - 5a7c56a5cc08 - - c78f3d7dd1db - - d033ffc1c161 - 6a457678efcb - b89cac5156ec - - d7c7ef3353fe - - 8834daeb9892 - f04a1264e2a2 + - '841557158611' + - d033ffc1c161 - a6619171428e - - 26de3a7b1cb9 - - 3b8b5bde0bd9 - 3f59ebfbfe3d - - f73435dc282b + - 8834daeb9892 - 81e66674859e - - '841557158611' + - 107d3ba7024a + - c78f3d7dd1db + - 3b8b5bde0bd9 + - f73435dc282b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 5b777002c2de + - 3b96e92e8ec3 + - a185b079b095 + - e75442c7f4da + - 4755f52427c4 + - 02b8758214b0 + - aa8cc71438cf - 659517798cc4 - b0af57c1a968 - 6283babe736e - - a185b079b095 + - 6a726db04d4b - df47d4845b62 - - 6223845127ea - - 3b96e92e8ec3 + - 88c4aa435ded + - 5b777002c2de - 7a2092844346 - 5fcd1ece3a6e - - 02b8758214b0 - - 88c4aa435ded - - 4755f52427c4 - - e75442c7f4da - - 6a726db04d4b - - aa8cc71438cf + - 6223845127ea tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - f97743d52b87 - - d1c340a5664b - b8476e82ac20 + - f97743d52b87 - 9b892d7f82cc - c1d53e95327f + - d1c340a5664b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 9e10ba792be2 - feb40665d7cd - - daddf188c13f - 128ba8da994f + - daddf188c13f + - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - 2f1019071464 - - 03ed9524dcd1 - - 5f8727ff21e7 + - a2099fb98cdb - ca337cce3888 - - 9d61d3fa046c + - abf6dbe8c9d7 + - 03ed9524dcd1 - 7bb8726be37c + - 9d61d3fa046c - 437e28791761 - - abf6dbe8c9d7 - - 2fa9d4f1b48f - - 42a174224817 + - 81804a978fc0 + - 83a69484cb87 - ca0d8cf80567 + - 5f8727ff21e7 - 3a43c3982401 - - b6abccb1f25b - - 36912871ccdc - - 83a69484cb87 - - a2099fb98cdb - b7e297c2ede6 + - 42a174224817 + - b6abccb1f25b - 14ae456b8cc5 - - 81804a978fc0 + - 2fa9d4f1b48f + - 36912871ccdc tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: raxml owner: iuc revisions: - - 29ff6a849eac + - a4b71be30c3c + - ea30d3089354 + - b1e68bbe4cef - 73a469f7dc96 - ba29b5e2a4be - - ea30d3089354 - - a4b71be30c3c + - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - f1ccc8a6eb05 - - 809e42326fc2 + - 15ac71df11a0 - dbe2b2204555 + - 809e42326fc2 - e88a7de55d6e - - 15ac71df11a0 - 91887494eb97 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 f6a4dbc1a..e56c64733 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - f6ced08779c4 - - 7d34178f2812 - f9242e01365a + - a1f0b3f4b781 - 881d7645d1bf - - b502c227b5e6 - - fc288950c3b7 - 1aac2a13842a - - a1f0b3f4b781 + - f6ced08779c4 + - fc288950c3b7 + - b502c227b5e6 + - 7d34178f2812 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 17a690cc1..1767bdfc7 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,14 +2,14 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - e4a053d67e24 - - c0e71cb2bd1b - - 7fbec959cf2b - eb085b3dbaf8 - - ca90d17ff51b + - e4a053d67e24 + - d00e15139065 - 5b85006245f3 - a58f7eb0df2c - - d00e15139065 + - ca90d17ff51b + - 7fbec959cf2b + - c0e71cb2bd1b - 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 5813d6b6a..bc67f047a 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -5,81 +5,81 @@ tools: - f28ad96b76dc - 0a18ac48ac53 - b18329a8ac14 - - b574b84afc4d - ece627528a78 - 277dc652246e + - b574b84afc4d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - bf06d196e23d - e215f71d7983 + - 525f201b86c1 - e988563cc6e5 - b41107d8fe89 - - 525f201b86c1 + - bf06d196e23d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - 8da3511c9467 - - bb6397b94018 - 4fbffddde8cd + - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - 528fb09022be - b8c79e70516d - f23d67e28cc8 - a8157342d9a3 - - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a69865da6f80 - - 25b83cbd596a - - a95a82eb4d50 - 80600735685d + - a95a82eb4d50 + - 25b83cbd596a - 59e85306eae5 + - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d - - 798da6bdff3d - - ed9ed1e6cca2 - f1897eb07081 + - ed9ed1e6cca2 + - 798da6bdff3d + - 611d80c0e29d - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - 74b61bf5bc4b - 5a35e3a8d013 + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - cc430977c8ff - 82f6c2f4332d - df2187f9013b - - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - 043f9c91f686 - - d2483487e077 - 10566783d718 - 1693b2126f30 + - d2483487e077 - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -98,8 +98,8 @@ tools: - name: diann owner: galaxyp revisions: - - ae4dc0c041f9 - 9fa3dbf06f17 + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -146,16 +146,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - d286ff4600dd - 160538a890a6 - e66f552a3c47 + - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -168,42 +168,42 @@ tools: - name: maxquant owner: galaxyp revisions: - - 837224ad1694 - 97a7f34fcb6a - - 7f432d87c82c - - 37d669de2828 + - 4d17fcdeb8ff - f522c08e900c + - 37d669de2828 - e42225f8a659 + - 1f39c833f65f + - 7f432d87c82c - 2133b0be850a + - 837224ad1694 - 8934bc76bb52 - - 4d17fcdeb8ff - - 1f39c833f65f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 - 85b8866f06d7 - - a72ac2c7cc5b - '860429737408' + - a72ac2c7cc5b + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 1974224d63c2 - 990b4560ead7 - - 4187b6df1a40 - 352b37c66d97 + - 1974224d63c2 + - 4187b6df1a40 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - - 99450519d727 - deaf035bbe9f + - 99450519d727 + - 4f359549383c - a1daafbf5233 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -211,9 +211,9 @@ tools: owner: galaxyp revisions: - e79958768a2c - - c1343e3389ca - c7745841de24 - 40ca115438d2 + - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat @@ -228,10 +228,10 @@ tools: - name: metaquantome_viz owner: galaxyp revisions: - - 1199751329b0 - 944b43462104 - 9bf325045235 - eb811f3018ea + - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -251,23 +251,23 @@ tools: revisions: - 28434abe6c5c - b7034eff0db1 - - 593839e1f2c3 - 8212e342e482 + - 593839e1f2c3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - a5e394b36d87 - bd1535813cfe + - a5e394b36d87 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: + - 8960fb791701 - 4e77b8f12cd3 - 01dbaf6a57e0 - - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -280,17 +280,17 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 - - 518b1730cf2a - - c9eff69a7c62 - f7fef900f5b2 + - c9eff69a7c62 + - 518b1730cf2a + - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 5e948629bc73 - dff6c756eee5 + - 5e948629bc73 - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -298,8 +298,8 @@ tools: owner: galaxyp revisions: - 658494a2cb00 - - 41859bbdc16e - 890025d6e426 + - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter @@ -313,105 +313,105 @@ tools: - name: openms_filefilter owner: galaxyp revisions: + - 05d5e1ddc985 - d6878d27f051 - 0bb5056cb775 - - 05d5e1ddc985 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - febd569ad26f - 52ba9695e752 + - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 39e8fde08881 - 92352a475eed - 27cba4c5fc42 + - 39e8fde08881 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: + - d413dc49d650 - 0efbc235f314 - 9e26f5c770f8 - - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - 3720e349ba2a - - c28f13cab67a - 8a04ed1c1d1b + - c28f13cab67a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - ca799a7246e7 - - 382cde407f81 - c55dddc5844a + - 382cde407f81 + - ca799a7246e7 - c427a8628cbe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 8ddb7bab1138 - - b5d0905419da - 39caaa778d2e + - b5d0905419da + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - 18f93351f8b6 - - 1c5f31b8d632 - - 8d4db262964c - f817513840a9 + - 8d4db262964c + - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - c69f69d7867a - - 111c3a00136d - 5d9f175dff81 + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 476b5e296979 - - 0e52c85f3b15 - be74a8cd7d66 + - 0e52c85f3b15 + - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - e133b5c8878f - 9866e1170611 + - e133b5c8878f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - c18d8efa4474 - 2b2a7551a857 - a407b6790342 + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 4e66c4e73909 - d0304fb829c0 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter @@ -432,8 +432,8 @@ tools: - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 8c01da82292c - 2a9ff56cb279 + - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -453,8 +453,8 @@ tools: - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - 0bddef8d144e - d4396637b9f5 + - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter @@ -474,8 +474,8 @@ tools: - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - 18826fb8e5db + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -488,8 +488,8 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - 5ae104d0da6e - 3d8d4ada5405 + - 5ae104d0da6e - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -497,9 +497,9 @@ tools: owner: galaxyp revisions: - e039cc5c7aed + - dd173849c3d8 - 539a3a4dcc9e - 5182338d5e7c - - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -518,8 +518,8 @@ tools: - name: openms_textexporter owner: galaxyp revisions: - - d063e2fe4ba4 - 9020199dba0a + - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator @@ -531,8 +531,8 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - 7f6a1f27553e - c8b225c69a7f + - 7f6a1f27553e - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -553,14 +553,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 943a34df6047 - - 7fdd9119cc4f - - 3634c90301af - - 07ff622ec007 - - 3ec27b4cee7c - - a72c48001f7c - 1beff3ddce58 + - 07ff622ec007 + - 7fdd9119cc4f - da885ca16cb2 + - a72c48001f7c + - 943a34df6047 + - 3ec27b4cee7c + - 3634c90301af tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -614,10 +614,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 12692567c7f9 - a371252a2cf6 - - 1a5690a5eedc - 265c35540faa + - 12692567c7f9 + - 1a5690a5eedc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index ba1a61cb4..a5ea0699f 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,44 +2,44 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 2f1d464ebfd2 - - 289b7d6b69a4 - - e345aadf914f - 42201b90e3f4 - - cd5f98911089 - 110a346daf36 + - e345aadf914f + - 2f1d464ebfd2 + - cd5f98911089 + - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 0cd2df8af811 - - c207119ba5f6 - - fcce77c09289 - 42d9087b4789 - 8501601a118d + - c207119ba5f6 + - fcce77c09289 - 0345dbaaa79b + - 0cd2df8af811 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - ad5ab22ffe24 - - 405a212b32ab - 421c33b8bf17 - - 89eb29319bf4 - 33486216eec0 + - 405a212b32ab + - 89eb29319bf4 + - ad5ab22ffe24 - 04db7fd6b238 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: + - fa51dc5e8386 - 7b72fde3d27e - 7370bb65bad4 - - f6e91108b7b1 - - fa51dc5e8386 - eb784fa07f80 + - f6e91108b7b1 - 1d839ead7ad3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -47,87 +47,87 @@ tools: owner: iuc revisions: - c9b77ced9a78 - - 3d70c2996730 - - a3e86cd9cac7 - d30e36c48c93 - - 8a55d29c8fcf + - a3e86cd9cac7 + - 3d70c2996730 - 1544278c272e + - 8a55d29c8fcf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - 7b881f5f5ad5 - e2db212d64ad - 887cf585cafc + - 564c33e5c3e3 - b242deb58952 + - 7b881f5f5ad5 - a5969aa9347e - - 564c33e5c3e3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - 9a171f9a450b - b4bab607eb05 - - bd5ff77e2036 + - 9a171f9a450b - e897c74a48bb - 8cff84759bf6 + - bd5ff77e2036 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 33f0793edf93 - - 887e0991eb24 + - adc7a7610d4f - 4f65e343ecdf - 6dafad990086 + - 887e0991eb24 - 5e10f396979e - - adc7a7610d4f + - 33f0793edf93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - c287418eb288 - 4e280b27a831 - - 97575d01f06b + - c5d7050e4ad7 - 17d39bf0a63a + - 97575d01f06b - 43e3eeb2e0ec - - c5d7050e4ad7 + - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 9586f08634c0 - 0b8c84a7fdb5 - - cd034465d4a4 - - d9bf483266a1 - 09b8edb56d80 + - cd034465d4a4 + - 9586f08634c0 - a819ec3b362d + - d9bf483266a1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 95351dd0fd3f - - 2645575d1bf2 - - a4b4bd84f69e - - bf0e43ab0416 - - a9c34a289493 - 69842dd5aa48 + - a9c34a289493 + - bf0e43ab0416 + - a4b4bd84f69e + - 2645575d1bf2 + - 95351dd0fd3f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - - 912f904a6e1e - - d1fda11e602f - d033e1ccb386 - - 8a35a3bc6752 + - 912f904a6e1e - bb0475c884ff + - cfb504394ae1 + - 8a35a3bc6752 + - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - 95286af4139b - d504d945a655 + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 7aa4bfc29..7e0361197 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,9 +2,9 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - 31f8063eedea - 2d4e3aff9dc7 - cf01dd6c6b1f - - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters @@ -18,8 +18,8 @@ tools: - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -64,16 +64,16 @@ tools: - name: cuffmerge owner: devteam revisions: - - 6a6717a5f421 - - 86285ddd4512 - cf747d1bd79a + - 86285ddd4512 + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -97,29 +97,29 @@ tools: - name: describe_samples owner: iuc revisions: - - 3b36efd62b3e - 8f0181aacb7a - - 0693ccd171c4 - e3b16fd7dd08 + - 3b36efd62b3e + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 9a882d108833 - - 0696db066a5b + - 24a09ca67621 - cd9874cb9019 - 6a3a025714d3 - d027d1f4984e - - 24a09ca67621 + - 9a882d108833 + - 0696db066a5b - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - b47c006d90c5 - 62adf13b86ea + - b47c006d90c5 - df929f257179 - 2872c633f07e tool_panel_section_label: RNA-seq @@ -128,15 +128,15 @@ tools: owner: iuc revisions: - 070900306913 - - 3d89af8a44f0 - - 555659de7321 - - f2843df56434 - - 9bdff28ae1b1 - - 0cb907a2a810 - a8305cf0c951 - - df0c8d0a5992 - 6e53e565fc6a - 334ce9b1bac5 + - 9bdff28ae1b1 + - 0cb907a2a810 + - f2843df56434 + - 3d89af8a44f0 + - 555659de7321 + - df0c8d0a5992 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -155,17 +155,17 @@ tools: - name: featurecounts owner: iuc revisions: - - a56fbe2d6ba7 + - ea04b737afa0 - f3a5f075498f + - af814359d244 + - a37612abf7f9 + - f9d49f5cb597 - 90d16db017d7 - e6a2a912677a + - a56fbe2d6ba7 - 6f66ae7c5f7a - - ea04b737afa0 - - af814359d244 - - 7db9d3ea71c9 - 38b6d12edc68 - - f9d49f5cb597 - - a37612abf7f9 + - 7db9d3ea71c9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -183,9 +183,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 3c97c841a443 - f99dd58de04f - 0f710191a66d - - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -197,20 +197,20 @@ tools: - name: hisat2 owner: iuc revisions: - - 6ab42baa56e9 + - f4af63aaf57a + - 26371a1df031 + - 6c19daec423d - d4b55e2beb12 - 3fb01a8c902d - a86e80d3c09c - - 26371a1df031 - - 6c19daec423d - - f4af63aaf57a + - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -222,18 +222,18 @@ tools: - name: kallisto_pseudo owner: iuc revisions: + - 5ae5c312d718 - 1c75aa5de15e + - 87c11c05d238 - 01247aaf0a10 - ce5d418183c5 - - 5ae5c312d718 - - 87c11c05d238 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 4f9c4e6566e5 - c971db6f0fe5 + - 4f9c4e6566e5 - 40985510cd98 - 10c98fab6c5a tool_panel_section_label: RNA-seq @@ -243,11 +243,11 @@ tools: revisions: - 708348a17fa1 - 97e06a4c7c75 + - 58c35179ebf0 - 0921444c832d - - 32511f586472 - e827f9aae031 - d6f5fa4ee473 - - 58c35179ebf0 + - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -297,18 +297,18 @@ tools: owner: iuc revisions: - 4df95e2d7f61 - - 5ec75f5dae3c - - b9e04854e2bb - - 0a563fd2f22e - - 79de45b5069b - - e132e7d02a3e + - 99b17b74a8cd + - c7c55b694974 - 7ed2edc1337f + - e132e7d02a3e - 3ea5a2a63fa2 - - 99b17b74a8cd + - b9e04854e2bb + - 0a563fd2f22e + - 5ec75f5dae3c + - 4074fc1940e2 - c772497b2c32 - 980d2a2e1180 - - 4074fc1940e2 - - c7c55b694974 + - 79de45b5069b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -322,31 +322,31 @@ tools: revisions: - ebab418107f5 - 49121db48873 + - cc05793bb896 - e3d32471da11 + - 53e9709776a0 - 15cd64d7c58b - - cc05793bb896 - 2c0ca397d302 - - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - fab6ff46e019 - c0fd285eb553 - - 56242ff81c84 - 8c28affc7c48 + - fab6ff46e019 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - ae618321f34a - 258d696dbd7e - - dd4df992d93d + - cef79931dda5 - 914cfcba0ec8 + - dd4df992d93d - 76d290331481 - - cef79931dda5 + - ae618321f34a - 1ebd14235b92 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -371,73 +371,73 @@ tools: - name: transdecoder owner: iuc revisions: - - c6334cb383ff - - ffd1300599a1 - d0d4cef4f967 + - ffd1300599a1 - 0db979fead3a + - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - 74217fbfba4d - ba3720d7e68b - bcc5f03f1900 + - 74217fbfba4d - d6a479fd4281 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - c2b82a94493e - - 478f36effca1 - 2fb4ee002432 - 56162e446004 + - c2b82a94493e + - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - 9ff3765e7172 - - 3f4094b6a565 - fab23c3b5258 + - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - 34a018cbee9c - - be3f26533209 - 4687ecf0eb2d - 870ac06dff8e + - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - c5fbddcac63a - - 33406f5a445c - - 05ab8d5e04a2 - - 65e7dea767ea - 5192f657f305 + - 65e7dea767ea + - 05ab8d5e04a2 + - 33406f5a445c + - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d + - e406ac71165d - a35cba31d904 - 6f0fb35b799c - - e406ac71165d + - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - 964b7efe2639 + - 7c7fbf13aadd - c2c039e421af - 37a1129c89d2 - - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -452,24 +452,24 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 - 9871104ea630 - - 3a4ac03d1266 - 1812dbc5bb7b + - 3a4ac03d1266 + - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - 8f1c3df4dd49 - - 32b86cd8eb50 - - db1f362cca3e + - d2bc35f3d1c5 - cee61b3fcf78 - - d84caa5a98ad - 48636f857c4b - - d2bc35f3d1c5 - - c9cfec002f71 + - 32b86cd8eb50 + - 8f1c3df4dd49 - 9fa24d5aac68 + - d84caa5a98ad + - db1f362cca3e + - c9cfec002f71 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 dfa03fca7..b2c45c52e 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: + - 1a052c827e88 - 080fd5739bb4 - 473382134e56 - - 1a052c827e88 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 20a64dff7..95a32fe00 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,6 +2,7 @@ tools: - name: bam_to_sam owner: devteam revisions: + - a53efedba9e7 - 10184eaa85fc - 88eedb4abea0 tool_panel_section_label: SAM/BAM @@ -9,8 +10,8 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 108db6635177 - cb20f99fd45b + - 108db6635177 - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -41,8 +42,8 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - 19ece8afbaab + - 5f8e69cc4c6e - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -67,15 +68,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - cf1ffd88f895 - 9bd1568619cd + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -87,8 +88,8 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 649a225999a5 - 56c31114ad4a + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -96,6 +97,7 @@ tools: revisions: - 12749212f61b - 46c6639921f1 + - 6856f8a01905 - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -110,59 +112,64 @@ tools: - name: samtools_fastx owner: iuc revisions: - - b3d99709fe1a - - 720217c23995 - a8d69aee190e + - 720217c23995 + - b3d99709fe1a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: + - db17d5321bad + - cc61ade70eb8 - fe34990e5ce7 + - fefd89ab563c - 22970df7a40e - - cc61ade70eb8 - - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 7def34e6cf4d - - 7a6034296ae9 - 88b8c2916784 + - fa5d3e61e429 - 811fc2d75ad4 + - 7a6034296ae9 + - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 36677f429310 - 740ce0a18f0d + - 65a38e8c8e2a - b40e2d865d52 + - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: + - b61f5d6a7f25 + - 8da515fbc1bf - 329deb17a9f7 - - 583abf29fc8e - 9da0311ab1dd - - 8da515fbc1bf + - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - 30388d878f81 - - db000c6007a0 - bb8cfc6f6e0c + - db000c6007a0 + - d7b4851d1971 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -176,44 +183,47 @@ tools: revisions: - 344fc91e1bfd - a4a10c7924d1 + - b5c88b7b153e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - e613c1ad4c4c - - 6c2c1836728b - cab3f8d35989 + - a577ea614bed + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: + - 135c85f4cfaf - 5d9ae78f34d3 - - b7f7826ef1cd - bcedabb53ddf - - 135c85f4cfaf + - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 145f6d74ff5e - - 5a08c09b9311 - 24c5d43cb545 + - 145f6d74ff5e - 3a0efe14891f - 1cc79f49b8d5 + - 5a08c09b9311 + - fed4aa48ba09 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - c370440f901e - - 5826298f6a73 - - 0dbf49c414ae - - bf328cec6a42 - - b72793637686 - b01db2684fa5 - 350bbc5c2ffd + - b72793637686 + - 0dbf49c414ae + - 5826298f6a73 + - bf328cec6a42 + - c370440f901e 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 e7378d8e5..606f5c833 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,9 +2,9 @@ tools: - name: ena_upload owner: iuc revisions: + - d147d6455873 - 6f6537780379 - 59bb6d34fca6 - - d147d6455873 - 480d9e9d156b - a62c4a11a67d - 4aab5ae907b6 diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index 1591141c5..7fcae715c 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -2,39 +2,39 @@ tools: - name: anndata_import owner: iuc revisions: - - cfc3f5a57dc6 - - fb9e030ffae4 - 55e35e9203cf + - cfc3f5a57dc6 - 00712416fdaa + - fb9e030ffae4 - 32e547223c9e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 39e945f0b2c1 - ee98d611afc6 + - 688357ad5e61 + - 39e945f0b2c1 - b9fac48532eb - 038e32885fec - - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - b85871dd69f9 - - 43cb7b5a6fe7 - - d4af736e7b83 + - 3d748954434b - 9bd945a03d7b + - d4af736e7b83 + - b85871dd69f9 - ed4996a16f7f - - 3d748954434b + - 43cb7b5a6fe7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils owner: iuc revisions: - - a9caad671439 - 8855361fcfc5 + - a9caad671439 - 2c1200fba922 - cdf4443d5625 tool_panel_section_label: Single-cell @@ -55,15 +55,15 @@ tools: - name: music_deconvolution owner: bgruening revisions: - - 2ba99a52bd44 - 56371b5a2da9 + - 2ba99a52bd44 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -89,37 +89,38 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - a6821f856a1e - df8e4e54d367 + - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 - 2af7c5086a96 + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - b2df381a6004 - - 77b91b9bdf52 - aaa5da8e73a9 + - 77b91b9bdf52 + - b2df381a6004 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - 3c86f71498bc - - b409c2486353 - a97abb8cd15b + - b409c2486353 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - 6bd82ed14acd + - 3081ff5c84a3 - 5e9171dc8244 - c5d3684f7c4c tool_panel_section_label: Single-cell @@ -128,56 +129,58 @@ tools: owner: iuc revisions: - 3bcd5445cd7a - - ab55fe8030b6 - a407e7f8bdc1 + - ab55fe8030b6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - 6adf98e782f3 - - dbbe1ea8ecb1 - aa0c474463c2 + - 9b0cdb8cf6be + - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: + - 215733a383f2 - bf2017df9837 + - 458e8f43a775 - f2f6c703da06 - - 215733a383f2 - 73ab2ac53d06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - fd808de478b1 - 8f333f90d8d6 - b834074a9aff + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: - - 7a365ec81b52 - b7ea9f09c02f - 652923ce664f + - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter owner: iuc revisions: + - ef4c80837bc5 - 2e41b35b5bdd - 81e5bdff4853 - - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca owner: iuc revisions: - - c99ba278dfa9 - 46fc6751d746 - 9e5c0bb18d08 + - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index e42515e3f..48549d19f 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 562f3c677828 + - 419027d822d6 - 4c07ddedc198 + - 562f3c677828 - 2f3c6f2dcf39 - - 419027d822d6 - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -56,23 +56,23 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 7a15159140d1 - - cb1c59d69557 - 6c29c7e347e8 + - cb1c59d69557 + - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - aef56d0e7a61 + - 9c3e1d3235c8 - 7442b94d6a1e - 4c4ec859c31a - - 840f29aad145 - - aef56d0e7a61 - b1eda492f063 - - 9c3e1d3235c8 + - 840f29aad145 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: + - 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tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives @@ -384,15 +384,15 @@ tools: - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes owner: devteam revisions: - - 84959112d9a6 - 70bc6ced57f7 + - 84959112d9a6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -405,22 +405,22 @@ tools: - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine owner: devteam revisions: - - 53edb91ed051 - 1f0ba67cc85a + - 53edb91ed051 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples @@ -433,23 +433,23 @@ tools: - name: vcfdistance owner: devteam revisions: - - 48e458c721b3 - 5822b40f3037 + - 48e458c721b3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - 6b935ab36d7b - fa24bf0598f4 - eae7c08ebb6f + - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -462,15 +462,15 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -483,8 +483,8 @@ tools: - name: vcfleftalign owner: devteam revisions: - - 29f9b782727e - d2406f98a782 + - 29f9b782727e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers @@ -497,8 +497,8 @@ 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 @@ -524,7 +524,7 @@ 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/viral_tools.yml b/usegalaxy.org.au/viral_tools.yml index 06370d956..15250eab7 100644 --- a/usegalaxy.org.au/viral_tools.yml +++ b/usegalaxy.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 18aad692772a - 9def47f3c1e4 + - 18aad692772a tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu