From 9081f81a71ef21b8ab457ab8bd3c7b2ba9c69a82 Mon Sep 17 00:00:00 2001 From: admin Date: Wed, 12 Jul 2023 04:58:26 +0000 Subject: [PATCH] Jenkins update build 156. --- automated_tool_installation_log.tsv | 18 ++ staging.usegalaxy.org.au/annotation.yml | 72 +++--- staging.usegalaxy.org.au/assembly.yml | 184 +++++++------- staging.usegalaxy.org.au/bacterial_typing.yml | 4 +- staging.usegalaxy.org.au/bb_tools.yml | 4 +- staging.usegalaxy.org.au/bed.yml | 14 +- staging.usegalaxy.org.au/blast.yml | 10 +- staging.usegalaxy.org.au/chemicaltoolbox.yml | 62 ++--- staging.usegalaxy.org.au/chip_seq.yml | 6 +- .../collection_operations.yml | 6 +- staging.usegalaxy.org.au/convert_formats.yml | 28 +-- staging.usegalaxy.org.au/deeptools.yml | 96 +++---- .../dna_metabarcoding.yml | 8 +- staging.usegalaxy.org.au/emboss.yml | 4 +- staging.usegalaxy.org.au/epigenetics.yml | 6 +- staging.usegalaxy.org.au/fastafastq.yml | 72 +++--- .../fastq_quality_control.yml | 24 +- staging.usegalaxy.org.au/filter_and_sort.yml | 2 +- staging.usegalaxy.org.au/gemini_tools.yml | 24 +- staging.usegalaxy.org.au/genome_editing.yml | 10 +- staging.usegalaxy.org.au/get_data.yml | 28 +-- .../graphdisplay_data.yml | 60 ++--- staging.usegalaxy.org.au/hca_single_cell.yml | 6 +- staging.usegalaxy.org.au/hicexplorer.yml | 12 +- staging.usegalaxy.org.au/imaging.yml | 15 +- staging.usegalaxy.org.au/ivar.yml | 72 +++--- .../join_subtract_and_group.yml | 6 +- staging.usegalaxy.org.au/machine_learning.yml | 20 +- staging.usegalaxy.org.au/mapping.yml | 38 +-- .../metagenomic_analysis.yml | 80 +++--- staging.usegalaxy.org.au/mothur.yml | 6 +- .../multiple_alignments.yml | 43 ++-- staging.usegalaxy.org.au/nanopore.yml | 28 +-- staging.usegalaxy.org.au/none.yml | 40 +-- staging.usegalaxy.org.au/phylogenetics.yml | 85 +++---- staging.usegalaxy.org.au/picard.yml | 10 +- staging.usegalaxy.org.au/proteomic_ai.yml | 6 +- staging.usegalaxy.org.au/proteomics.yml | 142 +++++------ staging.usegalaxy.org.au/rad_seq.yml | 64 ++--- staging.usegalaxy.org.au/rna_seq.yml | 135 +++++----- staging.usegalaxy.org.au/rseqc.yml | 2 +- staging.usegalaxy.org.au/sambam.yml | 46 ++-- staging.usegalaxy.org.au/send_data.yml | 6 +- staging.usegalaxy.org.au/single_cell.yml | 40 +-- staging.usegalaxy.org.au/statistics.yml | 24 +- .../text_manipulation.yml | 32 +-- staging.usegalaxy.org.au/variant_calling.yml | 36 +-- staging.usegalaxy.org.au/vcfbcf.yml | 238 +++++++++--------- staging.usegalaxy.org.au/viral_tools.yml | 2 +- usegalaxy.org.au/annotation.yml | 64 ++--- usegalaxy.org.au/assembly.yml | 192 +++++++------- usegalaxy.org.au/bacterial_typing.yml | 8 +- usegalaxy.org.au/bb_tools.yml | 2 +- usegalaxy.org.au/bed.yml | 14 +- usegalaxy.org.au/blast.yml | 10 +- usegalaxy.org.au/chemicaltoolbox.yml | 52 ++-- usegalaxy.org.au/chip_seq.yml | 8 +- usegalaxy.org.au/collection_operations.yml | 10 +- usegalaxy.org.au/convert_formats.yml | 30 +-- usegalaxy.org.au/deeptools.yml | 98 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 10 +- usegalaxy.org.au/emboss.yml | 4 +- usegalaxy.org.au/epigenetics.yml | 4 +- usegalaxy.org.au/fastafastq.yml | 66 ++--- usegalaxy.org.au/fastq_quality_control.yml | 20 +- usegalaxy.org.au/filter_and_sort.yml | 2 +- usegalaxy.org.au/gemini_tools.yml | 28 +-- usegalaxy.org.au/genome_editing.yml | 6 +- usegalaxy.org.au/get_data.yml | 26 +- usegalaxy.org.au/graphdisplay_data.yml | 50 ++-- usegalaxy.org.au/hca_single_cell.yml | 4 +- usegalaxy.org.au/hicexplorer.yml | 10 +- usegalaxy.org.au/imaging.yml | 23 +- usegalaxy.org.au/ivar.yml | 60 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 4 +- usegalaxy.org.au/machine_learning.yml | 24 +- usegalaxy.org.au/mapping.yml | 42 ++-- usegalaxy.org.au/metagenomic_analysis.yml | 82 +++--- usegalaxy.org.au/mothur.yml | 6 +- usegalaxy.org.au/multiple_alignments.yml | 39 +-- usegalaxy.org.au/nanopore.yml | 30 +-- usegalaxy.org.au/none.yml | 34 +-- usegalaxy.org.au/phylogenetics.yml | 87 +++---- usegalaxy.org.au/picard.yml | 8 +- usegalaxy.org.au/proteomic_ai.yml | 8 +- usegalaxy.org.au/proteomics.yml | 154 ++++++------ usegalaxy.org.au/rad_seq.yml | 76 +++--- usegalaxy.org.au/rna_seq.yml | 137 +++++----- usegalaxy.org.au/rseqc.yml | 4 +- usegalaxy.org.au/sambam.yml | 54 ++-- usegalaxy.org.au/send_data.yml | 4 +- usegalaxy.org.au/single_cell.yml | 40 +-- usegalaxy.org.au/statistics.yml | 22 +- usegalaxy.org.au/text_manipulation.yml | 38 +-- usegalaxy.org.au/variant_calling.yml | 32 +-- usegalaxy.org.au/vcfbcf.yml | 236 ++++++++--------- usegalaxy.org.au/viral_tools.yml | 2 +- 97 files changed, 1983 insertions(+), 1957 deletions(-) diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 3ccd8782c..33fff3e96 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -5231,3 +5231,21 @@ Update 155 05/07/23 14:53:58 openms_targetedfileconverter False Tests failed gal Update 155 05/07/23 14:56:02 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_155/install_log.txt Update 155 05/07/23 15:06:53 salmon False Tests failed bgruening 15cd64d7c58b 15cd64d7c58b Staging Testing 10/11 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_155/install_log.txt Install 1298 11/07/23 12:19:45 data_manager_build_bracken_database True Installed iuc 5c8a23ccb14a 5c8a23ccb14a 0/0 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1298/install_log.txt +Update 156 12/07/23 11:40:44 cactus_cactus False Tests failed galaxy-australia 9eeb13a92d79 9eeb13a92d79 Staging Testing 3/4 Multiple Alignments toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:01:56 cactus_export False Installed galaxy-australia d7ce0ec78e51 d7ce0ec78e51 5/5 5/5 Multiple Alignments toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:05:25 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_156/install_log.txt +Update 156 12/07/23 12:13:45 chipseeker False Tests failed rnateam 8bd92f2404dd 8bd92f2404dd Staging Testing 0/6 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:21:04 count_objects False Installed imgteam 5bf8eb50b280 5bf8eb50b280 1/1 1/1 Imaging toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:27:13 dada2_assigntaxonomyaddspecies False Tests failed iuc 76d3d2b10738 76d3d2b10738 Staging Testing 2/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:31:27 deeptools_plot_heatmap False Tests failed bgruening 25d830337d31 25d830337d31 Staging Testing 0/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:36:01 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_156/install_log.txt +Update 156 12/07/23 12:38:00 encyclopedia_searchtolib False Tests failed galaxyp fb192dd6658a fb192dd6658a Staging Testing 0/2 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:39:59 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_156/install_log.txt +Update 156 12/07/23 12:48:05 lastz False Tests failed devteam 37b497aa133f 37b497aa133f Staging Testing 8/10 Mapping toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:50:12 openms_decoydatabase False Tests failed galaxyp 25529df60a81 25529df60a81 Staging Testing 0/4 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 12:52:16 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_156/install_log.txt +Update 156 12/07/23 12:54:23 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_156/install_log.txt +Update 156 12/07/23 13:44:15 pangolin False Installed iuc 9d61d3fa046c 9d61d3fa046c 4/4 4/4 Phylogenetics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 13:54:09 salmon False Tests failed bgruening 15cd64d7c58b 15cd64d7c58b Staging Testing 10/11 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 14:54:14 seurat False Installed iuc fab6ff46e019 fab6ff46e019 4/4 4/4 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt +Update 156 12/07/23 14:58:07 uniprotxml_downloader False Tests failed galaxyp a371252a2cf6 a371252a2cf6 Staging Testing 0/7 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_156/install_log.txt diff --git a/staging.usegalaxy.org.au/annotation.yml b/staging.usegalaxy.org.au/annotation.yml index 1cfd34ddd..06be118a4 100644 --- a/staging.usegalaxy.org.au/annotation.yml +++ b/staging.usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 78c75f134c16 + - c2ef298da409 - 4efdca267d51 - - 6e9aea89e388 + - 78c75f134c16 - 3f3e247c053d - - c2ef298da409 + - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,20 +36,20 @@ tools: - name: annotatemyids owner: iuc revisions: - - fe3ca740a485 - - 1aae04680c4b - - b5d8e5475247 - - 4f2967b27e67 - - f29602ae449e - 133f36c29579 + - 1aae04680c4b + - fe3ca740a485 - 44018dd6b447 + - f29602ae449e + - 4f2967b27e67 + - b5d8e5475247 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 @@ -64,8 +64,8 @@ tools: owner: bgruening revisions: - ca6d970d931c - - 28433faa6e42 - 09855551d713 + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -78,8 +78,8 @@ tools: owner: iuc revisions: - 7355bbf5e05f - - 8fd427007e93 - fe48aa4ccd5e + - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: chipseeker @@ -116,17 +116,17 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 582fd74dc2a1 - 9f2455341fac - 14f588312c56 + - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 30fb23d4c31c - - a230ea445788 - 73428a792541 + - a230ea445788 + - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare @@ -140,17 +140,17 @@ tools: - name: funannotate_predict owner: iuc revisions: - - 7abc5f6dd595 - 2bba2ff070d9 + - 7abc5f6dd595 - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - 52af33194019 - b3cf4684e9c7 - d3af38b9c7e1 - - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -162,8 +162,8 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 79261884facd - 2aea122fbd25 + - 79261884facd - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -176,10 +176,10 @@ tools: - name: goseq owner: iuc revisions: + - 602de62d995b - ef2ad746b589 - - 8b3e3657034e - 43798b4caee0 - - 602de62d995b + - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -264,11 +264,11 @@ tools: - name: prokka owner: crs4 revisions: - - d643e3b03500 - - 8a22554cdde2 - - bf68eb663bc3 - a17498c603ec + - bf68eb663bc3 + - d643e3b03500 - eaee459f3d69 + - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -280,15 +280,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: rgi @@ -306,21 +306,21 @@ tools: - name: snpeff owner: iuc revisions: - - 68693743661e - 5c7b70713fb5 - - 5b80f544c67f + - 5a29ab10dba6 + - cfcf33df7fc0 - 268d162b9c49 + - 5b80f544c67f - 8f92c2b26e6d - - cfcf33df7fc0 - - 5a29ab10dba6 + - 68693743661e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - - 09d6806c609e - 5fab4f81391d + - 09d6806c609e + - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -344,22 +344,22 @@ tools: - name: tbprofiler owner: iuc revisions: - - ba6f87115e13 - - e1a9d6fd258d - - 037a11682176 - - 45083d070fb8 - ac8250086ac3 + - ba6f87115e13 - 37213cf56392 - - 200c378d85f3 + - e1a9d6fd258d - 2c68b0c38785 + - 45083d070fb8 + - 037a11682176 - 809dfc93d593 + - 200c378d85f3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: trna_prediction diff --git a/staging.usegalaxy.org.au/assembly.yml b/staging.usegalaxy.org.au/assembly.yml index 40c07fd9b..21723b5ed 100644 --- a/staging.usegalaxy.org.au/assembly.yml +++ b/staging.usegalaxy.org.au/assembly.yml @@ -3,23 +3,23 @@ tools: owner: iuc revisions: - fa5259cc561b + - 841084c5fc46 - 7547fcab5d19 - 8f1b150a2487 - 890b794c997d - - 841084c5fc46 - - 0e93176640ac - 553bfe8bd0b5 + - 0e93176640ac tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 94fe43e75ddc - ddddce450736 - - b9e31c5c01c7 - 067592b6b312 - - 21e491ad532a + - 94fe43e75ddc + - b9e31c5c01c7 - b2860df42e16 + - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -31,39 +31,39 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - - 5258e18bbe23 + - faee8629b460 - 3371c5bdc17a - a7f16f24e9a1 - - faee8629b460 + - 5258e18bbe23 + - 22286dab5aa1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 41030a6c03b7 - - 2dd755c1c6ff - cf13a1e03e5b - - e824f5d958d0 - 46ae58b1d792 + - 2dd755c1c6ff + - bb935709506a + - 0d243f458b53 + - 41030a6c03b7 - 1440ae06552f - - e4bd1e99bacf - - 5ecdeca79a0d - f18f0b887c31 + - 5ecdeca79a0d - 94170eee0ad8 - - bb935709506a - - 0d243f458b53 - 1e62c28ba91d - - 4048d82f0c88 + - e4bd1e99bacf + - e824f5d958d0 - 602fb8e63aa7 + - 4048d82f0c88 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - c5b7390290b1 - 5732f959936a - 86f150c8019d + - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -75,19 +75,19 @@ tools: - name: flye owner: bgruening revisions: - - 1ce9b1d72ec3 - - e27815e82dd4 + - 8d4f03b5fe9d - cb8dfd28c16f + - e27815e82dd4 - 276f5d8712d5 + - 1ce9b1d72ec3 - 3ee0ef312022 - - 8d4f03b5fe9d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 01210c4e9144 - b2f674562a18 + - 01210c4e9144 - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -102,10 +102,10 @@ tools: - name: gfastats owner: bgruening revisions: - - 3fba9c77550a - 3ef480892a9f - - 690c2caa367e + - 3fba9c77550a - 5127a713de83 + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -117,18 +117,18 @@ tools: - name: hifiasm owner: bgruening revisions: + - 9ef6920c3089 + - ec9e21e9c71b + - 2061fb3b81b4 - 6505bd37670d + - 5bec28269d95 - 71740308d412 - - ec9e21e9c71b + - 3f7be05a1597 + - 366a11d316a7 - f3c89da3af16 - 045c7c3d8e59 - - 5f625c63b8bc - - 2061fb3b81b4 - - 3f7be05a1597 - - 5bec28269d95 - da9d8bf98802 - - 9ef6920c3089 - - 366a11d316a7 + - 5f625c63b8bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -146,17 +146,17 @@ tools: - name: megahit owner: iuc revisions: + - 7518ee87b53d - de387b2b2803 - 14ddfc8ffb93 - - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 39edec572bae - f8113c25bc6b - 9d79beb19ac3 + - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl @@ -170,13 +170,13 @@ tools: - name: metaspades owner: nml revisions: - - 606b09cc9860 + - fd128c111ab0 - f338e9942b27 + - 3ca2d2a9068c - 2ecf5a570907 - eb7a370f6588 - - fd128c111ab0 + - 606b09cc9860 - e731ea24e48d - - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -188,11 +188,11 @@ tools: - name: miniasm owner: iuc revisions: + - 8dee0218ac7d - 8b6d0d85252b - a7b889b90140 - - 80d1250bd5fd - 73a3846701e1 - - 8dee0218ac7d + - 80d1250bd5fd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -220,71 +220,71 @@ tools: revisions: - 02831bf9e95f - bbe19ef04a74 - - 2b16ba799da9 - 8fef980d48b5 - - d256a51a656b - dfb8a4497339 + - 2b16ba799da9 + - d256a51a656b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: + - e9bd16ba5ebd - 76d4cbefff85 - a315c25dc813 - - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 7594365c546b - - 342a1d1fed7b - - 6fcbee531de6 + - ebb0dcdb621a - 875d0f36d66f - - 59db8ea8c845 - 3061c8b029e5 - - 675488238c96 - - ebb0dcdb621a - 72472698a2df + - 342a1d1fed7b + - 675488238c96 + - 7594365c546b + - 59db8ea8c845 + - 6fcbee531de6 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - aa39b19ca11e - - d865b62f501c - a199cd7ac344 - - cd06929b224b - 39bed8de8017 + - d865b62f501c + - cd06929b224b - e100a765370e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - f11b994b7eb2 - 33b7d8481a76 + - f8564b2d7f63 - 3edba9afc9bc + - f11b994b7eb2 - 2b2a352488fa - - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - 53c2bc8c2ae3 - 378e55aeeb25 + - 1d06c8b38e77 - e122f9101584 - - 53c2bc8c2ae3 - ef69617ecb42 - - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - ab5b7f6b7198 - - ba7b0f11e470 - 9a22227bb6d0 + - ba7b0f11e470 + - ab5b7f6b7198 - f77f7a7f3b83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -297,47 +297,47 @@ tools: - name: shovill owner: iuc revisions: + - ad80238462c1 - 865119fcb694 - - f698c7604b3b - - 83ead2be47b2 - 196a599ec43d - - ad80238462c1 + - 83ead2be47b2 + - f698c7604b3b - d9f6a00b6db7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - - 5e0825476fb7 - 5a0ddb4dc3a4 + - 5e0825476fb7 + - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: + - 904bf932cf78 + - 1fc82fe7ebef - 7490b213baa9 - 051fd2db8a27 - - 1fc82fe7ebef - - 904bf932cf78 - 1bb12736175c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - ad8b536d1caa - - 34305b013402 - 808b3a0a6716 - d6e617c4e338 + - 34305b013402 - fee85957cebe + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - b8002c3f7141 - 8d4b90bf9caf + - b8002c3f7141 - 6b5a5842531e - e5a3b75a271f - 21da31ed41a1 @@ -346,71 +346,71 @@ tools: - name: spades_metaviralspades owner: iuc revisions: - - 2a10645aeadd + - 9de69775f512 - f1532cb33c75 - - 86f66ab58e14 - 328aa71f0f3c - - 9de69775f512 + - 2a10645aeadd + - 86f66ab58e14 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 1708851f8804 - - 340bc17f49cf + - 6aad515a5270 - e41dcb0e913b - 85fb02c43042 - - 6aad515a5270 + - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b3490b036c5a - - d159735a6a9f - - 249f6a28c751 - d5fb354f745d + - 249f6a28c751 + - d159735a6a9f - b65a43f70b99 + - b3490b036c5a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d2d1df21dfb9 + - 7897763d14ec - b7829778729f + - 9006e5836729 - dd7ad84f3943 - 33368fec3b70 - - 9006e5836729 - - 7897763d14ec + - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ced385aa976d - 505a9833ab5d - - 8f631679571f + - ced385aa976d - 6f4c8ad6ea01 - 189e837009c9 + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - e59bee4565b3 + - d40ed4eb0c0e - 19bdfd1e6fe3 - - 9ded6109434a - 356afed970b4 - - d40ed4eb0c0e + - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 80a17897564d - 4688ae3b49b5 - b23249f81bc4 - ebd801e712bc - - 80a17897564d - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -418,49 +418,49 @@ tools: owner: iuc revisions: - b5e35a2ca4f3 + - 59bd28f6265d + - 937ea677d437 - b64696992ee9 - cb1e3db43020 - - 937ea677d437 - - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - 383bb5ad32e2 - 6015aa0303f2 + - cb4768eeca3b - 05bd7504fdb2 - - 383bb5ad32e2 - 2628f6790eda - - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - d10bdad2fd17 + - 6e26c9afd301 + - 9e3e80cc4ad4 - 0a3a602cd1e3 - e92675014ac9 - - 9e3e80cc4ad4 - - 6e26c9afd301 - - d10bdad2fd17 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f + - 8d09f8be269e - 920677cd220f - 5da9a0e2fb2d - - 8d09f8be269e + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - d81360ea69d8 - - 4a53b89fa703 - 37d88f41c810 - - 0e2b4e3f9ca1 + - 4a53b89fa703 - 82398ba86ba7 + - d81360ea69d8 + - 0e2b4e3f9ca1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/staging.usegalaxy.org.au/bacterial_typing.yml b/staging.usegalaxy.org.au/bacterial_typing.yml index b169fe5be..545fce894 100644 --- a/staging.usegalaxy.org.au/bacterial_typing.yml +++ b/staging.usegalaxy.org.au/bacterial_typing.yml @@ -15,17 +15,17 @@ tools: - name: mlst owner: iuc revisions: + - 31812e7a1315 - ded48b36f3b7 - 1f5641a52664 - 8e8dc9a1e3e5 - - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 17fcac7ddf54 - 5c8ff92e38a9 + - 17fcac7ddf54 - 24a7a95867b0 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/bb_tools.yml b/staging.usegalaxy.org.au/bb_tools.yml index 70adf3e9d..93b7c3d31 100644 --- a/staging.usegalaxy.org.au/bb_tools.yml +++ b/staging.usegalaxy.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 204a131e47db - - 159b04e36791 - a9c9d768b751 + - 159b04e36791 + - 204a131e47db tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/bed.yml b/staging.usegalaxy.org.au/bed.yml index ce2200037..da1bc1d78 100644 --- a/staging.usegalaxy.org.au/bed.yml +++ b/staging.usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - e19bebe96cd2 - - a8eabd2838f6 - - b28e0cfa7ba1 - ce3c7f062223 - - a1a923cd89e8 - - a68aa6c1204a - - 07e8b80f278c - 589e7e57fd6d - 0a5c785ac6db - - dde39ba9c031 + - a8eabd2838f6 - 87ee588b3d45 + - 07e8b80f278c + - dde39ba9c031 + - e19bebe96cd2 + - b28e0cfa7ba1 + - a68aa6c1204a + - a1a923cd89e8 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/blast.yml b/staging.usegalaxy.org.au/blast.yml index cc7cffdac..d5b422f28 100644 --- a/staging.usegalaxy.org.au/blast.yml +++ b/staging.usegalaxy.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - 54f751e413f4 - 62c9df8382c2 - - 1e3323a44643 + - 54f751e413f4 - f921014aba5a + - 1e3323a44643 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: - - e25d3acf6e68 - - 0e3cf9594bb7 + - 5edc472ec434 - 6f386c5dc4fb + - 0e3cf9594bb7 - acf4e47b734c - 2889433c7ae1 - - 5edc472ec434 + - e25d3acf6e68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.usegalaxy.org.au/chemicaltoolbox.yml b/staging.usegalaxy.org.au/chemicaltoolbox.yml index aa36432b8..1c7803f19 100644 --- a/staging.usegalaxy.org.au/chemicaltoolbox.yml +++ b/staging.usegalaxy.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 710301bc46fa - 27ee142314a9 - - 095ad4d096d1 - - 6ca543ec1bf8 - f4230f116196 + - 6ca543ec1bf8 - c8cdde00b105 + - 095ad4d096d1 - da6bd1975a71 + - 710301bc46fa tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -74,8 +74,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: enumerate_charges @@ -102,89 +102,89 @@ tools: revisions: - 3b8a9d5ced85 - 88076940fa94 - - 0fac8e2afc13 - - 79cfd9ead848 - bfb65cb551d8 + - 79cfd9ead848 + - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 715cd0e87781 - - b46d4b4d995c - f5d979cb4b54 - eb6564a60136 - - 55918daa5651 - d532b7e5f64b + - 715cd0e87781 + - b46d4b4d995c + - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 97872d87ba80 - - f26afd1b7104 - - 5579659312e6 - d2f955aea23a + - f26afd1b7104 + - 97872d87ba80 - fdf2cc80adb5 + - 5579659312e6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: + - 319a28774da9 - bc31d02be922 - d1d0efda35c0 - - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - 2c349b027a01 - - cac1886249a2 - 4da9ee404eab + - ed736e6eee39 + - cac1886249a2 - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 525ca7c8065f - - c0c9a5024177 - - da8753545526 - - d1f803b5943c - - 807aa4c9293d - - 73008ef1f487 - f197e34c33a9 + - 73008ef1f487 - 2e219a2d9327 + - 807aa4c9293d + - d1f803b5943c + - 525ca7c8065f + - da8753545526 + - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 61094e01eff9 - 1809414a9454 - - 2c8ed1b52bf7 + - 7568ae18908a + - 61094e01eff9 - 27ea4e1a3f95 + - 2c8ed1b52bf7 - c4fbab8e03c5 - - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: + - d7ec25187599 + - ba83f0923369 - ccfbd956a2d3 - 79e8ab8f1e81 - 730ef07b90ae - - ba83f0923369 - - d7ec25187599 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 9a3a1f698fc6 - 48d6a6eb438b + - 9a3a1f698fc6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: natural_product_likeness @@ -196,9 +196,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - - 1400d1977e7b - e6011617c748 + - 1400d1977e7b + - b59c91adeac1 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 - - d4c67ced6abc - bf99565cec1f + - d4c67ced6abc - 9b48456a96fe + - 85fad59f8168 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.usegalaxy.org.au/chip_seq.yml b/staging.usegalaxy.org.au/chip_seq.yml index 733f11408..f3350f6b9 100644 --- a/staging.usegalaxy.org.au/chip_seq.yml +++ b/staging.usegalaxy.org.au/chip_seq.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - c97a786e8fb5 - - fa56d93f7980 - 163688bb8f73 + - fa56d93f7980 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -22,8 +22,8 @@ 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 @@ -31,8 +31,8 @@ tools: revisions: - 640d3af5d833 - f5d67c722d67 - - 495a4173006f - 424aefbd7777 + - 495a4173006f tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 diff --git a/staging.usegalaxy.org.au/collection_operations.yml b/staging.usegalaxy.org.au/collection_operations.yml index cd0b73a09..5f2288772 100644 --- a/staging.usegalaxy.org.au/collection_operations.yml +++ b/staging.usegalaxy.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - 705ebd286b57 - cd6da887a5f4 + - 705ebd286b57 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - 830961c48e42 - - 90981f86000f - 33151a38533a + - 90981f86000f - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_to_collection diff --git a/staging.usegalaxy.org.au/convert_formats.yml b/staging.usegalaxy.org.au/convert_formats.yml index 5e501292c..c440ba21a 100644 --- a/staging.usegalaxy.org.au/convert_formats.yml +++ b/staging.usegalaxy.org.au/convert_formats.yml @@ -8,13 +8,13 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 4a6ee918c13a - - 5e1240a87bcb - 367b1ed91207 - a3b86937ead6 - - 0b3c3ad92827 - f3a19509108a - e3cbd2287f63 + - 0b3c3ad92827 + - 5e1240a87bcb + - 4a6ee918c13a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert @@ -22,19 +22,19 @@ tools: revisions: - 72ed72122deb - 1b5fc03380d4 - - 33c99804a32f - 54ccb7e1f49a + - e525f9ffb9ac - bd46669113b9 + - 33c99804a32f - 584008e574b2 - 501c21cce614 - - e525f9ffb9ac tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - 11c3eb512633 - a0d092f27fdf + - 11c3eb512633 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -60,8 +60,8 @@ tools: - name: fastq_to_tabular owner: devteam revisions: - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -73,8 +73,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -105,32 +105,32 @@ 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 owner: devteam revisions: - - 0a7799698fe5 - 0b4e36026794 + - 0a7799698fe5 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - 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: + - 26c6706bfb07 + - 92ac8e086317 - 19e45916daf9 - - b9b385097f13 - 63769c4217a7 - - 92ac8e086317 - - 26c6706bfb07 + - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.usegalaxy.org.au/deeptools.yml b/staging.usegalaxy.org.au/deeptools.yml index 38d974333..23d12ebf0 100644 --- a/staging.usegalaxy.org.au/deeptools.yml +++ b/staging.usegalaxy.org.au/deeptools.yml @@ -2,66 +2,66 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - de72ba3ed6f2 - a1ca9bccc7f2 - - 29451af70c52 - e821645ef8fc - 268e91e540ee + - de72ba3ed6f2 - 5f6d123679f4 + - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - bb1e4f63e0e6 - 0e143b4c3987 - - 2d2cf5c1ea8a - - 12af64f93288 - 5d11599b8a7d + - 12af64f93288 + - bb1e4f63e0e6 + - 2d2cf5c1ea8a - 7a7fd0f5f15d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 81b1e3e1fc6c - 195e98217334 - - 1d848bc4585f - - 7c1beb6d6eca + - 81b1e3e1fc6c - dc059492a995 + - 7c1beb6d6eca + - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 3d211717a775 - - 93eb012d9eed - - 26e7304d6737 - a67ac707496a - bfff7454b59a + - 93eb012d9eed + - 3d211717a775 - 71aa86af6762 + - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 2bc10a9ca58b - - 29fcfd36e90a - - b8858746dc1f - 56d5b797ce84 - 5be24eba848d + - 2bc10a9ca58b + - b8858746dc1f - dd0b7398bb96 + - 29fcfd36e90a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - ee3a1b0f45f1 - - 9384cd033f30 - - c3e012dfe21f - 7e6bcd2e5128 - - 7ef978dc1b8a + - c3e012dfe21f + - 9384cd033f30 - 72bfafe3330b + - ee3a1b0f45f1 + - 7ef978dc1b8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix @@ -69,44 +69,44 @@ tools: revisions: - b73e213add0c - 9470f29702f8 + - 167788df3b46 + - 514fa53b5efb - fd1275e01605 - fb9cf9c97ec4 - - 167788df3b46 - d9a637e83828 - - 514fa53b5efb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 5bffaa8354a1 + - c34d11ea4ba6 - ca0616bb2cdf - - 2c37ce318bc3 - a02cfa31e9cb + - 2c37ce318bc3 + - 5bffaa8354a1 - 86febdcc4283 - - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 78f405266706 + - 1fcb7adc39b8 + - 2d466b530754 - 004aea905d4d - 192ef85c0b0b - - 2d466b530754 - 69a8621ca2f0 - - 78f405266706 - - 1fcb7adc39b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - d580d6acd1df - 2f9e4843f480 - 3c9f0c486cca - - 459cfa861f0b - - d580d6acd1df - - d9ce4897dbb2 - 9ecba5e225a6 + - d9ce4897dbb2 + - 459cfa861f0b - db940c262830 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -114,75 +114,75 @@ tools: owner: bgruening revisions: - 2c66e43f1c86 + - 32e451def88c + - f264afa9fa6f - bd7db9e2f2cb - fd408d755394 - fbe773640707 - - 32e451def88c - - f264afa9fa6f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 7fda5607e777 - - 7e361d147872 - 3b9d990a0a0e - 4e12ea27f788 - - 9368fbc49c8b - 56bce3c82278 + - 9368fbc49c8b + - 7e361d147872 + - 7fda5607e777 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - c03c3384cd81 - e65d16fb2724 - - b1779366c8e9 - ce4ce3316f74 - - 94ca68515826 - d9114ef1c8a5 + - 94ca68515826 + - c03c3384cd81 + - b1779366c8e9 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 793665fff0f8 + - 23f7c5f1fdaf - d57251071381 - b88ebb3672a1 - - 23f7c5f1fdaf - - f8fc4e5aff9d - 2da482e408b8 + - 793665fff0f8 + - f8fc4e5aff9d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - 010e58e9d822 - - c60570fa602f - - 512155688d98 - - a7849312d328 - ba6efa77fb79 - a4dfb122e52b + - 512155688d98 + - a7849312d328 + - c60570fa602f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - 69264da0ce77 - - 4d678170d29b - 38e3f226248b - c899e0ccff8c - - 00d869ea03a1 - aa200e4f3939 + - 4d678170d29b + - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a - - a2d70c4fd406 + - 10301d137111 - d806504e96d9 + - a2d70c4fd406 + - c361b12d207a - aac8444d6681 - - 10301d137111 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/dna_metabarcoding.yml b/staging.usegalaxy.org.au/dna_metabarcoding.yml index bce6924fb..0d06819f5 100644 --- a/staging.usegalaxy.org.au/dna_metabarcoding.yml +++ b/staging.usegalaxy.org.au/dna_metabarcoding.yml @@ -16,22 +16,22 @@ tools: - name: obi_convert owner: iuc revisions: - - 374fd9feb032 - 4d705e3443a7 + - 374fd9feb032 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - fe7ec8a3d35e - e9e49cf06b42 + - fe7ec8a3d35e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 94f412098ac8 - 83fbdf93d51e + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 723a93febe89 - 39320fee9d70 + - 723a93febe89 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab diff --git a/staging.usegalaxy.org.au/emboss.yml b/staging.usegalaxy.org.au/emboss.yml index c87ebd957..52347455d 100644 --- a/staging.usegalaxy.org.au/emboss.yml +++ b/staging.usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - 63dd26468588 - dba489bfcd62 - - 832c20329690 - ce385837c160 + - 63dd26468588 + - 832c20329690 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/epigenetics.yml b/staging.usegalaxy.org.au/epigenetics.yml index 9d982d970..fb8edc8f2 100644 --- a/staging.usegalaxy.org.au/epigenetics.yml +++ b/staging.usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - 62f5fab76dfb - - 29bdbc353f20 - d82648ad25a3 + - 62f5fab76dfb - 6da3972210ee + - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -17,7 +17,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/fastafastq.yml b/staging.usegalaxy.org.au/fastafastq.yml index 51b1952bf..420d2770d 100644 --- a/staging.usegalaxy.org.au/fastafastq.yml +++ b/staging.usegalaxy.org.au/fastafastq.yml @@ -8,22 +8,22 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8665bcc8b847 - - c4b82dce8335 - - 660cffd8d92a - - 093678460093 - - c5e2e5902201 - - 49370cb85f0f + - 135b80fb1ac2 - e4691e1589d3 + - c5e2e5902201 + - 8c0175e03cee - 48f587c13075 - - c053d4cad713 - 5915ea1ec9b1 - - 44e2cc14f75b - - 8c0175e03cee - - 288f97432497 - 4e5056fefd88 - - 135b80fb1ac2 + - 8665bcc8b847 + - 44e2cc14f75b - de6cebe3c043 + - c053d4cad713 + - c4b82dce8335 + - 660cffd8d92a + - 288f97432497 + - 093678460093 + - 49370cb85f0f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -62,38 +62,38 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - e626b3ff9922 - 8cacfcf96a52 + - e626b3ff9922 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 9457a20156db - 859422bcb689 + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - f81d4362b6c1 - ec0b5076173a + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - cd0874854f51 - - 9c620a950d3a - 56022eb50bbd + - cd0874854f51 - 0dbb995c7d35 + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -105,8 +105,8 @@ tools: - name: fastp owner: iuc revisions: - - 65b93b623c77 - dbf9c561ef29 + - 65b93b623c77 - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -126,8 +126,8 @@ tools: - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - 10b75444feae + - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -140,15 +140,15 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -176,8 +176,8 @@ tools: owner: devteam revisions: - 249c8393f2d4 - - e39cc71d3ed6 - 35e38452bb3f + - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -189,15 +189,15 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 54053ea6c77e - 74db4cffab1f + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - f0e7deab6518 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -216,8 +216,8 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 09070cacefd8 - 567d5b3c52b1 + - 09070cacefd8 - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -231,24 +231,24 @@ tools: - name: fastx_clipper owner: devteam revisions: - - 736b8f6ee456 - cb1e251cac37 + - 736b8f6ee456 - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 421f0af4ee95 - 7ce1891db6f5 + - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 - 02f8a17a4ebd - 3599f5451ee2 + - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -282,8 +282,8 @@ tools: - name: pear owner: iuc revisions: - - b4c6f054210a - 2f804526f5fd + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -314,8 +314,8 @@ 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 @@ -334,11 +334,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f - - b557acca0b56 + - 8250ea3a1501 - a535cf1e5da4 - e654095ab143 - - 8250ea3a1501 + - 24013bf85a6f + - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -356,11 +356,11 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - f3759eec3018 + - 9fa7803d1c51 + - 7accf7407811 - 27ac32a22ad2 - 6a675c3aa610 - - 7accf7407811 - - 9fa7803d1c51 + - f3759eec3018 - 828dba98cdb4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/fastq_quality_control.yml b/staging.usegalaxy.org.au/fastq_quality_control.yml index 6cdc5536f..0046e6ed1 100644 --- a/staging.usegalaxy.org.au/fastq_quality_control.yml +++ b/staging.usegalaxy.org.au/fastq_quality_control.yml @@ -18,12 +18,12 @@ tools: owner: devteam revisions: - f2e8552cf1d0 - - 3d0c7bdf12f5 - - e7b2202befea - - 5ec9f6bceaee - ff9530579d1f - 9da02be9c6cc + - e7b2202befea + - 3d0c7bdf12f5 - 2b0c9d9fc6ca + - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -43,37 +43,37 @@ tools: - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - 8880fb74ef56 - - a72af9de6bf5 - 41b2ad601cf0 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 5e33b465d8d5 - - abfd8a6544d7 - - f7985e0479b9 - - b2f1f75d49c4 - bf675f34b056 - - 9a913cdee30e - - 3d93dd18d9f8 + - f7985e0479b9 - 75c93c70d094 + - abfd8a6544d7 + - 3d93dd18d9f8 + - 5e33b465d8d5 - 1c2db0054039 + - b2f1f75d49c4 + - 9a913cdee30e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 949f01671246 - 084bbd8ba7b8 - cd7e644cae1d + - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/filter_and_sort.yml b/staging.usegalaxy.org.au/filter_and_sort.yml index 5b44a1c25..7946b577d 100644 --- a/staging.usegalaxy.org.au/filter_and_sort.yml +++ b/staging.usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs diff --git a/staging.usegalaxy.org.au/gemini_tools.yml b/staging.usegalaxy.org.au/gemini_tools.yml index d7dc41b81..b9dc5ca01 100644 --- a/staging.usegalaxy.org.au/gemini_tools.yml +++ b/staging.usegalaxy.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 @@ -16,8 +16,8 @@ tools: - name: gemini_annotate owner: iuc revisions: - - 8f53b238a360 - 0c8f7322f8fc + - 8f53b238a360 - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -86,52 +86,52 @@ tools: - name: gemini_load owner: iuc revisions: + - cf61daf064fe - b2c25142267e - 45296e47d565 - - cf61daf064fe 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 owner: iuc revisions: - - 61343646155c - 00c2734b3bea + - 61343646155c tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways owner: iuc revisions: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - 840fb4850be3 - 666f60a9331a - da74170c55c7 + - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 05124dc72dba - 86f3aac4418d + - 05124dc72dba tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region @@ -144,8 +144,8 @@ tools: - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -165,7 +165,7 @@ tools: - 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/staging.usegalaxy.org.au/genome_editing.yml b/staging.usegalaxy.org.au/genome_editing.yml index 061f295f2..0fe27413f 100644 --- a/staging.usegalaxy.org.au/genome_editing.yml +++ b/staging.usegalaxy.org.au/genome_editing.yml @@ -2,35 +2,35 @@ 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: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/get_data.yml b/staging.usegalaxy.org.au/get_data.yml index a50c5a467..88515fe13 100644 --- a/staging.usegalaxy.org.au/get_data.yml +++ b/staging.usegalaxy.org.au/get_data.yml @@ -2,52 +2,52 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - e9df53a75f3c - b39347891609 - 983bf725dfc2 - c1b437242fee - - e9df53a75f3c 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: - aad3885b3216 - - c441583adae5 + - 1790dcf3c32d + - 7068f48d0ef9 + - 9a776b080193 + - 653e89d73fc4 - 4df8de2d0e48 - e08a7ad4378b - - 6ea73833cf67 - - 9a776b080193 - - 7068f48d0ef9 + - f5ea3ce9b9b0 - 69ebb7f46e45 - 83c7d564b128 + - c441583adae5 - 5e6237d58b0c - - 1790dcf3c32d - - f5ea3ce9b9b0 - - 653e89d73fc4 + - 6ea73833cf67 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 - 7863f1abcdda - - 34758ab8aaa4 - 75b3b3d0adbf + - 9aaa46d45472 + - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - af5eccf83605 - - bfdc6a7ffd3a - 054483e27a35 + - bfdc6a7ffd3a + - af5eccf83605 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/graphdisplay_data.yml b/staging.usegalaxy.org.au/graphdisplay_data.yml index a3d57c854..426be3ce9 100644 --- a/staging.usegalaxy.org.au/graphdisplay_data.yml +++ b/staging.usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: + - a64dc31ab7f2 - fd59d783248a - - 4b519282a05b - - 290a11559985 - - 740057a5126d - - ae9994cf526f - c4bde687c846 + - 290a11559985 - 7f13dc906cb9 - df7356989ac1 - - a64dc31ab7f2 + - 4b519282a05b + - 740057a5126d + - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,38 +34,38 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - '566197475670' - - 3b37b1b1c3a7 - ca7cb0eaad62 + - 53460afd5115 + - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 3d059e9c2fba - - 10515715c940 - 391a4cc45fea - - d3a9e32672ec + - 10515715c940 - da4c086cff5b + - 3d059e9c2fba + - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 299307abd804 - - 3b12bf9b4b87 + - 1acf88921176 - d0fc8b746d57 + - 299307abd804 - 5fe1dc76176e + - 3b12bf9b4b87 - e3a675da7fd0 - - 1acf88921176 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -91,24 +91,24 @@ 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: + - a6e57ff585c0 - 4542035c1075 + - 1cfc579079a6 + - 836d1aa3e89a - fd5dbf0f732e - - 2bb2e07a7a21 - ca2def38369c - 17359b808b01 - - 1cfc579079a6 + - 6cd09d7b5f37 - 667e17248bfe - - 836d1aa3e89a + - 2bb2e07a7a21 - 112eb40ba6cf - - 6cd09d7b5f37 - - a6e57ff585c0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -160,8 +160,8 @@ 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 @@ -173,22 +173,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 2824d77cd8f8 - - 360df4999907 - - 14e7c35f3d00 - - 7dd841a32245 - - 326a3db8d9d1 - a1abfa420d9d - - 59fd173ac850 + - 360df4999907 - 4ac4e7083b7e + - 59fd173ac850 + - 326a3db8d9d1 + - 7dd841a32245 + - 14e7c35f3d00 + - 2824d77cd8f8 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - - 73b8cb5bddcd - 83c573f2e73c + - 73b8cb5bddcd + - 44608d0193ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 @@ -200,7 +200,7 @@ 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.usegalaxy.org.au/hca_single_cell.yml b/staging.usegalaxy.org.au/hca_single_cell.yml index 73010e498..872bf3816 100644 --- a/staging.usegalaxy.org.au/hca_single_cell.yml +++ b/staging.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: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 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: - - 767a675b5254 - 0f98603d0116 + - 767a675b5254 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/staging.usegalaxy.org.au/hicexplorer.yml b/staging.usegalaxy.org.au/hicexplorer.yml index 43a049302..720d6d65b 100644 --- a/staging.usegalaxy.org.au/hicexplorer.yml +++ b/staging.usegalaxy.org.au/hicexplorer.yml @@ -3,39 +3,39 @@ tools: owner: bgruening revisions: - 921a2da49a0c - - 29f66c353bcb - 9edf8894a22d + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - 5746d61f0a91 - d404277cc87a - 78fb5e286609 - - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - 03dd3c16ae4e - - 4d511437b1e5 - 9e357a8b2ec3 + - 4d511437b1e5 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: + - 41dbf4d162a2 - 3b5b54ed6392 - 0ba4f56a3613 - - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 - - 7babd8a46fe0 - 5308ca68ef3d + - 7babd8a46fe0 + - 9939786dd9c9 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/imaging.yml b/staging.usegalaxy.org.au/imaging.yml index d74fa1eb6..1c5680083 100644 --- a/staging.usegalaxy.org.au/imaging.yml +++ b/staging.usegalaxy.org.au/imaging.yml @@ -46,6 +46,7 @@ tools: - name: count_objects owner: imgteam revisions: + - 5bf8eb50b280 - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -79,22 +80,22 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - 2484086dee41 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color @@ -121,22 +122,22 @@ tools: - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 91e03287f285 - 20dbb1f7ec7b + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity @@ -215,7 +216,7 @@ 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.usegalaxy.org.au/ivar.yml b/staging.usegalaxy.org.au/ivar.yml index 4d342983a..0374a687b 100644 --- a/staging.usegalaxy.org.au/ivar.yml +++ b/staging.usegalaxy.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - e4ee04da1c19 - - d6e72da3ec35 - - 78bbd17d0703 - - 3e4f434a69c6 - f362150bef41 - - a38934e303b9 - - 1069f6db0a0e - e319b5b65879 + - 3e4f434a69c6 + - 1069f6db0a0e + - d6e72da3ec35 + - 78bbd17d0703 - 17f911830a8c + - a38934e303b9 + - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - c88553ec696e - - 9537184d421f - - 1ef5b6e3e09d - 72ddd32392cd + - 9537184d421f + - c88553ec696e + - 0135f1d487a0 - 8f8df367470d - - f91cfb73d369 - 7fe36019c073 + - 1ef5b6e3e09d - 2b95d5c04908 - - 0135f1d487a0 + - f91cfb73d369 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 - - d7e79eb3bcb3 - ad0dc9f4c9e2 + - d7e79eb3bcb3 + - 2cf4a1cafc16 - fafb3d685fa9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - ee29337f905c - - 94df24c6bc00 - - 43aac8d29685 - bd2a7d1316b9 + - 69797fa273c3 - 3d18f8c3c0f6 - - 6a1515bb0687 - - 8c05afb547fa + - ee29337f905c + - 43aac8d29685 + - 28a6f1908fcc - ee2beb764a7b + - 94df24c6bc00 + - 7f1cfa4c0e32 - 8d36959b000d + - 6a1515bb0687 + - 8c05afb547fa - 9eaadf03e0df - - 7f1cfa4c0e32 - - 69797fa273c3 - - 28a6f1908fcc tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - c092052ed673 - - bcaa0d571ce2 + - 5671e1d3d5ee + - 5d6ed46cc101 + - 8858fa037a15 + - 0893a1dbb807 - 364f4ffec275 + - db536ad45f28 + - c092052ed673 - d37ede8589b2 + - cb903c9dc33d - 9f978da6528a + - bcaa0d571ce2 - e3bb03cf207a - - cb903c9dc33d - - 8858fa037a15 - - 0893a1dbb807 - - 5671e1d3d5ee - - 5d6ed46cc101 - - db536ad45f28 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 584beffa972b - - 3b6a16d82c1b - - 230b05597996 - e1a015876aa9 - - ed28dd32141c - - 045d6d00f606 - - f95f403841ad + - 49236b03e4fd + - 230b05597996 + - 584beffa972b - 12d66d0d05ac + - f95f403841ad + - ed28dd32141c + - 3b6a16d82c1b - c5c9f02b6167 + - 045d6d00f606 - 38b91a3190cd - - 49236b03e4fd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/join_subtract_and_group.yml b/staging.usegalaxy.org.au/join_subtract_and_group.yml index 53622b4f0..eba36b66e 100644 --- a/staging.usegalaxy.org.au/join_subtract_and_group.yml +++ b/staging.usegalaxy.org.au/join_subtract_and_group.yml @@ -2,18 +2,18 @@ tools: - name: datamash_reverse owner: iuc revisions: - - f198773344e4 - 0f1724dd59d2 - - b8a457820315 + - f198773344e4 - 17e3b698dd52 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ba0c40780ecf - 374cb875d38a - 22c2a1ac7ae3 - ac092723240d + - ba0c40780ecf tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/machine_learning.yml b/staging.usegalaxy.org.au/machine_learning.yml index cc49266c4..575751fd8 100644 --- a/staging.usegalaxy.org.au/machine_learning.yml +++ b/staging.usegalaxy.org.au/machine_learning.yml @@ -15,16 +15,16 @@ tools: owner: bgruening revisions: - f1b9a42d6809 - - b6ef6d0cb6b7 - e1317b5502fa + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 947c2eacccb8 - - 05143043ca13 - c80db5d6fd8c + - 05143043ca13 + - 947c2eacccb8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction @@ -39,42 +39,42 @@ tools: owner: bgruening revisions: - 841a6cc5fc58 - - 1a53edc4b438 - - 53616c8b0865 - a07ab242b0b5 + - 53616c8b0865 + - 1a53edc4b438 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - dc4b5fd604a6 - - 91c4e3331208 - 2fc89dcd41c8 + - 91c4e3331208 - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - e5a5ad882f1f - 25ab6b4e376e - c6ae57f774c6 - 301e07345c93 + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 4ed102b922cb - - f9639b488779 - b7c3e9a3b954 - 02d2be90dedb + - f9639b488779 + - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - ec69cbe34b73 + - 14180f9c831e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/mapping.yml b/staging.usegalaxy.org.au/mapping.yml index ef33ee926..a01e06605 100644 --- a/staging.usegalaxy.org.au/mapping.yml +++ b/staging.usegalaxy.org.au/mapping.yml @@ -3,14 +3,14 @@ tools: owner: devteam revisions: - 03e9b2fbc005 + - 937aa69e715f + - 3ba8d4563129 - f6877ad76b00 - - 749c918495f7 - - 17062a0decb7 - - a6d65b0c67af - 017aba02828d + - a6d65b0c67af + - 17062a0decb7 - cd659e8cc5fa - - 937aa69e715f - - 3ba8d4563129 + - 749c918495f7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -28,11 +28,11 @@ tools: - name: bwa owner: devteam revisions: - - dfd8b7f78c37 - 3fe632431b68 + - dfd8b7f78c37 + - 53646aaaafef - 64f11cf59c6e - e188dc7a68e6 - - 53646aaaafef tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -44,41 +44,41 @@ tools: - name: lastz owner: devteam revisions: + - 3e1ea2facca6 + - 60afcc2c1d05 - 2ff111fac1d7 - e7f19d6a9af8 - - 60afcc2c1d05 - - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 8c6cd2650d1f + - c0c2d0941de8 - 77b2770508f6 + - 3f4d6399997b + - 8c6cd2650d1f - be1d967337e4 - - 53c0b7a1a0c3 + - b3eab4b67562 + - 037c6e54df11 - 6b1e195506a3 - 11a0d50a54e6 - - 037c6e54df11 - 09b53c1d4ab1 + - 53c0b7a1a0c3 - f54f5baedfdd - - b3eab4b67562 - - c0c2d0941de8 - - 3f4d6399997b tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 9ee34ba73ebf + - e403d27e8f24 - 1cd2511a396e + - 9ee34ba73ebf + - ec9cbd6b9a49 + - 13022c3d3076 - 178bdbdb6d24 - 79b885ce78d7 - 00fbfac99d39 - b8f5f6e87f5c - - 13022c3d3076 - - e403d27e8f24 - - ec9cbd6b9a49 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.usegalaxy.org.au/metagenomic_analysis.yml b/staging.usegalaxy.org.au/metagenomic_analysis.yml index 41d9a8e85..d1347a46b 100644 --- a/staging.usegalaxy.org.au/metagenomic_analysis.yml +++ b/staging.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_prepare @@ -34,8 +34,8 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 5b5a7af9fbb4 - 63f86089423e + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada @@ -49,24 +49,24 @@ tools: - name: dada2_filterandtrim owner: iuc revisions: - - f732237754fc - - a9f4a217dcd6 - 34e55239e68b + - a9f4a217dcd6 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 04c15826a0b8 - 8c202e741d68 - 0776d824d896 - - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - e96bbb9e24ea - 8470de786d47 + - e96bbb9e24ea - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -74,16 +74,16 @@ tools: owner: iuc revisions: - 306a40d4bb8f - - 1d75bd0595e2 - 84743da21318 + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - 555ccac8a4c5 - - 8daf4564ccda - ac72310b038a + - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile @@ -97,17 +97,17 @@ tools: - name: dada2_removebimeradenovo owner: iuc revisions: + - 04144473e59e - 1bc3657cd694 - 7f3b59dee073 - - 04144473e59e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: + - 9058d8943303 - d943081510da - 0a1224c4b781 - - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -134,8 +134,8 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - 6c84982ee6f7 + - 654548ae1357 - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -157,16 +157,16 @@ tools: owner: iuc revisions: - c6676a890f50 - - d77397f09da1 - b084117133af + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - cad93abecac9 - - 7f208f1eb64f - 9704f1a3b32d + - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -178,54 +178,54 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 - c409a495841f - 79706f10d680 + - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - d24841f5c3d2 - - 714d5a28cc5c - 172920f67a84 - 71ea608ddfa3 + - d24841f5c3d2 + - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 12fb63b5f63f - - 4137b492233e - d7e9a3c41657 - a4d7148ccee4 + - 12fb63b5f63f + - 4137b492233e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - 6fcb8ac37a3e - 64bc7acc22a9 - - 75bedfb2078b - - cf87759761eb - e2c71b852aba + - cf87759761eb + - 6fcb8ac37a3e + - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c - 5e5a999ffaa9 - - c82508e76ad1 - 4033827c76b8 + - 080ea153677c + - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: + - 95bf7479d53c - 6b7622dda516 - 2cd76b089570 - - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -305,8 +305,8 @@ 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 @@ -325,8 +325,8 @@ 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_kreport2krona @@ -357,18 +357,18 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 2cff76cf35c6 - - 0270541aaf46 + - e073891b2afc - 27250f92a01a + - 0270541aaf46 - 4fd3b5d8706b - - e073891b2afc + - 2cff76cf35c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 76bc4efa1aeb - 708abf08a626 + - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -434,20 +434,20 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 1a6cdf55390f + - ff8f55893e7d - 6dee4abadccb - - a92a632c4d9b + - a16313517e55 - 2131d7dca455 + - a92a632c4d9b - b89b0765695d - - ff8f55893e7d - - a16313517e55 + - 1a6cdf55390f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -477,8 +477,8 @@ 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 @@ -527,11 +527,11 @@ tools: - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 + - 4b9a8031ab74 + - 4d83eccf5f81 - aeaa20b96ef2 + - 2fd4d4c9c5c2 - be818ae858e4 - - 4d83eccf5f81 - - 4b9a8031ab74 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -562,7 +562,7 @@ tools: owner: iuc revisions: - b3c7199d8786 - - 9495df9dd6ef - 576963db5f1b + - 9495df9dd6ef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/mothur.yml b/staging.usegalaxy.org.au/mothur.yml index 61b197735..3a4bc2787 100644 --- a/staging.usegalaxy.org.au/mothur.yml +++ b/staging.usegalaxy.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 @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 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: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.usegalaxy.org.au/multiple_alignments.yml b/staging.usegalaxy.org.au/multiple_alignments.yml index fbfe94250..3398635e5 100644 --- a/staging.usegalaxy.org.au/multiple_alignments.yml +++ b/staging.usegalaxy.org.au/multiple_alignments.yml @@ -2,33 +2,34 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 9422c5a87ee2 - - cd07731e4434 - - 2263989660f5 - - bdfbaf0c10aa - - 9baa871cb1d1 - - 48c13389050d - 6ae5a7b5a0a2 - 8b67dd48fec1 - - 80f03df2e2ce + - 48c13389050d - a74dbfee5a86 + - 2263989660f5 + - cd07731e4434 + - 9baa871cb1d1 + - bdfbaf0c10aa + - 9422c5a87ee2 + - 80f03df2e2ce tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f14193ec1f50 - - aaa0d6a8b808 + - d7ce0ec78e51 + - be78f13134e2 - f0af8936ed41 - - d390fe1567dc - - '764845535798' - bc3831dd65c1 - - be78f13134e2 + - f14193ec1f50 + - fc2e49f91e52 - 5abf2c2249aa + - '764845535798' + - d390fe1567dc - 4a60927aaca5 - - c18157c68134 - 2e093badc689 - - fc2e49f91e52 + - c18157c68134 + - aaa0d6a8b808 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -40,8 +41,8 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -60,18 +61,18 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f - 15974dd17515 - f1a5908ea2cb - - c5908940967d - a65296ffb4a0 + - 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 @@ -84,8 +85,8 @@ 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 @@ -98,14 +99,14 @@ tools: - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 636b049e6141 + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - 959c1f8dae95 + - b4124df98b26 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/nanopore.yml b/staging.usegalaxy.org.au/nanopore.yml index bdb940317..b3140f676 100644 --- a/staging.usegalaxy.org.au/nanopore.yml +++ b/staging.usegalaxy.org.au/nanopore.yml @@ -8,33 +8,33 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - 0e9e7fcdd543 - 72b5e9dda577 - cb34f00cc10f - - 79e9a869f40e - a7228a7ea146 - - 0e9e7fcdd543 + - 79e9a869f40e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - fa11aa8103b2 - - d6cddc06aeae - 682d1e2c8be4 - db25ec99c3ea + - fa11aa8103b2 + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - 0f5f4a208660 - - 43815fa60f3a + - edf6d4003fad - 19f3b583a9b3 - cc36773a3681 - - 2bf63b38ee9b - ec699520444c - - edf6d4003fad + - 0f5f4a208660 - 222669c4afb6 + - 2bf63b38ee9b + - 43815fa60f3a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -53,9 +53,9 @@ tools: - name: nanoplot owner: iuc revisions: - - 645159bcee2d - edbb6c5028f5 - a3c4fe6f49ab + - 645159bcee2d - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -69,8 +69,8 @@ tools: - name: nanopolish_methylation owner: bgruening revisions: - - be95355fef8d - a8d4be409446 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya @@ -83,16 +83,16 @@ 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: + - 543cbeef3949 - 93d623d9979c - 5f76b20953e5 - - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -137,15 +137,15 @@ 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: - - ce8af9373061 - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/staging.usegalaxy.org.au/none.yml b/staging.usegalaxy.org.au/none.yml index c75e1dfdc..a7063df49 100644 --- a/staging.usegalaxy.org.au/none.yml +++ b/staging.usegalaxy.org.au/none.yml @@ -21,8 +21,8 @@ tools: - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 96d2000977ab - 58341ad4fb42 + - 96d2000977ab tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -59,8 +59,8 @@ tools: - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 83da94c0e4a6 - 9dd107db92c2 + - 83da94c0e4a6 - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -74,8 +74,8 @@ tools: owner: iuc revisions: - 2f27f3b86827 - - ed1518ce2237 - edacc4bcd3cb + - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -100,9 +100,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - 48a42ca61006 - 5711fc06a63e + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -142,17 +142,17 @@ 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: - - 5bcf0e24f42c - b4b2b284230a - - 27a6a256cd23 - 172815da3d41 + - 27a6a256cd23 + - 5bcf0e24f42c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -164,8 +164,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -177,16 +177,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: + - 19bbd19b74b3 - fea85c467896 - 87febc68b45b - - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 7776cb18fdf8 - 0df47f8552f6 + - 7776cb18fdf8 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -210,9 +210,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 5fe20c915fa6 - 9c43baa60906 - 4ba60cb14cb0 + - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -224,33 +224,33 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: + - 0db22932bc39 - aec831b54a5b - 9d09724f2bf1 - - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: + - df30a2f1db55 + - 29c738066906 - 6e24e79d3d69 - ed7a967cb11b - - 29c738066906 - - df30a2f1db55 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 + - 1865e693d8b2 + - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - d107d20dc6bd - def511e8e005 + - d107d20dc6bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -262,9 +262,9 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: + - d63c1442407f - c520a52b5174 - 64deddb6a8ec - - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder @@ -1016,8 +1016,8 @@ 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 @@ -1030,9 +1030,9 @@ tools: - name: rdock_rbdock owner: bgruening revisions: - - a22969b08177 - e4b7d1507a75 - c362398df83b + - a22969b08177 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/staging.usegalaxy.org.au/phylogenetics.yml b/staging.usegalaxy.org.au/phylogenetics.yml index 9427ec982..47ad26b3b 100644 --- a/staging.usegalaxy.org.au/phylogenetics.yml +++ b/staging.usegalaxy.org.au/phylogenetics.yml @@ -20,61 +20,61 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_absrel owner: iuc revisions: - - d7c7ef3353fe - - 5a7c56a5cc08 - - cce7b18495e4 - 26de3a7b1cb9 - - 3f59ebfbfe3d - - 107d3ba7024a - - 81e66674859e - - c78f3d7dd1db - - 6a457678efcb - '841557158611' - 3b8b5bde0bd9 - - b89cac5156ec + - 6a457678efcb + - d7c7ef3353fe + - 5a7c56a5cc08 - d033ffc1c161 + - f04a1264e2a2 + - 107d3ba7024a + - 3f59ebfbfe3d - 8834daeb9892 + - b89cac5156ec + - cce7b18495e4 + - c78f3d7dd1db + - 81e66674859e - f73435dc282b - - f04a1264e2a2 - a6619171428e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 88c4aa435ded - - 6a726db04d4b - - 5b777002c2de - - 5fcd1ece3a6e - b0af57c1a968 - - 02b8758214b0 - - df47d4845b62 + - 6283babe736e + - e75442c7f4da - 7a2092844346 + - 5fcd1ece3a6e + - 6223845127ea + - df47d4845b62 + - 5b777002c2de - aa8cc71438cf - - 659517798cc4 - - 4755f52427c4 + - 02b8758214b0 - 3b96e92e8ec3 - - e75442c7f4da - - 6223845127ea - - 6283babe736e + - 6a726db04d4b + - 4755f52427c4 + - 659517798cc4 - a185b079b095 + - 88c4aa435ded tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - d1c340a5664b + - f97743d52b87 + - b8476e82ac20 - 524d31add34a + - d1c340a5664b - 9b892d7f82cc - - b8476e82ac20 - - f97743d52b87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade @@ -82,30 +82,31 @@ tools: revisions: - feb40665d7cd - 9e10ba792be2 - - daddf188c13f - 128ba8da994f + - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 81804a978fc0 - - 36912871ccdc + - 42a174224817 - 14ae456b8cc5 - - 03ed9524dcd1 + - 7bb8726be37c - ca0d8cf80567 + - b6abccb1f25b - a2099fb98cdb - - 7bb8726be37c + - 2fa9d4f1b48f + - 81804a978fc0 + - 83a69484cb87 - b7e297c2ede6 - - 3a43c3982401 - - 42a174224817 - - b6abccb1f25b + - ca337cce3888 - abf6dbe8c9d7 - 437e28791761 + - 03ed9524dcd1 - 5f8727ff21e7 - - 83a69484cb87 - - 2fa9d4f1b48f - - ca337cce3888 + - 36912871ccdc + - 3a43c3982401 + - 9d61d3fa046c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -117,21 +118,21 @@ tools: - name: raxml owner: iuc revisions: - - 29ff6a849eac + - ea30d3089354 - 73a469f7dc96 - a4b71be30c3c - ba29b5e2a4be - - ea30d3089354 + - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - f1ccc8a6eb05 - - dbe2b2204555 - - 91887494eb97 + - e88a7de55d6e - 809e42326fc2 - 15ac71df11a0 - - e88a7de55d6e + - 91887494eb97 + - f1ccc8a6eb05 + - dbe2b2204555 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/picard.yml b/staging.usegalaxy.org.au/picard.yml index 94af46824..ae98282c4 100644 --- a/staging.usegalaxy.org.au/picard.yml +++ b/staging.usegalaxy.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - 1aac2a13842a - - a1f0b3f4b781 - - b502c227b5e6 - 7d34178f2812 - - 585027e65f3b - - f6ced08779c4 - 881d7645d1bf + - b502c227b5e6 + - 1aac2a13842a + - f6ced08779c4 + - a1f0b3f4b781 - fc288950c3b7 + - 585027e65f3b tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/proteomic_ai.yml b/staging.usegalaxy.org.au/proteomic_ai.yml index cda1fd9c5..588f1d835 100644 --- a/staging.usegalaxy.org.au/proteomic_ai.yml +++ b/staging.usegalaxy.org.au/proteomic_ai.yml @@ -2,12 +2,12 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - eb085b3dbaf8 - c0e71cb2bd1b - - d00e15139065 - - 5b85006245f3 + - eb085b3dbaf8 - 3bd420ec162d + - d00e15139065 - ca90d17ff51b + - 5b85006245f3 - 7fbec959cf2b - a58f7eb0df2c tool_panel_section_label: Proteomic AI diff --git a/staging.usegalaxy.org.au/proteomics.yml b/staging.usegalaxy.org.au/proteomics.yml index 47aa5c85f..daae4febc 100644 --- a/staging.usegalaxy.org.au/proteomics.yml +++ b/staging.usegalaxy.org.au/proteomics.yml @@ -3,19 +3,19 @@ tools: owner: galaxyp revisions: - b18329a8ac14 - - 0a18ac48ac53 + - b574b84afc4d - 277dc652246e - f28ad96b76dc - - b574b84afc4d + - 0a18ac48ac53 - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - e215f71d7983 - bf06d196e23d - 525f201b86c1 + - e215f71d7983 - b41107d8fe89 - e988563cc6e5 tool_panel_section_label: Proteomics @@ -23,64 +23,64 @@ tools: - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - 8da3511c9467 - bb6397b94018 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - b8c79e70516d - 528fb09022be - f23d67e28cc8 - - b8c79e70516d - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 - 80600735685d - - 25b83cbd596a - - a95a82eb4d50 - a69865da6f80 + - a95a82eb4d50 + - 59e85306eae5 + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - e0669b1854b1 - - 611d80c0e29d - 798da6bdff3d + - 611d80c0e29d - f1897eb07081 - ed9ed1e6cca2 + - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - 74b61bf5bc4b - - a7fb9b395ddf - 5a35e3a8d013 + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - df2187f9013b - 82f6c2f4332d + - df2187f9013b - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - c5aa9fca18c6 - - 043f9c91f686 - - 1693b2126f30 - 10566783d718 + - c5aa9fca18c6 - d2483487e077 + - 1693b2126f30 + - 043f9c91f686 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -112,8 +112,8 @@ tools: owner: galaxyp revisions: - 1c5cbf8f79ce - - 0fa397f4f40b - 4081e4faa4ab + - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -138,8 +138,8 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - e66f552a3c47 + - 160538a890a6 - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -160,43 +160,43 @@ tools: - name: maxquant owner: galaxyp revisions: - - f522c08e900c - - 37d669de2828 - e42225f8a659 - - 1f39c833f65f - - 8934bc76bb52 - 2133b0be850a - 7f432d87c82c - - 837224ad1694 - 4d17fcdeb8ff + - 837224ad1694 - 97a7f34fcb6a + - 37d669de2828 + - 1f39c833f65f + - 8934bc76bb52 + - f522c08e900c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: + - 0ed07016d668 + - 85b8866f06d7 - a72ac2c7cc5b - '860429737408' - - 85b8866f06d7 - - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 990b4560ead7 - - 4187b6df1a40 - 352b37c66d97 - 1974224d63c2 + - 990b4560ead7 + - 4187b6df1a40 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - a1daafbf5233 - - deaf035bbe9f - - 4f359549383c - 99450519d727 + - 4f359549383c + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample @@ -220,10 +220,10 @@ tools: - name: metaquantome_viz owner: galaxyp revisions: - - 1199751329b0 - - eb811f3018ea - - 944b43462104 - 9bf325045235 + - 944b43462104 + - eb811f3018ea + - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -241,25 +241,25 @@ tools: - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - - 593839e1f2c3 - 8212e342e482 + - 593839e1f2c3 - b7034eff0db1 + - 28434abe6c5c 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 @@ -271,18 +271,18 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 518b1730cf2a - 9cdf15d3cfc8 - - f7fef900f5b2 + - 518b1730cf2a - c9eff69a7c62 + - f7fef900f5b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - - 5e948629bc73 - ca88bd28f116 + - 5e948629bc73 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter @@ -296,16 +296,16 @@ tools: - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - - 9b7977080f6d - 6634cad7d797 + - 9b7977080f6d + - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 0bb5056cb775 - 05d5e1ddc985 + - 0bb5056cb775 - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -328,17 +328,17 @@ tools: - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 0efbc235f314 - 9e26f5c770f8 + - 0efbc235f314 - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - - c28f13cab67a - 3720e349ba2a + - c28f13cab67a + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter @@ -346,8 +346,8 @@ tools: revisions: - ca799a7246e7 - 382cde407f81 - - c55dddc5844a - c427a8628cbe + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper @@ -361,56 +361,56 @@ tools: - name: openms_idmerger owner: galaxyp revisions: - - f817513840a9 - - 18f93351f8b6 - 1c5f31b8d632 - 8d4db262964c + - f817513840a9 + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a - - 5d9f175dff81 - 111c3a00136d + - 5d9f175dff81 + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - be74a8cd7d66 - 0e52c85f3b15 - 476b5e296979 + - be74a8cd7d66 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: - - a407b6790342 - c18d8efa4474 - 2b2a7551a857 + - a407b6790342 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 owner: galaxyp revisions: + - 8098330f6d91 - bf32e0bcf554 - ee860980edc6 - - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer @@ -423,8 +423,8 @@ 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 @@ -437,15 +437,15 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - f861ec9fbe59 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - d4396637b9f5 - 0bddef8d144e + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter @@ -458,8 +458,8 @@ tools: - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f9ed7e074900 - 05ec9fb05ed1 + - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer @@ -479,18 +479,18 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - 5ae104d0da6e + - decc397c3b7e - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - - 5182338d5e7c - dd173849c3d8 + - 5182338d5e7c - 539a3a4dcc9e + - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -509,8 +509,8 @@ 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 @@ -522,16 +522,16 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - c8b225c69a7f - 7f6a1f27553e + - c8b225c69a7f - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate @@ -544,13 +544,13 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 943a34df6047 - - 7fdd9119cc4f + - 3634c90301af - 1beff3ddce58 - - 3ec27b4cee7c - a72c48001f7c - - 3634c90301af + - 3ec27b4cee7c - 07ff622ec007 + - 7fdd9119cc4f + - 943a34df6047 - da885ca16cb2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -605,9 +605,9 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 265c35540faa - - 12692567c7f9 - 1a5690a5eedc + - 12692567c7f9 + - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.usegalaxy.org.au/rad_seq.yml b/staging.usegalaxy.org.au/rad_seq.yml index 0e54dcf15..3cf41d2bf 100644 --- a/staging.usegalaxy.org.au/rad_seq.yml +++ b/staging.usegalaxy.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 42201b90e3f4 - - 289b7d6b69a4 - - e345aadf914f - 110a346daf36 - - 2f1d464ebfd2 - cd5f98911089 + - 2f1d464ebfd2 + - 289b7d6b69a4 + - 42201b90e3f4 + - e345aadf914f 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: - - fcce77c09289 - - c207119ba5f6 - - 0345dbaaa79b - - 42d9087b4789 - 0cd2df8af811 - 8501601a118d + - 42d9087b4789 + - fcce77c09289 + - 0345dbaaa79b + - c207119ba5f6 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: + - 405a212b32ab - 421c33b8bf17 - 89eb29319bf4 + - ad5ab22ffe24 - 04db7fd6b238 - - 405a212b32ab - 33486216eec0 - - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - 7b72fde3d27e - - fa51dc5e8386 - - 1d839ead7ad3 - eb784fa07f80 - - 7370bb65bad4 + - 1d839ead7ad3 - f6e91108b7b1 + - fa51dc5e8386 + - 7b72fde3d27e + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -71,11 +71,11 @@ tools: owner: iuc revisions: - 8a55d29c8fcf - - 1544278c272e - - c9b77ced9a78 - - 3d70c2996730 - d30e36c48c93 + - c9b77ced9a78 - a3e86cd9cac7 + - 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: + - 887cf585cafc - b242deb58952 - - a5969aa9347e - e2db212d64ad - - 7b881f5f5ad5 - 564c33e5c3e3 - - 887cf585cafc + - a5969aa9347e + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -105,8 +105,8 @@ tools: owner: iuc revisions: - 9a171f9a450b - - b4bab607eb05 - bd5ff77e2036 + - b4bab607eb05 - 8cff84759bf6 - e897c74a48bb tool_panel_section_label: RAD-seq @@ -120,11 +120,11 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 5e10f396979e - 6dafad990086 - - 33f0793edf93 - adc7a7610d4f + - 33f0793edf93 - 4f65e343ecdf + - 5e10f396979e - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: + - 4e280b27a831 - 97575d01f06b - 43e3eeb2e0ec - c287418eb288 - 17d39bf0a63a - c5d7050e4ad7 - - 4e280b27a831 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - 9586f08634c0 - 0b8c84a7fdb5 - - cd034465d4a4 + - 9586f08634c0 - d9bf483266a1 - a819ec3b362d - 09b8edb56d80 + - cd034465d4a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -172,11 +172,11 @@ tools: owner: iuc revisions: - bf0e43ab0416 - - 69842dd5aa48 - a4b4bd84f69e - a9c34a289493 - - 2645575d1bf2 + - 69842dd5aa48 - 95351dd0fd3f + - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - - bb0475c884ff - 912f904a6e1e - d033e1ccb386 - d1fda11e602f - 8a35a3bc6752 + - bb0475c884ff + - cfb504394ae1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: + - d504d945a655 - 95286af4139b - d1fad35bdb4a - - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -267,8 +267,8 @@ 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/staging.usegalaxy.org.au/rna_seq.yml b/staging.usegalaxy.org.au/rna_seq.yml index ef4a981f2..f7bdee7b6 100644 --- a/staging.usegalaxy.org.au/rna_seq.yml +++ b/staging.usegalaxy.org.au/rna_seq.yml @@ -2,15 +2,15 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 2d4e3aff9dc7 - 31f8063eedea + - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - 32e542c2a773 + - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -46,8 +46,8 @@ 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 @@ -61,8 +61,8 @@ tools: owner: devteam revisions: - 6a6717a5f421 - - cf747d1bd79a - 86285ddd4512 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -74,8 +74,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -99,10 +99,10 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 + - e3b16fd7dd08 - 57f477b57c35 - 8f0181aacb7a - - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -114,12 +114,12 @@ tools: - name: deseq2 owner: iuc revisions: - - 24a09ca67621 - - 0696db066a5b - d027d1f4984e - - cd9874cb9019 - - 8fe98f7094de + - 0696db066a5b - 6a3a025714d3 + - 8fe98f7094de + - 24a09ca67621 + - cd9874cb9019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -131,10 +131,10 @@ tools: - name: dexseq owner: iuc revisions: - - 62adf13b86ea - - 2872c633f07e - b47c006d90c5 + - 62adf13b86ea - df929f257179 + - 2872c633f07e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -146,11 +146,11 @@ tools: - name: edger owner: iuc revisions: + - 9bdff28ae1b1 - df0c8d0a5992 + - 6e53e565fc6a - f2843df56434 - - 9bdff28ae1b1 - 555659de7321 - - 6e53e565fc6a - 3d89af8a44f0 - 334ce9b1bac5 tool_panel_section_label: RNA-seq @@ -164,8 +164,8 @@ tools: - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -183,16 +183,16 @@ tools: - name: featurecounts owner: iuc revisions: + - 7db9d3ea71c9 - ea04b737afa0 - 6f66ae7c5f7a - 38b6d12edc68 - - e6a2a912677a - a37612abf7f9 - - 90d16db017d7 + - e6a2a912677a + - af814359d244 - a56fbe2d6ba7 - - 7db9d3ea71c9 + - 90d16db017d7 - f3a5f075498f - - af814359d244 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -216,9 +216,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - f99dd58de04f - 3c97c841a443 + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -236,13 +236,13 @@ tools: - name: hisat2 owner: iuc revisions: + - 6c19daec423d - f4af63aaf57a - - 26371a1df031 - a86e80d3c09c - - 6c19daec423d + - 6ab42baa56e9 - 3fb01a8c902d - d4b55e2beb12 - - 6ab42baa56e9 + - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -260,8 +260,8 @@ tools: - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -280,9 +280,9 @@ tools: owner: iuc revisions: - ce5d418183c5 - - 87c11c05d238 - - 1c75aa5de15e - 01247aaf0a10 + - 1c75aa5de15e + - 87c11c05d238 - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -295,10 +295,10 @@ tools: - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 + - 4f9c4e6566e5 - 10c98fab6c5a + - c971db6f0fe5 - 40985510cd98 - - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -310,13 +310,13 @@ tools: - name: limma_voom owner: iuc revisions: - - 32511f586472 - - 708348a17fa1 - - 97e06a4c7c75 - - e827f9aae031 - - 0921444c832d - d6f5fa4ee473 + - 0921444c832d - 58c35179ebf0 + - e827f9aae031 + - 32511f586472 + - 97e06a4c7c75 + - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -377,18 +377,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - 3ea5a2a63fa2 + - c7c55b694974 - c772497b2c32 - - e132e7d02a3e - - b9e04854e2bb - - 0a563fd2f22e - - 7ed2edc1337f - 4df95e2d7f61 - - 99b17b74a8cd + - 7ed2edc1337f + - 980d2a2e1180 + - 3ea5a2a63fa2 + - b9e04854e2bb - 5ec75f5dae3c - - c7c55b694974 + - e132e7d02a3e + - 99b17b74a8cd + - 0a563fd2f22e - 4074fc1940e2 - - 980d2a2e1180 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -414,9 +414,9 @@ tools: revisions: - 2c0ca397d302 - ebab418107f5 + - 49121db48873 - cc05793bb896 - 53e9709776a0 - - 49121db48873 - e3d32471da11 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -429,20 +429,21 @@ tools: - name: seurat owner: iuc revisions: - - c0fd285eb553 - 56242ff81c84 + - c0fd285eb553 + - fab6ff46e019 - 8c28affc7c48 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - ae618321f34a - - dd4df992d93d - 1ebd14235b92 + - dd4df992d93d - 76d290331481 - - 258d696dbd7e + - ae618321f34a - 914cfcba0ec8 + - 258d696dbd7e - cef79931dda5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -474,9 +475,9 @@ tools: owner: iuc revisions: - d0d4cef4f967 - - 0db979fead3a - c6334cb383ff - ffd1300599a1 + - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -488,10 +489,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - d6a479fd4281 - - bcc5f03f1900 - a009c96c5c18 - 74217fbfba4d + - d6a479fd4281 + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -504,9 +505,9 @@ tools: owner: iuc revisions: - c2b82a94493e - - 478f36effca1 - - 75f4e1859ed7 - 56162e446004 + - 75f4e1859ed7 + - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -532,10 +533,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 41db7569b4ba + - 4687ecf0eb2d - be3f26533209 - 34a018cbee9c - - 4687ecf0eb2d + - 41db7569b4ba tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -547,11 +548,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 05ab8d5e04a2 - 5192f657f305 - 33406f5a445c - ae501908a17f - c5fbddcac63a + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -563,10 +564,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - e406ac71165d + - 1fdb25a8384d - 6f0fb35b799c + - e406ac71165d - aa38fa8c5815 - - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -593,10 +594,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 1d689e4e1caf - - 047c22569787 - eafea3083352 - c63338cf419f + - 047c22569787 + - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -608,10 +609,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 3a4ac03d1266 - - 9871104ea630 - 1812dbc5bb7b + - 3a4ac03d1266 - 1b1a25f93f80 + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -623,14 +624,14 @@ tools: - name: trinity owner: iuc revisions: - - c9cfec002f71 - - 48636f857c4b - d2bc35f3d1c5 - - 77cf519a812e - 32b86cd8eb50 + - db1f362cca3e + - c9cfec002f71 + - 48636f857c4b - cee61b3fcf78 - d84caa5a98ad - - db1f362cca3e + - 77cf519a812e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -642,10 +643,10 @@ tools: - name: trinotate owner: iuc revisions: - - 4383070d29ed - - 2b093007fab9 - 6fd16fad465d + - 2b093007fab9 - 9e61bc67866f + - 4383070d29ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.usegalaxy.org.au/rseqc.yml b/staging.usegalaxy.org.au/rseqc.yml index ee91e8906..b41c54fe8 100644 --- a/staging.usegalaxy.org.au/rseqc.yml +++ b/staging.usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: + - 080fd5739bb4 - 1a052c827e88 - 473382134e56 - - 080fd5739bb4 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/sambam.yml b/staging.usegalaxy.org.au/sambam.yml index 1b64b8977..7a484bf7d 100644 --- a/staging.usegalaxy.org.au/sambam.yml +++ b/staging.usegalaxy.org.au/sambam.yml @@ -2,8 +2,8 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 88eedb4abea0 - 10184eaa85fc + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -35,8 +35,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -54,8 +54,8 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - e7fd6754d093 + - 5f8e69cc4c6e - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -81,8 +81,8 @@ 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 @@ -108,16 +108,16 @@ 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: - - 12749212f61b - 46c6639921f1 - 9149ad20699a + - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -143,9 +143,9 @@ 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_fastx @@ -158,8 +158,8 @@ tools: owner: devteam revisions: - 22970df7a40e - - cc61ade70eb8 - fe34990e5ce7 + - cc61ade70eb8 - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -172,10 +172,10 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 7a6034296ae9 - 88b8c2916784 - - 811fc2d75ad4 - 7def34e6cf4d + - 811fc2d75ad4 + - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -187,8 +187,8 @@ tools: - name: samtools_merge owner: iuc revisions: - - 36677f429310 - b40e2d865d52 + - 36677f429310 - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -196,9 +196,9 @@ tools: owner: devteam revisions: - 583abf29fc8e + - 9da0311ab1dd - 329deb17a9f7 - fa7ad9b89f4a - - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -210,8 +210,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -243,8 +243,8 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - a4a10c7924d1 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -257,8 +257,8 @@ tools: owner: devteam revisions: - cab3f8d35989 - - 6c2c1836728b - e613c1ad4c4c + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -270,10 +270,10 @@ tools: - name: samtools_split owner: devteam revisions: + - 135c85f4cfaf - bcedabb53ddf - 5d9ae78f34d3 - b7f7826ef1cd - - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -285,11 +285,11 @@ tools: - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f + - 5a08c09b9311 - 145f6d74ff5e - - 24c5d43cb545 - 1cc79f49b8d5 - - 5a08c09b9311 + - 24c5d43cb545 + - 3a0efe14891f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -301,13 +301,13 @@ tools: - name: samtools_view owner: iuc revisions: + - b01db2684fa5 + - 350bbc5c2ffd - bf328cec6a42 - - c370440f901e - 5826298f6a73 - b72793637686 - - 350bbc5c2ffd + - c370440f901e - 0dbf49c414ae - - b01db2684fa5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.usegalaxy.org.au/send_data.yml b/staging.usegalaxy.org.au/send_data.yml index 318da763c..518290d49 100644 --- a/staging.usegalaxy.org.au/send_data.yml +++ b/staging.usegalaxy.org.au/send_data.yml @@ -2,10 +2,10 @@ tools: - name: ena_upload owner: iuc revisions: - - d147d6455873 - - 4aab5ae907b6 - - 59bb6d34fca6 - 6f6537780379 + - 4aab5ae907b6 + - d147d6455873 - a62c4a11a67d + - 59bb6d34fca6 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/single_cell.yml b/staging.usegalaxy.org.au/single_cell.yml index 5ea01ddb6..37fc1e5b8 100644 --- a/staging.usegalaxy.org.au/single_cell.yml +++ b/staging.usegalaxy.org.au/single_cell.yml @@ -2,11 +2,11 @@ tools: - name: anndata_import owner: iuc revisions: - - 00712416fdaa - cfc3f5a57dc6 - - fb9e030ffae4 - - 55e35e9203cf + - 00712416fdaa - 32e547223c9e + - 55e35e9203cf + - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -19,10 +19,10 @@ tools: owner: iuc revisions: - 39e945f0b2c1 - - ee98d611afc6 + - b9fac48532eb - 688357ad5e61 - 038e32885fec - - b9fac48532eb + - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -34,11 +34,11 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 3d748954434b + - d4af736e7b83 + - b85871dd69f9 - 43cb7b5a6fe7 - 9bd945a03d7b - - b85871dd69f9 - - d4af736e7b83 + - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -52,8 +52,8 @@ tools: revisions: - cdf4443d5625 - 8855361fcfc5 - - 2c1200fba922 - a9caad671439 + - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -71,15 +71,15 @@ 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 owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -132,9 +132,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - a6821f856a1e - 69018f285aa3 - df8e4e54d367 + - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -174,9 +174,9 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 3c86f71498bc - a97abb8cd15b - b409c2486353 + - 3c86f71498bc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -188,10 +188,10 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - 6c145a6868cc - c5d3684f7c4c - - 5e9171dc8244 - cc0deb593fc8 + - 6c145a6868cc + - 5e9171dc8244 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -218,8 +218,8 @@ tools: owner: iuc revisions: - 6adf98e782f3 - - dbbe1ea8ecb1 - aa0c474463c2 + - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -231,9 +231,9 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - bf2017df9837 - 215733a383f2 - f2f6c703da06 + - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -260,8 +260,8 @@ tools: owner: iuc revisions: - 7a365ec81b52 - - b7ea9f09c02f - 652923ce664f + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -273,9 +273,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - - ef4c80837bc5 - 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.usegalaxy.org.au/statistics.yml b/staging.usegalaxy.org.au/statistics.yml index 053ea7149..2584d29d4 100644 --- a/staging.usegalaxy.org.au/statistics.yml +++ b/staging.usegalaxy.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 562f3c677828 - - 746e8e4bf929 - - 4c07ddedc198 - - 2f3c6f2dcf39 - 419027d822d6 + - 2f3c6f2dcf39 + - 4c07ddedc198 + - 746e8e4bf929 + - 562f3c677828 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: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 6c29c7e347e8 - cb1c59d69557 - 7a15159140d1 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -121,34 +121,34 @@ tools: owner: bgruening revisions: - 9c3e1d3235c8 - - b1eda492f063 - 840f29aad145 + - b1eda492f063 - aef56d0e7a61 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 07843f917990 - d0352e8b4c10 - 375bbd555f4a + - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 2c58b83c9bad - 4cc980df6265 - cd02bf168d23 + - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - 7dd3fb35904f + - 1dd433d2c92c - ad7e0b4291ee - 4bbaf77573ef - - 1dd433d2c92c tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.usegalaxy.org.au/text_manipulation.yml b/staging.usegalaxy.org.au/text_manipulation.yml index 2da82b313..3aa195265 100644 --- a/staging.usegalaxy.org.au/text_manipulation.yml +++ b/staging.usegalaxy.org.au/text_manipulation.yml @@ -20,21 +20,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - f18f67056946 - 6c6d26ff01ff + - f18f67056946 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - be25c075ed54 - 9cd341095afd - 6e8d94597139 - - 6595517c2dd8 - - 464b9305180e - 02026300aa45 + - be25c075ed54 - 626658afe4cb - 13b6f0007d9e + - 464b9305180e + - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -46,8 +46,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -72,9 +72,9 @@ tools: owner: iuc revisions: - 34d29339abab - - 4d5aae46f850 - - 9cc411a62277 - 37cde8134c6a + - 9cc411a62277 + - 4d5aae46f850 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -99,27 +99,27 @@ tools: owner: devteam revisions: - f2aac0c5c60d - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 83069b38aa85 - - 1ea4e668bf73 - cf34c344508d - 2e8f945f7285 + - 83069b38aa85 - 33d61c89fb8d - 623f3eb7aa48 + - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - 503bcd6ebe4b - 399da6b5ec21 - ae8c4b2488e7 - - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -131,16 +131,16 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - c29d2f80a066 - bce29ec10b78 - b722161a845a + - c29d2f80a066 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 60ff16842fcd - 3bf5661c0280 + - 60ff16842fcd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing @@ -148,10 +148,10 @@ tools: revisions: - a6f147a050a2 - ddf54b12c295 - - f46f0e4f75c4 - - 74a8bef53a00 + - d698c222f354 - 0a8c6b61f0f4 + - f46f0e4f75c4 - 9ff72e942410 - - d698c222f354 + - 74a8bef53a00 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/variant_calling.yml b/staging.usegalaxy.org.au/variant_calling.yml index 6ff77eb17..679f5417f 100644 --- a/staging.usegalaxy.org.au/variant_calling.yml +++ b/staging.usegalaxy.org.au/variant_calling.yml @@ -3,8 +3,8 @@ tools: owner: iuc revisions: - 85c57cc9b558 - - 82fb5e3bb93e - 0d18a3ba2d1c + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -16,47 +16,47 @@ tools: - name: freebayes owner: devteam revisions: - - 04fa42777df9 - - 156b60c1530f - - a5937157062f - ef2c525bd8cd - 57def2d7c093 + - a5937157062f + - 156b60c1530f + - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - 09d6e4693887 + - 791f73caa0c8 - 435b157bed6d - e61c9ac190ad - - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 3b4b2121842f - - 4805fe3d8fda - - e1461b5c52a0 - dfadc322b065 - - 03627f24605f - - 65432c3abf6c - 074d44697036 + - 4805fe3d8fda + - 65432c3abf6c + - 03627f24605f + - 3b4b2121842f + - e1461b5c52a0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 7dfca164d2e3 - 701d134358ad - 9cb929f21cfa - - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - c27549b9aa1f - f4473557ffc7 + - c27549b9aa1f - 971e07ca4456 - 426d707dfc47 tool_panel_section_label: Variant Calling @@ -64,9 +64,9 @@ tools: - name: lofreq_viterbi owner: iuc revisions: - - cdaab621d454 - - dbd9f2db9ed8 - aa35ee7f3ab2 + - dbd9f2db9ed8 + - cdaab621d454 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: - - 9bccc8404a3c + - fa016f1eea1a - c9a8ef2aa380 - 5bbf9eada9c2 - - fa016f1eea1a - d220115f882b + - 9bccc8404a3c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -132,16 +132,16 @@ tools: revisions: - e7aff4a85df5 - 3b1e7c170b10 - - ee4a90760848 - 40f0591deda0 + - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - 02d81b994ef5 - - 4934c0ac6197 - adc0645b945c + - 4934c0ac6197 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_somatic diff --git a/staging.usegalaxy.org.au/vcfbcf.yml b/staging.usegalaxy.org.au/vcfbcf.yml index f834b80a4..ea5e9ff06 100644 --- a/staging.usegalaxy.org.au/vcfbcf.yml +++ b/staging.usegalaxy.org.au/vcfbcf.yml @@ -2,13 +2,13 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - e075b1be5abb - - 3f62d4939d54 - - 265fe0f9ea64 + - 8a2e296c07ef - b7ea370b8f5d - - ebe5fc018e72 - 6a88248893c4 - - 8a2e296c07ef + - 3f62d4939d54 + - ebe5fc018e72 + - 265fe0f9ea64 + - e075b1be5abb 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: - - 0fba2c15b40d + - 22637b1a55bf - b03984136ce4 - f0d44631365f - - 544cb432072b - c37b684e7f4e + - 0fba2c15b40d - 21687e35f066 - - 22637b1a55bf + - 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: - - 8408bffd5616 - 0238f68ad641 - - 01d6b7d6365e - - 8ca3647c90fd - 8627b2b383b4 - - bf1f4994f104 - 6d35a3780bfd + - 8408bffd5616 - 3a7084316a6e + - bf1f4994f104 + - 8ca3647c90fd + - 01d6b7d6365e 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: - 6b6c992d3a14 - - 81426b3cf18b - 08296952d12f - - f430a1ec7ee4 - - 9b5abbf50d23 - 03e0645395d2 + - 9b5abbf50d23 + - 81426b3cf18b - 62ca6da715bf - d144af39073a + - f430a1ec7ee4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -76,13 +76,13 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - d37e313a41be - - 2363ef414c9b - e522022137f6 - - 95c6f3f4c77f + - 147de996e34f - d3081540d175 + - d37e313a41be - 1829900b5dcd - - 147de996e34f + - 2363ef414c9b + - 95c6f3f4c77f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -95,11 +95,11 @@ tools: owner: iuc revisions: - 09f37afb3621 - - 9b29129fb491 - b14ff40958cb - 348cd212dbad - - 92c0aff8b53e + - 9b29129fb491 - cacc9970727a + - 92c0aff8b53e - 1137ce8efc1e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -112,12 +112,12 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - ecc9192912b8 - - 55c0e906c14c - - 367ba501b6eb - - de68c11034f6 - 1f2183a23823 + - de68c11034f6 + - 367ba501b6eb + - ecc9192912b8 - 4935320a59a8 + - 55c0e906c14c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -130,11 +130,11 @@ tools: owner: iuc revisions: - 039ea3f1dea9 + - 64a8f7dae3ad - ae68ceb4cca3 - 7cbf3c66d4ad - - f01b2c9506b9 - - 64a8f7dae3ad - 6c790a091c7c + - f01b2c9506b9 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 - - 6ea7170a016d + - e7452697afd9 - 656a916779fe + - 963a3635b2e1 - cdb7b4927742 - - 33bd9301568c - - e7452697afd9 - 277719af4dd7 + - 33bd9301568c + - 6ea7170a016d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -164,12 +164,12 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 5a321fab1fe4 - 3eac729e66c9 - b7f0f59baa7e - - a1213a0b7b66 - a29a2f40b665 + - a1213a0b7b66 - 501bfb078342 + - 5a321fab1fe4 - 26d97cdd5410 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -182,14 +182,14 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 768d04526638 - - 97d19c008d15 - - c803c34361e0 + - 709dd8291b83 - d7d1663559e9 - - 63aabc920911 - - 5f27e814a119 + - c803c34361e0 - 81e4014fa809 - - 709dd8291b83 + - 5f27e814a119 + - 97d19c008d15 + - 768d04526638 + - 63aabc920911 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: - - af163c712539 - - 85ee7e6c4204 - - b1eba148b35b - - 7ba36babba2d - 86296490704e - b931e65638b8 + - 85ee7e6c4204 - 2215287d5cc9 + - b1eba148b35b + - af163c712539 + - 7ba36babba2d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -220,14 +220,14 @@ tools: owner: iuc revisions: - 9c711df3258d - - 5660b21a0dbd + - f506df85c652 + - 31ea13dfe5e6 - ce9396ddcb2b - 37757ffb4c5f - - 03191140c66a - cf06b44624c7 - - 31ea13dfe5e6 + - 5660b21a0dbd - 4e1d23e5c691 - - f506df85c652 + - 03191140c66a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -239,10 +239,10 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 48291658fdf6 - - ebb2e12a6de1 - 021693fdadaa - a404f786a94c + - 48291658fdf6 + - ebb2e12a6de1 - 6deb4d549bc9 - 19905c025d2a tool_panel_section_label: VCF/BCF @@ -256,13 +256,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - be6b217710af - - c450406f722b - 5ad5d4243987 + - 97e8145d7e30 - 71c78e0eea52 + - c450406f722b + - be6b217710af - f7879f1e77f9 - 69d8b7567281 - - 97e8145d7e30 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -275,12 +275,12 @@ tools: owner: iuc revisions: - 89720ec3d58e - - d31a2e310a52 - - 2514e684f8a3 + - 0fe007201caf - 79f7a1acc2cd - 52f9e4a660e3 - cc7f9a4e186b - - 0fe007201caf + - d31a2e310a52 + - 2514e684f8a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -292,13 +292,13 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 230e424bde67 - - 80e6e399ccd0 - - 0a62420cb9cd - - 1411bef27a75 - 026a989b7cee - 99f4a81a47be + - 0a62420cb9cd + - 230e424bde67 + - 1411bef27a75 - 75ddd081f608 + - 80e6e399ccd0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -310,13 +310,13 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - 444e6a756c35 - - 5808f77b2bb6 - - ba20340426fe - bca7ce81688f - - 5acfca5a76af + - ba20340426fe + - 5808f77b2bb6 - c01be0ab9806 - e493702b19eb + - 444e6a756c35 + - 5acfca5a76af tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -328,13 +328,13 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - d52b8947b269 - 4d236c696844 + - d52b8947b269 + - 12152af85697 - 7fe09ad6a939 + - 68fec03a63b7 - 157ffcdd3fa7 - - 12152af85697 - f2482aa4862e - - 68fec03a63b7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -346,11 +346,11 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 6f8e223f78f3 + - 27e2611639a9 - 8f2fc0ab30fb - - 29ba253e2e05 + - 6f8e223f78f3 - 0e5d11004815 - - 27e2611639a9 + - 29ba253e2e05 - 8dbce095986c - cbe39e530cbf tool_panel_section_label: VCF/BCF @@ -364,13 +364,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 3ff5654b4e7d - - a367a15c6de5 + - e0a856def0b0 - 88bb477f45f7 - a8630d4fbaf8 - - e0a856def0b0 - - 9708e3086f32 - af36eb5418fe + - 9708e3086f32 + - 3ff5654b4e7d + - a367a15c6de5 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: - - 5c9729d54721 - - 31c096c6b156 - - 6ce175385dd9 - 2f4eef1f0d22 - - 03e30f06f15f - 96d0145c041a - 4ed46189d6c6 + - 6ce175385dd9 + - 31c096c6b156 + - 03e30f06f15f + - 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: - - 46eb13bc2c73 + - 40daf124be88 - a1aad8b559c6 - 09f5e45a8212 - - 2c4941386820 - - 40daf124be88 - 262bba5b90ef - 11af7fce71cf + - 2c4941386820 + - 46eb13bc2c73 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: - - 0594ea1417c8 - - 882b2e649602 - - f272b8ba0983 - - 6cbb9c47795c - - 4b796b58938b - 743cd1472aeb - 12038f59c0f4 + - f272b8ba0983 + - 4b796b58938b + - 882b2e649602 - 8cb121b6a1d2 + - 0594ea1417c8 + - 6cbb9c47795c 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: - - 238f78e38a8b - - 18cf9de1cf73 + - dba06328556a - eccb508bb678 + - 8c3ff4ef1190 - cced6715f926 + - 18cf9de1cf73 - adee7e8b746f - - 8c3ff4ef1190 - - dba06328556a + - 238f78e38a8b 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: - - 9f36041495a3 - - c9935c9e8a24 - - e0ad88dec40d - f64e7ca2efd2 + - e0ad88dec40d + - e53501abf992 + - 9f36041495a3 - a850902cac64 + - c9935c9e8a24 - 3ce32adc55b2 - - e53501abf992 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: + - d43eb39b989e - 8057cf55fa41 + - 79489d5685dd + - d68c43202172 - fd3539749127 - - d43eb39b989e - b7be725976b6 - - d68c43202172 - 4db0695a6fc7 - - 79489d5685dd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -492,12 +492,12 @@ tools: owner: iuc revisions: - bdc67eeb0bc9 + - 78cd8b69da4c - 1ccf0e7fb4f6 - 58091e1be01b - - 5296d26b0373 - 6a636d58dfc2 + - 5296d26b0373 - b0d39ef600a7 - - 78cd8b69da4c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -509,13 +509,13 @@ tools: - name: bcftools_stats owner: iuc revisions: - - 4d3ce9dc1525 + - e8af591435d1 - a2f8dc22d7c0 - '388983871932' - - e8af591435d1 - b641062a2587 - - b17394940c7a - baa8823f8073 + - b17394940c7a + - 4d3ce9dc1525 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: - - abc3ced31cd1 - 3ca3de4e5291 - - e6b5cbbf449b - 59fa8742285e - - 38d75661c235 - d1f8f55f564d + - abc3ced31cd1 + - e6b5cbbf449b - 3a233c8eb814 + - 38d75661c235 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -545,36 +545,36 @@ tools: - name: vcf2tsv owner: devteam revisions: - - 285060661b45 - e92b3c0f9224 + - 285060661b45 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 owner: devteam revisions: - - 57a16b310fe8 - a8a4f94aa321 + - 57a16b310fe8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 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 @@ -601,37 +601,37 @@ tools: - name: vcfcombine owner: devteam revisions: - - 53edb91ed051 - 1f0ba67cc85a + - 53edb91ed051 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples owner: devteam revisions: - - f1852ecef841 - 254f285dbaaa + - f1852ecef841 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - eae7c08ebb6f - fa24bf0598f4 - 6b935ab36d7b + - eae7c08ebb6f 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 @@ -665,36 +665,36 @@ 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 owner: devteam revisions: - - 17096387c0e6 - d226a7327946 + - 17096387c0e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample owner: devteam revisions: - - 6257ee3b50d3 - 12b570dd0bc5 + - 6257ee3b50d3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples owner: devteam revisions: - - 2ba3b87f904f - 958b6484a7f1 + - 2ba3b87f904f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort owner: devteam revisions: - - dd44c3f416c3 - 5b7120c66efc + - dd44c3f416c3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/staging.usegalaxy.org.au/viral_tools.yml b/staging.usegalaxy.org.au/viral_tools.yml index 06370d956..15250eab7 100644 --- a/staging.usegalaxy.org.au/viral_tools.yml +++ b/staging.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 diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 5f0e9ace1..4b4831aeb 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 6e9aea89e388 - 78c75f134c16 - 3f3e247c053d - - c2ef298da409 + - 6e9aea89e388 - 4efdca267d51 + - c2ef298da409 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -37,34 +37,34 @@ tools: owner: iuc revisions: - 4f2967b27e67 - - b5d8e5475247 - - 1aae04680c4b - 133f36c29579 - - fe3ca740a485 - f29602ae449e - 44018dd6b447 + - 1aae04680c4b + - b5d8e5475247 + - 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: - 7be22100e5e1 - - 6519ebe25019 - dc027fa56d55 + - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - 28433faa6e42 + - 09855551d713 - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -97,8 +97,8 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf - 63662ae295d6 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -116,41 +116,41 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 582fd74dc2a1 - - 9f2455341fac - 14f588312c56 + - 9f2455341fac + - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 73428a792541 - 30fb23d4c31c + - 73428a792541 - a230ea445788 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - 563a19373357 - 30f08d74024f + - 494f0bb4a993 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 7abc5f6dd595 - 2bba2ff070d9 + - 7abc5f6dd595 - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - d3af38b9c7e1 - 52af33194019 - b3cf4684e9c7 - - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -176,8 +176,8 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b - ef2ad746b589 + - 602de62d995b - 8b3e3657034e - 43798b4caee0 tool_panel_section_label: Annotation @@ -197,15 +197,15 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -224,16 +224,16 @@ tools: - name: maker_map_ids owner: iuc revisions: - - 326f9c294b09 - e906fa778440 + - 326f9c294b09 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: + - 3c1a01127868 - 370c210d9541 - d46d803ca6cc - - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 @@ -264,10 +264,10 @@ tools: - name: prokka owner: crs4 revisions: - - d643e3b03500 + - 8a22554cdde2 - bf68eb663bc3 + - d643e3b03500 - a17498c603ec - - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -299,20 +299,20 @@ tools: - name: snpeff owner: iuc revisions: - - cfcf33df7fc0 + - 8f92c2b26e6d - 68693743661e + - cfcf33df7fc0 - 5a29ab10dba6 + - 5b80f544c67f - 268d162b9c49 - 5c7b70713fb5 - - 8f92c2b26e6d - - 5b80f544c67f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - 2b3e65a4252f + - 5fab4f81391d - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -337,22 +337,22 @@ tools: - name: tbprofiler owner: iuc revisions: - - 45083d070fb8 + - 809dfc93d593 + - 200c378d85f3 + - ac8250086ac3 - 2c68b0c38785 - e1a9d6fd258d - - ac8250086ac3 - - 200c378d85f3 - - 37213cf56392 - - 809dfc93d593 - 037a11682176 + - 37213cf56392 + - 45083d070fb8 - ba6f87115e13 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: trna_prediction diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index f775b9577..bae048f6b 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,24 +2,24 @@ tools: - name: abyss owner: iuc revisions: - - 841084c5fc46 - fa5259cc561b - 7547fcab5d19 - - 8f1b150a2487 - 553bfe8bd0b5 - - 0e93176640ac - 890b794c997d + - 0e93176640ac + - 8f1b150a2487 + - 841084c5fc46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 94fe43e75ddc - - b9e31c5c01c7 - 067592b6b312 - - 21e491ad532a - - ddddce450736 - b2860df42e16 + - ddddce450736 + - 21e491ad532a + - b9e31c5c01c7 + - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -31,37 +31,37 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - a7f16f24e9a1 - - 5258e18bbe23 - 22286dab5aa1 - - 3371c5bdc17a + - a7f16f24e9a1 - faee8629b460 + - 3371c5bdc17a + - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 1e62c28ba91d - - e824f5d958d0 + - 0d243f458b53 - cf13a1e03e5b - - 94170eee0ad8 - - 2dd755c1c6ff - - 46ae58b1d792 - - 4048d82f0c88 - 1440ae06552f + - bb935709506a + - e824f5d958d0 + - 46ae58b1d792 - 5ecdeca79a0d - - 602fb8e63aa7 - - 0d243f458b53 - - 41030a6c03b7 - e4bd1e99bacf - - bb935709506a + - 2dd755c1c6ff + - 41030a6c03b7 + - 4048d82f0c88 + - 602fb8e63aa7 + - 94170eee0ad8 + - 1e62c28ba91d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 86f150c8019d - 5732f959936a + - 86f150c8019d - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -74,8 +74,8 @@ tools: - name: flye owner: bgruening revisions: - - 3ee0ef312022 - 276f5d8712d5 + - 3ee0ef312022 - 8d4f03b5fe9d - cb8dfd28c16f - 1ce9b1d72ec3 @@ -86,25 +86,25 @@ tools: owner: iuc revisions: - b2f674562a18 - - 01210c4e9144 - 3169a38c2656 + - 01210c4e9144 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: + - 611219887a48 - 06bcf65179fb - 8b330a577046 - - 611219887a48 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 3fba9c77550a + - 5127a713de83 - 3ef480892a9f - 690c2caa367e - - 5127a713de83 + - 3fba9c77550a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -116,18 +116,18 @@ tools: - name: hifiasm owner: bgruening revisions: - - 3f7be05a1597 - - f3c89da3af16 - - 6505bd37670d - - 2061fb3b81b4 - - 045c7c3d8e59 + - 366a11d316a7 - 5bec28269d95 - - 5f625c63b8bc - - da9d8bf98802 - - ec9e21e9c71b - 9ef6920c3089 - 71740308d412 - - 366a11d316a7 + - 045c7c3d8e59 + - f3c89da3af16 + - da9d8bf98802 + - 5f625c63b8bc + - ec9e21e9c71b + - 6505bd37670d + - 2061fb3b81b4 + - 3f7be05a1597 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -153,9 +153,9 @@ tools: - name: merqury owner: iuc revisions: + - 9d79beb19ac3 - 39edec572bae - f8113c25bc6b - - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl @@ -169,12 +169,12 @@ tools: - name: metaspades owner: nml revisions: - - 2ecf5a570907 - - e731ea24e48d - f338e9942b27 - - 606b09cc9860 - 3ca2d2a9068c - eb7a370f6588 + - e731ea24e48d + - 2ecf5a570907 + - 606b09cc9860 - fd128c111ab0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -187,11 +187,11 @@ tools: - name: miniasm owner: iuc revisions: - - a7b889b90140 - - 8b6d0d85252b - 8dee0218ac7d - 73a3846701e1 + - 8b6d0d85252b - 80d1250bd5fd + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -217,55 +217,55 @@ tools: - name: pretext_map owner: iuc revisions: - - bbe19ef04a74 - - 8fef980d48b5 - 2b16ba799da9 - - d256a51a656b - 02831bf9e95f + - d256a51a656b + - 8fef980d48b5 - dfb8a4497339 + - bbe19ef04a74 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - 76d4cbefff85 - - a315c25dc813 - e9bd16ba5ebd + - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 59db8ea8c845 - - 7594365c546b - - 72472698a2df - - 3061c8b029e5 - 342a1d1fed7b - - 6fcbee531de6 + - 7594365c546b - 675488238c96 - ebb0dcdb621a + - 3061c8b029e5 + - 59db8ea8c845 + - 6fcbee531de6 + - 72472698a2df - 875d0f36d66f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 39bed8de8017 + - e100a765370e - aa39b19ca11e + - cd06929b224b - a199cd7ac344 + - 39bed8de8017 - d865b62f501c - - cd06929b224b - - e100a765370e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: + - 33b7d8481a76 + - 3edba9afc9bc - f8564b2d7f63 - f11b994b7eb2 - 2b2a352488fa - - 3edba9afc9bc - - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades @@ -273,9 +273,9 @@ tools: revisions: - ef69617ecb42 - 1d06c8b38e77 + - e122f9101584 - 378e55aeeb25 - 53c2bc8c2ae3 - - e122f9101584 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa @@ -296,50 +296,50 @@ tools: - name: shovill owner: iuc revisions: - - 83ead2be47b2 - - 865119fcb694 - - ad80238462c1 - 196a599ec43d + - 865119fcb694 - f698c7604b3b + - 83ead2be47b2 - d9f6a00b6db7 + - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: + - 5e0825476fb7 - 24e471d13fe9 - 5a0ddb4dc3a4 - - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 904bf932cf78 - 1fc82fe7ebef - - 1bb12736175c - - 7490b213baa9 - 051fd2db8a27 + - 7490b213baa9 + - 1bb12736175c + - 904bf932cf78 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 808b3a0a6716 - - ad8b536d1caa - - d6e617c4e338 - fee85957cebe - 34305b013402 + - d6e617c4e338 + - 808b3a0a6716 + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - e5a3b75a271f - - 8d4b90bf9caf - b8002c3f7141 - - 21da31ed41a1 + - 8d4b90bf9caf + - e5a3b75a271f - 6b5a5842531e + - 21da31ed41a1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades @@ -347,109 +347,109 @@ tools: revisions: - 2a10645aeadd - f1532cb33c75 - - 9de69775f512 - - 328aa71f0f3c - 86f66ab58e14 + - 328aa71f0f3c + - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 340bc17f49cf - - e41dcb0e913b - 1708851f8804 - - 85fb02c43042 - 6aad515a5270 + - e41dcb0e913b + - 85fb02c43042 + - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - d5fb354f745d - b3490b036c5a - - b65a43f70b99 - d159735a6a9f + - b65a43f70b99 - 249f6a28c751 - - d5fb354f745d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - dd7ad84f3943 - - b7829778729f - - 7897763d14ec - - d2d1df21dfb9 - 33368fec3b70 + - b7829778729f - 9006e5836729 + - dd7ad84f3943 + - d2d1df21dfb9 + - 7897763d14ec tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: + - ced385aa976d + - 6f4c8ad6ea01 - 505a9833ab5d - 189e837009c9 - 8f631679571f - - ced385aa976d - - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - d40ed4eb0c0e + - 9ded6109434a + - e59bee4565b3 - 356afed970b4 - 19bdfd1e6fe3 - - e59bee4565b3 - - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 6dd935e4984b + - ebd801e712bc - b23249f81bc4 + - 6dd935e4984b - 4688ae3b49b5 - - ebd801e712bc - 80a17897564d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b5e35a2ca4f3 - - 937ea677d437 + - cb1e3db43020 - b64696992ee9 + - 937ea677d437 - 59bd28f6265d - - cb1e3db43020 + - b5e35a2ca4f3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6015aa0303f2 - 05bd7504fdb2 - - cb4768eeca3b - - 2628f6790eda + - 6015aa0303f2 - 383bb5ad32e2 + - 2628f6790eda + - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - d10bdad2fd17 - e92675014ac9 - - 6e26c9afd301 - 0a3a602cd1e3 + - 6e26c9afd301 - 9e3e80cc4ad4 + - d10bdad2fd17 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 920677cd220f - 5da9a0e2fb2d - 8d09f8be269e + - 08256557922f + - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index 8645caa44..d03ebf792 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: - - 31812e7a1315 - - 1f5641a52664 - 8e8dc9a1e3e5 + - 1f5641a52664 + - 31812e7a1315 - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 24a7a95867b0 - 5c8ff92e38a9 + - 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 35dcfef42..26700f340 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: - - a9c9d768b751 - 204a131e47db + - a9c9d768b751 - 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 798d228c5..3dab6b7f7 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: + - 07e8b80f278c - a1a923cd89e8 - - a8eabd2838f6 - - e19bebe96cd2 - 87ee588b3d45 - - dde39ba9c031 - - 07e8b80f278c - - a68aa6c1204a - - ce3c7f062223 - - b28e0cfa7ba1 + - a8eabd2838f6 - 589e7e57fd6d + - ce3c7f062223 - 0a5c785ac6db + - e19bebe96cd2 + - b28e0cfa7ba1 + - a68aa6c1204a + - dde39ba9c031 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 9fa148897..931221670 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,20 +8,20 @@ tools: - name: diamond owner: bgruening revisions: + - 62c9df8382c2 - f921014aba5a - - 1e3323a44643 - 54f751e413f4 - - 62c9df8382c2 + - 1e3323a44643 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - 2889433c7ae1 - - 0e3cf9594bb7 - - e25d3acf6e68 - 6f386c5dc4fb + - 0e3cf9594bb7 - 5edc472ec434 + - 2889433c7ae1 + - e25d3acf6e68 - acf4e47b734c 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 0383131c9..ac0ed951a 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: + - 27ee142314a9 + - 6ca543ec1bf8 - 710301bc46fa - f4230f116196 - da6bd1975a71 - - 6ca543ec1bf8 - - c8cdde00b105 - - 27ee142314a9 - 095ad4d096d1 + - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -74,8 +74,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: enumerate_charges @@ -100,21 +100,21 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 88076940fa94 - - 79cfd9ead848 - - 0fac8e2afc13 - 3b8a9d5ced85 + - 0fac8e2afc13 - bfb65cb551d8 + - 79cfd9ead848 + - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 715cd0e87781 - eb6564a60136 - - b46d4b4d995c - d532b7e5f64b + - 715cd0e87781 - 55918daa5651 + - b46d4b4d995c - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -123,49 +123,49 @@ tools: revisions: - f26afd1b7104 - 5579659312e6 + - dae135dfd519 - fdf2cc80adb5 - d2f955aea23a - - dae135dfd519 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - 319a28774da9 + - bc31d02be922 - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - cac1886249a2 - - 4da9ee404eab - 2c349b027a01 - - 070e3ecc3fda + - 4da9ee404eab - ed736e6eee39 + - cac1886249a2 + - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - da8753545526 - - d1f803b5943c - - f197e34c33a9 - - 807aa4c9293d - - c0c9a5024177 - - 73008ef1f487 - 525ca7c8065f + - 73008ef1f487 + - 807aa4c9293d + - f197e34c33a9 - 2e219a2d9327 + - c0c9a5024177 + - d1f803b5943c + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 61094e01eff9 - c4fbab8e03c5 - - 1809414a9454 - 7568ae18908a + - 1809414a9454 + - 61094e01eff9 - 27ea4e1a3f95 - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox @@ -173,11 +173,11 @@ tools: - name: md_converter owner: chemteam revisions: - - ccfbd956a2d3 - - 79e8ab8f1e81 - d7ec25187599 - - 730ef07b90ae - ba83f0923369 + - 730ef07b90ae + - ccfbd956a2d3 + - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -197,8 +197,8 @@ tools: owner: bgruening revisions: - b59c91adeac1 - - e6011617c748 - e2c36f62e22f + - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index fa07f8057..9b7149c7c 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - c97a786e8fb5 - - 163688bb8f73 - fa56d93f7980 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -16,16 +16,16 @@ 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: + - 495a4173006f - 424aefbd7777 - 640d3af5d833 - - 495a4173006f - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,7 +39,7 @@ tools: - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 6ea678946..eec283421 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,30 +9,30 @@ tools: - name: collapse_collections owner: nml revisions: - - 90981f86000f + - 33151a38533a - 25136a2b0cfe - 830961c48e42 - - 33151a38533a + - 90981f86000f tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - 6cbe2f30c2d7 + - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 0c8150d1c..d9a85e395 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -8,26 +8,26 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 4a6ee918c13a - - 5e1240a87bcb - - 0b3c3ad92827 - e3cbd2287f63 - - a3b86937ead6 - f3a19509108a - 367b1ed91207 + - a3b86937ead6 + - 5e1240a87bcb + - 0b3c3ad92827 + - 4a6ee918c13a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 584008e574b2 - - e525f9ffb9ac - - bd46669113b9 - - 33c99804a32f - 54ccb7e1f49a - - 501c21cce614 - 72ed72122deb - 1b5fc03380d4 + - 33c99804a32f + - 501c21cce614 + - 584008e574b2 + - e525f9ffb9ac + - bd46669113b9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -52,8 +52,8 @@ tools: - name: fastq_to_fasta owner: devteam revisions: - - 186b8d913e6c - 8979c288aefb + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -66,8 +66,8 @@ 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 @@ -79,8 +79,8 @@ 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 @@ -111,18 +111,18 @@ 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: - - 92ac8e086317 + - 26c6706bfb07 - 19e45916daf9 - b9b385097f13 - - 26c6706bfb07 - 63769c4217a7 + - 92ac8e086317 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 7d11fe9cf..970e53ab8 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,166 +2,166 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 5f6d123679f4 - de72ba3ed6f2 - - 29451af70c52 - 268e91e540ee - - e821645ef8fc - a1ca9bccc7f2 + - e821645ef8fc + - 29451af70c52 + - 5f6d123679f4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - bb1e4f63e0e6 - - 5d11599b8a7d - 0e143b4c3987 - - 7a7fd0f5f15d - 2d2cf5c1ea8a + - 7a7fd0f5f15d + - bb1e4f63e0e6 + - 5d11599b8a7d - 12af64f93288 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: + - 1d848bc4585f + - 7c1beb6d6eca - 81b1e3e1fc6c - dc059492a995 - - 7c1beb6d6eca - - 1d848bc4585f - 195e98217334 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: + - 71aa86af6762 - 3d211717a775 - - a67ac707496a - 26e7304d6737 - - 93eb012d9eed - - 71aa86af6762 - bfff7454b59a + - 93eb012d9eed + - a67ac707496a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 2bc10a9ca58b - - b8858746dc1f + - dd0b7398bb96 - 29fcfd36e90a - - 5be24eba848d + - b8858746dc1f - 56d5b797ce84 - - dd0b7398bb96 + - 2bc10a9ca58b + - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - c3e012dfe21f - - 9384cd033f30 - - 7ef978dc1b8a - 7e6bcd2e5128 - 72bfafe3330b + - 7ef978dc1b8a + - 9384cd033f30 - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: + - b73e213add0c - 514fa53b5efb - 167788df3b46 - - fd1275e01605 - - 9470f29702f8 - d9a637e83828 + - 9470f29702f8 - fb9cf9c97ec4 - - b73e213add0c + - fd1275e01605 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - c34d11ea4ba6 - - 5bffaa8354a1 - - a02cfa31e9cb + - 2c37ce318bc3 - 86febdcc4283 + - a02cfa31e9cb - ca0616bb2cdf - - 2c37ce318bc3 + - c34d11ea4ba6 + - 5bffaa8354a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 192ef85c0b0b + - 004aea905d4d + - 1fcb7adc39b8 - 78f405266706 - 2d466b530754 - - 1fcb7adc39b8 - 69a8621ca2f0 - - 192ef85c0b0b - - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 2f9e4843f480 + - 9ecba5e225a6 - 3c9f0c486cca - d9ce4897dbb2 - - 2f9e4843f480 - db940c262830 - d580d6acd1df - - 9ecba5e225a6 - 459cfa861f0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fd408d755394 - - bd7db9e2f2cb - - fbe773640707 - 2c66e43f1c86 + - fd408d755394 - f264afa9fa6f + - fbe773640707 - 32e451def88c + - bd7db9e2f2cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - 7fda5607e777 - - 9368fbc49c8b - - 7e361d147872 - - 4e12ea27f788 - 3b9d990a0a0e - 56bce3c82278 + - 7e361d147872 + - 4e12ea27f788 + - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - d9114ef1c8a5 - - b1779366c8e9 - - ce4ce3316f74 - - c03c3384cd81 - e65d16fb2724 + - c03c3384cd81 - 94ca68515826 + - ce4ce3316f74 + - b1779366c8e9 + - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - d57251071381 - f8fc4e5aff9d - - 793665fff0f8 - b88ebb3672a1 - - 2da482e408b8 - 23f7c5f1fdaf + - d57251071381 + - 2da482e408b8 + - 793665fff0f8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - c60570fa602f + - 512155688d98 - 010e58e9d822 - a7849312d328 - ba6efa77fb79 - - 512155688d98 - a4dfb122e52b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -169,20 +169,20 @@ tools: owner: bgruening revisions: - 38e3f226248b - - 00d869ea03a1 - - aa200e4f3939 - - 69264da0ce77 - c899e0ccff8c + - 69264da0ce77 - 4d678170d29b + - 00d869ea03a1 + - aa200e4f3939 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 10301d137111 - - aac8444d6681 - - c361b12d207a - d806504e96d9 + - c361b12d207a - a2d70c4fd406 + - 10301d137111 + - aac8444d6681 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 b2545f0c2..6a009173b 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -16,15 +16,15 @@ tools: - name: obi_convert owner: iuc revisions: - - 374fd9feb032 - 4d705e3443a7 + - 374fd9feb032 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - fe7ec8a3d35e - e9e49cf06b42 + - fe7ec8a3d35e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 3bf57dadf7cd + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -51,15 +51,15 @@ tools: - name: obi_stat owner: iuc revisions: - - 723a93febe89 - 39320fee9d70 + - 723a93febe89 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - 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/emboss.yml b/usegalaxy.org.au/emboss.yml index c20dc3f9c..e1f7bb3ff 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - 63dd26468588 - 832c20329690 - - ce385837c160 - dba489bfcd62 - - 63dd26468588 + - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index b31cba3aa..35a842c4d 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -2,9 +2,9 @@ tools: - name: bwameth owner: iuc revisions: - - d82648ad25a3 - 6da3972210ee - 62f5fab76dfb + - d82648ad25a3 - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -17,7 +17,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 558a7556e..51b5576e2 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,22 +8,22 @@ tools: - name: cutadapt owner: lparsons revisions: - - 288f97432497 - - 44e2cc14f75b - - 135b80fb1ac2 - - de6cebe3c043 - - 48f587c13075 + - 8665bcc8b847 - 093678460093 - - 8c0175e03cee - - c4b82dce8335 + - e4691e1589d3 - c053d4cad713 - 660cffd8d92a - - 8665bcc8b847 - - e4691e1589d3 + - de6cebe3c043 - 49370cb85f0f + - c4b82dce8335 + - 48f587c13075 + - 44e2cc14f75b + - 4e5056fefd88 + - 288f97432497 + - 135b80fb1ac2 - c5e2e5902201 + - 8c0175e03cee - 5915ea1ec9b1 - - 4e5056fefd88 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -36,8 +36,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - de2db1bdfbf8 - 7d37cfda8e00 + - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -77,24 +77,24 @@ tools: owner: iuc revisions: - 9c620a950d3a - - 56022eb50bbd - cd0874854f51 + - 56022eb50bbd - 0dbb995c7d35 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - 1d8fe9bc4cb0 - - 65b93b623c77 - dbf9c561ef29 + - 65b93b623c77 + - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -107,8 +107,8 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 8611b80a14d6 - 47e5dbc3e790 + - 8611b80a14d6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -121,15 +121,15 @@ 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 owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -149,30 +149,30 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - e39cc71d3ed6 - 249c8393f2d4 + - e39cc71d3ed6 - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - - 74db4cffab1f - 54053ea6c77e + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - b1cea1b2fcd0 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -185,8 +185,8 @@ tools: owner: devteam revisions: - d5e9e83cd3d8 - - 09070cacefd8 - 567d5b3c52b1 + - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -199,8 +199,8 @@ tools: - name: fastx_clipper owner: devteam revisions: - - bdf1ce174e39 - 736b8f6ee456 + - bdf1ce174e39 - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -214,25 +214,25 @@ tools: - name: fastx_renamer owner: devteam revisions: + - 3599f5451ee2 - 02f8a17a4ebd - b29d37ca9e41 - - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: + - 6027ef51ef91 - 0c2907307ba4 - e246088b6e34 - - 6027ef51ef91 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: + - 547e8d00f11c - 377ac2829eac - 61b4cedc8934 - - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -264,25 +264,25 @@ 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: - - 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 - e654095ab143 - - b557acca0b56 - a535cf1e5da4 - 8250ea3a1501 - - 24013bf85a6f + - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -294,11 +294,11 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - f3759eec3018 - 6a675c3aa610 - - 27ac32a22ad2 + - f3759eec3018 - 828dba98cdb4 - 7accf7407811 + - 27ac32a22ad2 - 9fa7803d1c51 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 f368fa8a1..855300817 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -3,27 +3,27 @@ tools: owner: devteam revisions: - 7b4468117008 - - ce9cd02d5b88 - e41385662e5e + - 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: - f2e8552cf1d0 - - 5ec9f6bceaee + - e7b2202befea - ff9530579d1f + - 5ec9f6bceaee - 9da02be9c6cc - 3d0c7bdf12f5 - 2b0c9d9fc6ca - - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -36,15 +36,15 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - ad116ae3f4d9 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong @@ -59,14 +59,14 @@ tools: owner: iuc revisions: - b2f1f75d49c4 - - 5e33b465d8d5 - - c1a4b5f3b432 - 3d93dd18d9f8 - - 75c93c70d094 - - abfd8a6544d7 - 1c2db0054039 + - c1a4b5f3b432 + - 75c93c70d094 + - 5e33b465d8d5 - bf675f34b056 - 9a913cdee30e + - abfd8a6544d7 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 5b44a1c25..7946b577d 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: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 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 ddd29b4fd..94a739cb2 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,16 +9,16 @@ 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 - f2f3bc622a16 - 0c8f7322f8fc - - 8f53b238a360 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -45,22 +45,22 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump owner: iuc revisions: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -79,23 +79,23 @@ 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 owner: iuc revisions: - - b2c25142267e - cf61daf064fe - 45296e47d565 + - b2c25142267e 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 @@ -122,44 +122,44 @@ tools: - name: gemini_query owner: iuc revisions: - - 666f60a9331a - 840fb4850be3 + - 666f60a9331a - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 86f3aac4418d - 05124dc72dba + - 86f3aac4418d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region owner: iuc revisions: - - 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: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 34c4db133..9844ff03b 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,15 +2,15 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index e4cee0d37..2a47769af 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,45 +2,45 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - 983bf725dfc2 - - e9df53a75f3c - b39347891609 + - e9df53a75f3c + - 983bf725dfc2 - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - - 28587613264f - 1c58de56d587 + - 28587613264f + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: + - 9a776b080193 - 83c7d564b128 - 7068f48d0ef9 + - 4df8de2d0e48 + - 6ea73833cf67 - f5ea3ce9b9b0 - - 69ebb7f46e45 - - 9a776b080193 - - 653e89d73fc4 + - 1790dcf3c32d - 5e6237d58b0c + - e08a7ad4378b - c441583adae5 + - 69ebb7f46e45 - aad3885b3216 - - 1790dcf3c32d - - 4df8de2d0e48 - - 6ea73833cf67 - - e08a7ad4378b + - 653e89d73fc4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 34758ab8aaa4 - 75b3b3d0adbf - - 9aaa46d45472 - 7863f1abcdda + - 9aaa46d45472 + - 34758ab8aaa4 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 b5367674b..bb73211f2 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: - - 7f13dc906cb9 - 740057a5126d - - df7356989ac1 - - 4b519282a05b - - fd59d783248a - c4bde687c846 + - 290a11559985 + - fd59d783248a - ae9994cf526f + - df7356989ac1 - a64dc31ab7f2 - - 290a11559985 + - 4b519282a05b + - 7f13dc906cb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -37,29 +37,29 @@ tools: revisions: - 53460afd5115 - '566197475670' - - ca7cb0eaad62 - 3b37b1b1c3a7 + - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 3d059e9c2fba - - d3a9e32672ec - 391a4cc45fea + - 3d059e9c2fba - da4c086cff5b - 10515715c940 + - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 - - 3b12bf9b4b87 - - 299307abd804 - d0fc8b746d57 - - e3a675da7fd0 + - 299307abd804 + - 1acf88921176 - 5fe1dc76176e + - e3a675da7fd0 + - 3b12bf9b4b87 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -71,8 +71,8 @@ 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 @@ -91,17 +91,17 @@ tools: - name: jbrowse owner: iuc revisions: + - fd5dbf0f732e - 836d1aa3e89a + - ca2def38369c - 667e17248bfe - a6e57ff585c0 + - 1cfc579079a6 - 2bb2e07a7a21 - 112eb40ba6cf + - 17359b808b01 - 6cd09d7b5f37 - 4542035c1075 - - fd5dbf0f732e - - ca2def38369c - - 1cfc579079a6 - - 17359b808b01 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -119,8 +119,8 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - fe154a7af404 + - f1691de443a7 - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -153,8 +153,8 @@ 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 @@ -166,22 +166,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 - - 4ac4e7083b7e - - 326a3db8d9d1 - - 59fd173ac850 - 14e7c35f3d00 + - 59fd173ac850 + - 4ac4e7083b7e + - 7dd841a32245 + - 360df4999907 - 2824d77cd8f8 + - 326a3db8d9d1 - a1abfa420d9d - - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 44608d0193ed - 83c573f2e73c - 73b8cb5bddcd - - 44608d0193ed 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 84644b2ba..b2f0159e2 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -173,8 +173,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - 0f98603d0116 + - 767a675b5254 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index ad62fd84a..d4df78e59 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,40 +2,40 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 921a2da49a0c - 29f66c353bcb + - 921a2da49a0c - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - d404277cc87a - 78fb5e286609 - 5746d61f0a91 + - d404277cc87a tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 9e357a8b2ec3 - 4d511437b1e5 - 03dd3c16ae4e + - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 41dbf4d162a2 - - 0ba4f56a3613 - 3b5b54ed6392 + - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 - 7babd8a46fe0 - 5308ca68ef3d + - 9939786dd9c9 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 9542964f0..34e198daf 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -33,8 +33,8 @@ tools: - name: bfconvert owner: imgteam revisions: - - b07f4839ca77 - f3360fbeda64 + - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -46,6 +46,7 @@ tools: - name: count_objects owner: imgteam revisions: + - 5bf8eb50b280 - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -79,8 +80,8 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: - - 2484086dee41 - 6a7da2e5f696 + - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -93,22 +94,22 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f8fa0f6718a3 - d0178bdcd00e + - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - ad271f78a87a + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - 993faa34333b + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -121,15 +122,15 @@ tools: - name: cp_mask_image owner: bgruening revisions: - - 3a05117669cf - b178453ea8d1 + - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied @@ -149,8 +150,8 @@ tools: - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - 6f4715b8540a + - e972e07c7845 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -163,15 +164,15 @@ tools: - name: cp_measure_object_size_shape owner: bgruening revisions: - - 79e10d12d90a - acf3aa487283 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - 80b200ae516b + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -183,8 +184,8 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 8083a87d2fdf - 3a3033222f61 + - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index ba30a8880..b7547736f 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - d6e72da3ec35 - e4ee04da1c19 - f362150bef41 - - 17f911830a8c - - a38934e303b9 - - 78bbd17d0703 - 3e4f434a69c6 - e319b5b65879 + - 78bbd17d0703 + - a38934e303b9 - 1069f6db0a0e + - d6e72da3ec35 + - 17f911830a8c tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - f91cfb73d369 - 0135f1d487a0 - - 2b95d5c04908 - - 8f8df367470d - 7fe36019c073 - - c88553ec696e + - f91cfb73d369 - 72ddd32392cd - - 1ef5b6e3e09d + - 8f8df367470d + - c88553ec696e - 9537184d421f + - 2b95d5c04908 + - 1ef5b6e3e09d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - fafb3d685fa9 + - d7e79eb3bcb3 - 2cf4a1cafc16 + - fafb3d685fa9 - ad0dc9f4c9e2 - - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 6a1515bb0687 - 28a6f1908fcc - 43aac8d29685 + - 6a1515bb0687 - 7f1cfa4c0e32 - - 8c05afb547fa - bd2a7d1316b9 + - 8d36959b000d - 3d18f8c3c0f6 - - 94df24c6bc00 - - 69797fa273c3 - ee2beb764a7b - 9eaadf03e0df + - 69797fa273c3 + - 8c05afb547fa + - 94df24c6bc00 - ee29337f905c - - 8d36959b000d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - db536ad45f28 - - 364f4ffec275 - - e3bb03cf207a - - 5d6ed46cc101 - cb903c9dc33d - - d37ede8589b2 - - 0893a1dbb807 - - 9f978da6528a - 8858fa037a15 + - 5d6ed46cc101 - c092052ed673 - - bcaa0d571ce2 - 5671e1d3d5ee + - db536ad45f28 + - d37ede8589b2 + - e3bb03cf207a + - bcaa0d571ce2 + - 9f978da6528a + - 364f4ffec275 + - 0893a1dbb807 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: + - 045d6d00f606 + - 49236b03e4fd - e1a015876aa9 - - ed28dd32141c - - 230b05597996 + - 3b6a16d82c1b - c5c9f02b6167 + - ed28dd32141c + - f95f403841ad - 38b91a3190cd - - 3b6a16d82c1b - - 49236b03e4fd - 12d66d0d05ac + - 230b05597996 - 584beffa972b - - 045d6d00f606 - - f95f403841ad 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 afd8acc4a..6335c4a57 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,10 +2,10 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 17e3b698dd52 + - f198773344e4 - 0f1724dd59d2 - b8a457820315 - - f198773344e4 + - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index a258ee6b7..3bad0a4bd 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -15,60 +15,60 @@ tools: owner: bgruening revisions: - f1b9a42d6809 - - b6ef6d0cb6b7 - e1317b5502fa + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - - 05143043ca13 - 947c2eacccb8 + - 05143043ca13 + - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 83228baae3c5 - 1552b8cb4a94 - 29e4122c90de + - 83228baae3c5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - a07ab242b0b5 - - 53616c8b0865 - - 1a53edc4b438 - 841a6cc5fc58 + - 1a53edc4b438 + - 53616c8b0865 + - a07ab242b0b5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 40f4447733b2 + - dc4b5fd604a6 - 2fc89dcd41c8 + - 40f4447733b2 - 91c4e3331208 - - dc4b5fd604a6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 301e07345c93 - e5a5ad882f1f - 25ab6b4e376e - c6ae57f774c6 + - 301e07345c93 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - f9639b488779 - - 4ed102b922cb - - b7c3e9a3b954 - 02d2be90dedb + - b7c3e9a3b954 + - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 2276b08c7..d9742da5e 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -3,14 +3,14 @@ tools: owner: devteam revisions: - 03e9b2fbc005 - - 17062a0decb7 - - 937aa69e715f - - a6d65b0c67af - - 749c918495f7 - - f6877ad76b00 - cd659e8cc5fa - 017aba02828d + - a6d65b0c67af - 3ba8d4563129 + - 749c918495f7 + - 17062a0decb7 + - 937aa69e715f + - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -28,11 +28,11 @@ tools: - name: bwa owner: devteam revisions: - - 64f11cf59c6e - 53646aaaafef - dfd8b7f78c37 - - 3fe632431b68 - e188dc7a68e6 + - 64f11cf59c6e + - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -44,41 +44,41 @@ tools: - name: lastz owner: devteam revisions: - - e7f19d6a9af8 - - 3e1ea2facca6 - 60afcc2c1d05 + - 3e1ea2facca6 + - e7f19d6a9af8 - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - b3eab4b67562 - - 6b1e195506a3 - - 53c0b7a1a0c3 - c0c2d0941de8 - f54f5baedfdd - - 11a0d50a54e6 - - 3f4d6399997b - 8c6cd2650d1f - - be1d967337e4 - - 09b53c1d4ab1 + - 6b1e195506a3 + - b3eab4b67562 + - 53c0b7a1a0c3 + - 3f4d6399997b - 77b2770508f6 + - 11a0d50a54e6 + - be1d967337e4 - 037c6e54df11 + - 09b53c1d4ab1 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 13022c3d3076 - - 1cd2511a396e - - ec9cbd6b9a49 + - 00fbfac99d39 - 178bdbdb6d24 + - 9ee34ba73ebf - b8f5f6e87f5c - - 00fbfac99d39 - 79b885ce78d7 + - 13022c3d3076 - e403d27e8f24 - - 9ee34ba73ebf + - 1cd2511a396e + - ec9cbd6b9a49 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 80951ad96..439698430 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 @@ -29,16 +29,16 @@ tools: - name: dada2_dada owner: iuc revisions: - - 1c35dadbe76f - - 84fd33a60b35 - 18a502a9d287 + - 84fd33a60b35 + - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - 34e55239e68b - f732237754fc + - 34e55239e68b - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -53,24 +53,24 @@ tools: - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - - 8470de786d47 - e96bbb9e24ea + - 8470de786d47 + - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 306a40d4bb8f - 84743da21318 + - 306a40d4bb8f - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a - 8daf4564ccda + - ac72310b038a - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,16 +78,16 @@ tools: owner: iuc revisions: - d60df8727f59 - - f947b4bb5107 - a58e4a43f49c + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - 04144473e59e - - 7f3b59dee073 - 1bc3657cd694 + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts @@ -101,8 +101,8 @@ tools: - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - e005e659ae21 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf @@ -115,15 +115,15 @@ tools: - 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 owner: iuc revisions: - - 6d364c65c946 - 6c84982ee6f7 + - 6d364c65c946 - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -136,17 +136,17 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - bd7a9c6efb10 - e66ab198ec15 - 6aad8ca3918b + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - b084117133af - d77397f09da1 - c6676a890f50 + - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways @@ -167,53 +167,53 @@ tools: owner: iuc revisions: - 79706f10d680 - - c409a495841f - 31c6d107e7a5 + - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 71ea608ddfa3 - 172920f67a84 - - 714d5a28cc5c - d24841f5c3d2 + - 714d5a28cc5c + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a4d7148ccee4 + - 12fb63b5f63f - d7e9a3c41657 + - a4d7148ccee4 - 4137b492233e - - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - e2c71b852aba - 75bedfb2078b + - cf87759761eb - 6fcb8ac37a3e + - e2c71b852aba - 64bc7acc22a9 - - cf87759761eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - c82508e76ad1 + - 5e5a999ffaa9 - 4033827c76b8 - 080ea153677c - - 5e5a999ffaa9 + - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 2cd76b089570 - - 6b7622dda516 - 95bf7479d53c + - 6b7622dda516 + - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -274,8 +274,8 @@ tools: owner: iuc revisions: - 4a9da2b6c2e3 - - e674066930b2 - 328c607150ff + - e674066930b2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -294,8 +294,8 @@ 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 @@ -307,8 +307,8 @@ tools: - name: kraken owner: devteam revisions: - - 8ba2174315aa - aec58624706f + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona @@ -339,11 +339,11 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 27250f92a01a + - 4fd3b5d8706b - e073891b2afc - 2cff76cf35c6 - 0270541aaf46 - - 4fd3b5d8706b - - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 @@ -416,20 +416,20 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - a92a632c4d9b + - ff8f55893e7d - a16313517e55 + - 6dee4abadccb - 1a6cdf55390f - - 2131d7dca455 - b89b0765695d - - 6dee4abadccb - - ff8f55893e7d + - 2131d7dca455 + - a92a632c4d9b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -478,8 +478,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 3bd5f5afb9b1 - 2e62e32d4f33 + - 3bd5f5afb9b1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -497,18 +497,18 @@ tools: - name: staramr owner: nml revisions: - - 4d83eccf5f81 - - aeaa20b96ef2 - - 4b9a8031ab74 - be818ae858e4 - 2fd4d4c9c5c2 + - 4b9a8031ab74 + - 4d83eccf5f81 + - aeaa20b96ef2 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 9b6a140d4..ebae25323 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - 4e9136c2c4c3 - ab12df91b47f + - 4e9136c2c4c3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 0d7501633..025b98990 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,33 +2,34 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: + - 48c13389050d + - cd07731e4434 + - 2263989660f5 + - 9422c5a87ee2 + - bdfbaf0c10aa + - 80f03df2e2ce - 9baa871cb1d1 - 6ae5a7b5a0a2 - - bdfbaf0c10aa - a74dbfee5a86 - - 9422c5a87ee2 - - 48c13389050d - 8b67dd48fec1 - - 2263989660f5 - - 80f03df2e2ce - - cd07731e4434 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - bc3831dd65c1 - - f0af8936ed41 - - '764845535798' - - aaa0d6a8b808 - - d390fe1567dc - 2e093badc689 - - be78f13134e2 - - f14193ec1f50 + - d390fe1567dc - c18157c68134 - - 4a60927aaca5 + - f14193ec1f50 - fc2e49f91e52 + - aaa0d6a8b808 - 5abf2c2249aa + - 4a60927aaca5 + - f0af8936ed41 + - bc3831dd65c1 + - d7ce0ec78e51 + - be78f13134e2 + - '764845535798' tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -47,8 +48,8 @@ tools: - name: clustalw owner: devteam revisions: - - 4daabc25df00 - d6694932c5e0 + - 4daabc25df00 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -60,11 +61,11 @@ tools: - name: mafft owner: rnateam revisions: - - a65296ffb4a0 - - f0d493f8f84f - f1a5908ea2cb - - c5908940967d - 15974dd17515 + - c5908940967d + - a65296ffb4a0 + - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter @@ -105,7 +106,7 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - 959c1f8dae95 + - b4124df98b26 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 8d650a5ce..cebdec0eb 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,33 +2,33 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - a7228a7ea146 - - 72b5e9dda577 - 79e9a869f40e - - cb34f00cc10f - 0e9e7fcdd543 + - 72b5e9dda577 + - a7228a7ea146 + - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - d6cddc06aeae - - 682d1e2c8be4 - fa11aa8103b2 + - 682d1e2c8be4 - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - 43815fa60f3a - - 2bf63b38ee9b - ec699520444c - edf6d4003fad + - 2bf63b38ee9b + - cc36773a3681 + - 43815fa60f3a - 19f3b583a9b3 - 0f5f4a208660 - 222669c4afb6 - - cc36773a3681 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -49,15 +49,15 @@ tools: revisions: - 645159bcee2d - edbb6c5028f5 - - a3c4fe6f49ab - 0f1c34698076 + - a3c4fe6f49ab 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 @@ -70,30 +70,30 @@ tools: - 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 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 - 543cbeef3949 + - 93d623d9979c - 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 @@ -131,8 +131,8 @@ 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 diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index f3c9a7a82..3da0c5e2b 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: - - adfd6bf710bd - 3e73c97f025d + - adfd6bf710bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - 83da94c0e4a6 - - 1586b111d2a3 - 9dd107db92c2 + - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -42,8 +42,8 @@ tools: owner: iuc revisions: - 19b6a2f0dbe2 - - 2f27f3b86827 - ed1518ce2237 + - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -69,8 +69,8 @@ tools: owner: iuc revisions: - 48a42ca61006 - - 38ccd4589990 - 5711fc06a63e + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -110,17 +110,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 9a40272f56d0 - 6287d0ee459e + - 9a40272f56d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - b4b2b284230a - 52b6a4d98009 - - 27a6a256cd23 - 172815da3d41 + - 27a6a256cd23 + - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -145,9 +145,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 19bbd19b74b3 - - fea85c467896 - 87febc68b45b + - fea85c467896 + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -178,9 +178,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 4ba60cb14cb0 - 5fe20c915fa6 - 9c43baa60906 - - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -192,26 +192,26 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - 0db22932bc39 - 9d09724f2bf1 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - 29c738066906 - - 6e24e79d3d69 + - df30a2f1db55 - ed7a967cb11b + - 6e24e79d3d69 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - 3e4d45aca422 - - ad90c2da4f38 - 1865e693d8b2 + - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -230,17 +230,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - 64deddb6a8ec + - d63c1442407f - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 94a50db37d1a - 9946bc39c834 - 625fd9476402 + - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -288,8 +288,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 564ca749c..f30dcaea9 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -27,85 +27,86 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - f04a1264e2a2 - - b89cac5156ec + - cce7b18495e4 + - d033ffc1c161 + - '841557158611' - 3b8b5bde0bd9 - - d7c7ef3353fe - 8834daeb9892 - - '841557158611' - - a6619171428e - - d033ffc1c161 - - 6a457678efcb - - 107d3ba7024a + - 81e66674859e - c78f3d7dd1db - - f73435dc282b - - cce7b18495e4 + - 3f59ebfbfe3d - 26de3a7b1cb9 - 5a7c56a5cc08 - - 3f59ebfbfe3d - - 81e66674859e + - d7c7ef3353fe + - 6a457678efcb + - f73435dc282b + - 107d3ba7024a + - b89cac5156ec + - f04a1264e2a2 + - a6619171428e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: + - 6a726db04d4b + - df47d4845b62 + - 5fcd1ece3a6e - aa8cc71438cf - - 88c4aa435ded - a185b079b095 - - 5fcd1ece3a6e - - df47d4845b62 - - 6283babe736e - - b0af57c1a968 - - 02b8758214b0 + - 3b96e92e8ec3 - 5b777002c2de - 6223845127ea - - 6a726db04d4b - - e75442c7f4da - - 4755f52427c4 - - 3b96e92e8ec3 + - b0af57c1a968 + - 6283babe736e - 659517798cc4 - 7a2092844346 + - 02b8758214b0 + - 4755f52427c4 + - 88c4aa435ded + - e75442c7f4da tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - d1c340a5664b - - b8476e82ac20 - - 9b892d7f82cc - - f97743d52b87 - c1d53e95327f + - f97743d52b87 + - 9b892d7f82cc + - b8476e82ac20 + - d1c340a5664b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - - 9e10ba792be2 - feb40665d7cd - 128ba8da994f + - daddf188c13f + - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - b6abccb1f25b - - abf6dbe8c9d7 + - b7e297c2ede6 + - 03ed9524dcd1 + - 9d61d3fa046c + - a2099fb98cdb - 14ae456b8cc5 + - 3a43c3982401 - 2fa9d4f1b48f - - 03ed9524dcd1 + - 5f8727ff21e7 - 7bb8726be37c - 437e28791761 - - 42a174224817 - - b7e297c2ede6 + - b6abccb1f25b - 83a69484cb87 - - a2099fb98cdb - - 5f8727ff21e7 - - ca0d8cf80567 - - ca337cce3888 - 36912871ccdc + - ca0d8cf80567 - 81804a978fc0 - - 3a43c3982401 + - ca337cce3888 + - 42a174224817 + - abf6dbe8c9d7 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -117,21 +118,21 @@ tools: - name: raxml owner: iuc revisions: - - a4b71be30c3c - ba29b5e2a4be + - 73a469f7dc96 - ea30d3089354 + - a4b71be30c3c - 29ff6a849eac - - 73a469f7dc96 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: + - 809e42326fc2 + - f1ccc8a6eb05 + - e88a7de55d6e - 15ac71df11a0 - dbe2b2204555 - 91887494eb97 - - 809e42326fc2 - - e88a7de55d6e - - f1ccc8a6eb05 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 c446b79ef..7ae6f100b 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - a1f0b3f4b781 - - 7d34178f2812 - b502c227b5e6 - - 585027e65f3b - - f6ced08779c4 - 881d7645d1bf - 1aac2a13842a + - f6ced08779c4 - fc288950c3b7 + - 7d34178f2812 + - a1f0b3f4b781 + - 585027e65f3b 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 3be8db0a3..f2977000e 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -3,12 +3,12 @@ tools: owner: galaxy-australia revisions: - 3bd420ec162d - - ca90d17ff51b - - d00e15139065 - - c0e71cb2bd1b - a58f7eb0df2c - - 7fbec959cf2b + - c0e71cb2bd1b - eb085b3dbaf8 + - 7fbec959cf2b + - d00e15139065 - 5b85006245f3 + - ca90d17ff51b 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 4adb83331..296fbc5ba 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,83 +2,83 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - f28ad96b76dc - 0a18ac48ac53 - - 277dc652246e - - ece627528a78 - b574b84afc4d + - ece627528a78 - b18329a8ac14 + - 277dc652246e + - f28ad96b76dc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - e988563cc6e5 - - bf06d196e23d - 525f201b86c1 - e215f71d7983 + - bf06d196e23d + - e988563cc6e5 - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: + - 4fbffddde8cd - 8da3511c9467 - bb6397b94018 - - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - f23d67e28cc8 + - b8c79e70516d - a8157342d9a3 - 528fb09022be - - b8c79e70516d - - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - a95a82eb4d50 + - a69865da6f80 - 25b83cbd596a - 80600735685d - - a69865da6f80 - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d - e0669b1854b1 + - 611d80c0e29d - ed9ed1e6cca2 - - 798da6bdff3d - f1897eb07081 + - 798da6bdff3d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 - - a7fb9b395ddf - 74b61bf5bc4b + - a7fb9b395ddf + - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - df2187f9013b - - cc430977c8ff - 82f6c2f4332d + - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - 043f9c91f686 - - c5aa9fca18c6 - 1693b2126f30 + - c5aa9fca18c6 - 10566783d718 - d2483487e077 tool_panel_section_label: Proteomics @@ -111,9 +111,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - 0fa397f4f40b - 1c5cbf8f79ce + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -139,15 +139,15 @@ tools: owner: galaxyp revisions: - e66f552a3c47 - - d286ff4600dd - 160538a890a6 + - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -160,70 +160,70 @@ tools: - name: maxquant owner: galaxyp revisions: - - 8934bc76bb52 + - 97a7f34fcb6a + - 4d17fcdeb8ff + - 7f432d87c82c - f522c08e900c + - 8934bc76bb52 - 1f39c833f65f - - 837224ad1694 - e42225f8a659 - - 4d17fcdeb8ff - - 7f432d87c82c - - 2133b0be850a - 37d669de2828 - - 97a7f34fcb6a + - 837224ad1694 + - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - - 85b8866f06d7 - 0ed07016d668 + - 85b8866f06d7 - '860429737408' + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - 1974224d63c2 - - 990b4560ead7 - - 4187b6df1a40 - 352b37c66d97 + - 4187b6df1a40 + - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: + - 99450519d727 - deaf035bbe9f - - 4f359549383c - a1daafbf5233 - - 99450519d727 + - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - 40ca115438d2 - e79958768a2c - - c7745841de24 - c1343e3389ca + - 40ca115438d2 + - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b648e45fd3cf - - da986f83631b - - d46d64e7964d - d2eac53666f0 + - d46d64e7964d + - da986f83631b + - b648e45fd3cf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 1199751329b0 + - 9bf325045235 - 944b43462104 + - 1199751329b0 - eb811f3018ea - - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -241,10 +241,10 @@ tools: - name: msstats owner: galaxyp revisions: - - b7034eff0db1 - 28434abe6c5c - 593839e1f2c3 - 8212e342e482 + - b7034eff0db1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -258,8 +258,8 @@ tools: owner: galaxyp revisions: - 4e77b8f12cd3 - - 8960fb791701 - 01dbaf6a57e0 + - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -271,66 +271,66 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - c9eff69a7c62 - f7fef900f5b2 - 9cdf15d3cfc8 - 518b1730cf2a + - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - 5e948629bc73 - - dff6c756eee5 - ca88bd28f116 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: + - 41859bbdc16e - 890025d6e426 - 658494a2cb00 - - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - 9b7977080f6d + - 5ad0b5bf1deb - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 05d5e1ddc985 - d6878d27f051 + - 05d5e1ddc985 - 0bb5056cb775 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - febd569ad26f + - 5ad830edc021 - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 27cba4c5fc42 - 39e8fde08881 - 92352a475eed + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 9e26f5c770f8 - - 0efbc235f314 - d413dc49d650 + - 0efbc235f314 + - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver @@ -344,87 +344,87 @@ tools: - name: openms_idfilter owner: galaxyp revisions: - - ca799a7246e7 - - c427a8628cbe - 382cde407f81 - c55dddc5844a + - c427a8628cbe + - ca799a7246e7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - b5d0905419da - 8ddb7bab1138 - 39caaa778d2e + - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 8d4db262964c - - 1c5f31b8d632 - f817513840a9 + - 1c5f31b8d632 + - 8d4db262964c - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a - - 111c3a00136d - 5d9f175dff81 + - 111c3a00136d + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - 476b5e296979 - - 0e52c85f3b15 - be74a8cd7d66 + - 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 owner: galaxyp revisions: - - 4e66c4e73909 - d0304fb829c0 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - ee860980edc6 - bf32e0bcf554 - 8098330f6d91 - - ee860980edc6 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 owner: galaxyp revisions: - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -451,15 +451,15 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 8b814eafce2c - 89254095cbf6 + - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f9ed7e074900 - 05ec9fb05ed1 + - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer @@ -472,32 +472,32 @@ tools: - name: openms_openswathworkflow owner: galaxyp revisions: - - 2aebe58de46e - bc63b4d12779 + - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - - 5ae104d0da6e - 3d8d4ada5405 + - 5ae104d0da6e + - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - dd173849c3d8 - - 5182338d5e7c + - e039cc5c7aed - 539a3a4dcc9e + - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 8a45fd5a608a - 16026cdb1330 + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter @@ -522,36 +522,36 @@ 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 owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 7fdd9119cc4f - 07ff622ec007 - - 943a34df6047 - 1beff3ddce58 + - da885ca16cb2 - a72c48001f7c + - 7fdd9119cc4f - 3ec27b4cee7c - 3634c90301af - - da885ca16cb2 + - 943a34df6047 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -606,8 +606,8 @@ tools: owner: galaxyp revisions: - 265c35540faa - - 12692567c7f9 - 1a5690a5eedc + - 12692567c7f9 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 38f9cc804..067fd1c86 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,19 +2,19 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - e345aadf914f - - cd5f98911089 + - 110a346daf36 - 42201b90e3f4 - - 289b7d6b69a4 - 2f1d464ebfd2 - - 110a346daf36 + - 289b7d6b69a4 + - e345aadf914f + - cd5f98911089 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - c207119ba5f6 - 8501601a118d + - c207119ba5f6 - fcce77c09289 - 42d9087b4789 - 0345dbaaa79b @@ -26,108 +26,108 @@ tools: revisions: - 89eb29319bf4 - 405a212b32ab - - ad5ab22ffe24 - 04db7fd6b238 - - 421c33b8bf17 - 33486216eec0 + - 421c33b8bf17 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - eb784fa07f80 - - 7370bb65bad4 - - 7b72fde3d27e - 1d839ead7ad3 - fa51dc5e8386 - f6e91108b7b1 + - eb784fa07f80 + - 7b72fde3d27e + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - 1544278c272e - - a3e86cd9cac7 - - d30e36c48c93 - c9b77ced9a78 - - 8a55d29c8fcf + - a3e86cd9cac7 - 3d70c2996730 + - 8a55d29c8fcf + - d30e36c48c93 + - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: + - a5969aa9347e - e2db212d64ad + - 564c33e5c3e3 - b242deb58952 - - a5969aa9347e - - 887cf585cafc - 7b881f5f5ad5 - - 564c33e5c3e3 + - 887cf585cafc tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - 8cff84759bf6 - - 9a171f9a450b - - bd5ff77e2036 - e897c74a48bb + - 8cff84759bf6 - b4bab607eb05 + - bd5ff77e2036 + - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 887e0991eb24 - - 6dafad990086 - - 5e10f396979e - 4f65e343ecdf - 33f0793edf93 + - 887e0991eb24 + - 6dafad990086 - adc7a7610d4f + - 5e10f396979e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - c287418eb288 - - 4e280b27a831 - - 17d39bf0a63a - - 43e3eeb2e0ec - 97575d01f06b + - 4e280b27a831 - c5d7050e4ad7 + - 43e3eeb2e0ec + - c287418eb288 + - 17d39bf0a63a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 09b8edb56d80 - - 9586f08634c0 - d9bf483266a1 - - a819ec3b362d - 0b8c84a7fdb5 + - 9586f08634c0 - cd034465d4a4 + - a819ec3b362d + - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 69842dd5aa48 - - 2645575d1bf2 - - bf0e43ab0416 - - a4b4bd84f69e - a9c34a289493 + - a4b4bd84f69e - 95351dd0fd3f + - 2645575d1bf2 + - 69842dd5aa48 + - bf0e43ab0416 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - d1fda11e602f - 8a35a3bc6752 - - d033e1ccb386 - - bb0475c884ff + - d1fda11e602f - 912f904a6e1e - cfb504394ae1 + - d033e1ccb386 + - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 73b1ae863..50fc855dd 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,8 +2,8 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 31f8063eedea - 2d4e3aff9dc7 + - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters @@ -46,8 +46,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -60,16 +60,16 @@ tools: - name: cuffmerge owner: devteam revisions: - - 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 @@ -93,42 +93,42 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - - 57f477b57c35 - e3b16fd7dd08 + - 0693ccd171c4 - 8f0181aacb7a + - 57f477b57c35 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - cd9874cb9019 + - 0696db066a5b - d027d1f4984e + - 24a09ca67621 - 6a3a025714d3 + - cd9874cb9019 - 8fe98f7094de - - 24a09ca67621 - - 0696db066a5b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 62adf13b86ea - - 2872c633f07e - b47c006d90c5 + - 2872c633f07e - df929f257179 + - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - f2843df56434 - - 6e53e565fc6a - df0c8d0a5992 - - 3d89af8a44f0 + - f2843df56434 + - 334ce9b1bac5 - 555659de7321 - 9bdff28ae1b1 - - 334ce9b1bac5 + - 3d89af8a44f0 + - 6e53e565fc6a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -147,16 +147,16 @@ tools: - name: featurecounts owner: iuc revisions: - - 38b6d12edc68 - - 7db9d3ea71c9 + - f3a5f075498f - a37612abf7f9 - - af814359d244 - - 6f66ae7c5f7a - - 90d16db017d7 + - ea04b737afa0 + - 7db9d3ea71c9 + - 38b6d12edc68 - a56fbe2d6ba7 - - f3a5f075498f - e6a2a912677a - - ea04b737afa0 + - 6f66ae7c5f7a + - af814359d244 + - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -188,12 +188,12 @@ tools: - name: hisat2 owner: iuc revisions: - - f4af63aaf57a - - 6c19daec423d - - 6ab42baa56e9 - 3fb01a8c902d - - d4b55e2beb12 + - 6ab42baa56e9 + - 6c19daec423d - a86e80d3c09c + - f4af63aaf57a + - d4b55e2beb12 - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -214,31 +214,31 @@ tools: owner: iuc revisions: - 5ae5c312d718 - - ce5d418183c5 - 87c11c05d238 - 1c75aa5de15e - 01247aaf0a10 + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 - 40985510cd98 - - 10c98fab6c5a - 4f9c4e6566e5 + - 10c98fab6c5a + - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 97e06a4c7c75 - - 0921444c832d - - d6f5fa4ee473 - - 708348a17fa1 - e827f9aae031 + - d6f5fa4ee473 + - 0921444c832d - 32511f586472 + - 97e06a4c7c75 - 58c35179ebf0 + - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -250,8 +250,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -287,18 +287,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - 7ed2edc1337f - - c7c55b694974 - - 0a563fd2f22e - - 980d2a2e1180 - - e132e7d02a3e - 4074fc1940e2 - b9e04854e2bb - - 4df95e2d7f61 - - c772497b2c32 + - 5ec75f5dae3c + - 980d2a2e1180 - 3ea5a2a63fa2 + - c7c55b694974 + - 7ed2edc1337f + - e132e7d02a3e - 99b17b74a8cd - - 5ec75f5dae3c + - 0a563fd2f22e + - c772497b2c32 + - 4df95e2d7f61 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -310,31 +310,32 @@ tools: - name: salmon owner: bgruening revisions: - - cc05793bb896 - - e3d32471da11 - 49121db48873 + - cc05793bb896 - 2c0ca397d302 - - 53e9709776a0 - ebab418107f5 + - e3d32471da11 + - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - 8c28affc7c48 - - 56242ff81c84 - c0fd285eb553 + - fab6ff46e019 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 76d290331481 - - dd4df992d93d - 1ebd14235b92 + - dd4df992d93d + - 76d290331481 + - 258d696dbd7e - 914cfcba0ec8 - cef79931dda5 - - 258d696dbd7e - ae618321f34a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -368,34 +369,34 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - - 74217fbfba4d - - d6a479fd4281 - a009c96c5c18 + - d6a479fd4281 + - 74217fbfba4d + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - c2b82a94493e - - 75f4e1859ed7 - 478f36effca1 + - 75f4e1859ed7 - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - c0096052b35b - fab23c3b5258 + - c0096052b35b - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 41db7569b4ba - 34a018cbee9c + - 41db7569b4ba - be3f26533209 - 4687ecf0eb2d tool_panel_section_label: RNA-seq @@ -403,59 +404,59 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 33406f5a445c - 5192f657f305 - - 05ab8d5e04a2 - c5fbddcac63a - ae501908a17f + - 33406f5a445c + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - aa38fa8c5815 - - 6f0fb35b799c - - 1fdb25a8384d - e406ac71165d + - 1fdb25a8384d + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - - ba460ccf0006 - 964b7efe2639 - c2c039e421af + - 37a1129c89d2 + - ba460ccf0006 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - 1d689e4e1caf - - 047c22569787 - eafea3083352 + - 047c22569787 - c63338cf419f + - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - 3a4ac03d1266 - 9871104ea630 - 1b1a25f93f80 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - cee61b3fcf78 - - c9cfec002f71 - d84caa5a98ad - - db1f362cca3e - - 32b86cd8eb50 - 77cf519a812e + - cee61b3fcf78 + - 32b86cd8eb50 + - c9cfec002f71 - 48636f857c4b + - db1f362cca3e - d2bc35f3d1c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index ba833d62f..b41c54fe8 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 - - 1a052c827e88 - 080fd5739bb4 + - 1a052c827e88 + - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index c487f5cc4..d2990a759 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -9,9 +9,9 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 108db6635177 - - 1dfd95ee241e - cb20f99fd45b + - 1dfd95ee241e + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -41,9 +41,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - - e7fd6754d093 - 19ece8afbaab + - e7fd6754d093 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -67,8 +67,8 @@ 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 @@ -87,24 +87,24 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 56c31114ad4a - 649a225999a5 + - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 46c6639921f1 - - 9149ad20699a - 12749212f61b + - 9149ad20699a + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 33208952b99d - 06dc50b7b711 - 92ec40abcdcf + - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -118,51 +118,51 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - 22970df7a40e - cc61ade70eb8 - - db17d5321bad + - 22970df7a40e - fe34990e5ce7 + - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 7a6034296ae9 + - 88b8c2916784 - 811fc2d75ad4 - 7def34e6cf4d - - 88b8c2916784 + - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 36677f429310 - - b40e2d865d52 - 740ce0a18f0d + - b40e2d865d52 + - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 8da515fbc1bf + - 329deb17a9f7 - 583abf29fc8e + - 8da515fbc1bf - 9da0311ab1dd - - 329deb17a9f7 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: + - db000c6007a0 - bb8cfc6f6e0c - 30388d878f81 - - db000c6007a0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -182,16 +182,16 @@ tools: owner: devteam revisions: - 6c2c1836728b - - e613c1ad4c4c - cab3f8d35989 + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - 5d9ae78f34d3 - - 135c85f4cfaf - b7f7826ef1cd + - 135c85f4cfaf - bcedabb53ddf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -199,21 +199,21 @@ tools: owner: devteam revisions: - 3a0efe14891f - - 145f6d74ff5e - 5a08c09b9311 - - 24c5d43cb545 + - 145f6d74ff5e - 1cc79f49b8d5 + - 24c5d43cb545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - 0dbf49c414ae - 5826298f6a73 - - c370440f901e - - b72793637686 - - b01db2684fa5 - 350bbc5c2ffd - bf328cec6a42 + - b01db2684fa5 + - 0dbf49c414ae + - c370440f901e + - b72793637686 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 de2d0e5ef..c5aa9ca9d 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,10 +2,10 @@ tools: - name: ena_upload owner: iuc revisions: + - 59bb6d34fca6 - 4aab5ae907b6 - - d147d6455873 - a62c4a11a67d - 6f6537780379 - - 59bb6d34fca6 + - d147d6455873 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index 7737718fe..ca6e8f699 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -4,38 +4,38 @@ tools: revisions: - fb9e030ffae4 - cfc3f5a57dc6 - - 55e35e9203cf - - 32e547223c9e - 00712416fdaa + - 32e547223c9e + - 55e35e9203cf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - ee98d611afc6 - - 688357ad5e61 - - 038e32885fec - b9fac48532eb + - 038e32885fec + - ee98d611afc6 - 39e945f0b2c1 + - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - 43cb7b5a6fe7 - - 9bd945a03d7b - 3d748954434b - d4af736e7b83 - b85871dd69f9 + - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils owner: iuc revisions: - a9caad671439 - - 8855361fcfc5 - cdf4443d5625 - 2c1200fba922 + - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -47,22 +47,22 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 282819d09a4f - 7ffaa0968da3 + - 282819d09a4f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 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 @@ -81,8 +81,8 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - f3eb2291da05 - 2b0d3e2f402a + - f3eb2291da05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -111,39 +111,39 @@ tools: 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: - - c5d3684f7c4c - 5e9171dc8244 + - c5d3684f7c4c 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_plot owner: iuc revisions: - - 6adf98e782f3 - aa0c474463c2 + - 6adf98e782f3 - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: + - 215733a383f2 - f2f6c703da06 - bf2017df9837 - - 215733a383f2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -157,24 +157,24 @@ tools: - 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: - - 81e5bdff4853 - - ef4c80837bc5 - 2e41b35b5bdd + - ef4c80837bc5 + - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca owner: iuc revisions: - 9e5c0bb18d08 - - c99ba278dfa9 - 46fc6751d746 + - 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 ce05afdb2..0d2aaed01 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 - - 2f3c6f2dcf39 - 419027d822d6 - - 4c07ddedc198 - 746e8e4bf929 + - 2f3c6f2dcf39 + - 4c07ddedc198 + - 562f3c677828 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: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - 7a15159140d1 - - 6c29c7e347e8 - cb1c59d69557 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,18 +120,18 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - b1eda492f063 + - 840f29aad145 - aef56d0e7a61 - 9c3e1d3235c8 - - 840f29aad145 + - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - d0352e8b4c10 - - 375bbd555f4a - 07843f917990 + - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier @@ -147,8 +147,8 @@ tools: revisions: - 7dd3fb35904f - 4bbaf77573ef - - ad7e0b4291ee - 1dd433d2c92c + - ad7e0b4291ee tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 2c62940e2..fc4bf5856 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -27,13 +27,13 @@ tools: - name: column_maker owner: devteam revisions: - - be25c075ed54 - - 02026300aa45 - - 9cd341095afd - - 464b9305180e - - 6595517c2dd8 - 13b6f0007d9e + - 6595517c2dd8 - 6e8d94597139 + - 9cd341095afd + - 02026300aa45 + - 464b9305180e + - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -70,10 +70,10 @@ tools: - name: filter_tabular owner: iuc revisions: - - 37cde8134c6a - - 4d5aae46f850 - 9cc411a62277 + - 37cde8134c6a - 34d29339abab + - 4d5aae46f850 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -97,26 +97,26 @@ tools: - name: merge_cols owner: devteam revisions: - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 623f3eb7aa48 - - 1ea4e668bf73 - - cf34c344508d - 33d61c89fb8d - - 2e8f945f7285 - 83069b38aa85 + - 2e8f945f7285 + - cf34c344508d + - 1ea4e668bf73 + - 623f3eb7aa48 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - ae8c4b2488e7 - 503bcd6ebe4b + - ae8c4b2488e7 - 399da6b5ec21 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -129,26 +129,26 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - c29d2f80a066 - - bce29ec10b78 - b722161a845a + - bce29ec10b78 + - c29d2f80a066 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 60ff16842fcd - 3bf5661c0280 + - 60ff16842fcd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - ddf54b12c295 - - d698c222f354 - 9ff72e942410 + - f46f0e4f75c4 + - d698c222f354 + - ddf54b12c295 - 74a8bef53a00 - a6f147a050a2 - - f46f0e4f75c4 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml index cf5f40239..53f3ed1a2 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -2,9 +2,9 @@ tools: - name: breseq owner: iuc revisions: + - 0d18a3ba2d1c - 82fb5e3bb93e - 85c57cc9b558 - - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -16,9 +16,9 @@ tools: - name: freebayes owner: devteam revisions: + - ef2c525bd8cd - a5937157062f - 156b60c1530f - - ef2c525bd8cd - 57def2d7c093 - 04fa42777df9 tool_panel_section_label: Variant Calling @@ -26,47 +26,47 @@ tools: - name: lofreq_alnqual owner: iuc revisions: - - 435b157bed6d - e61c9ac190ad - - 09d6e4693887 - 791f73caa0c8 + - 09d6e4693887 + - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 65432c3abf6c - - 03627f24605f - - dfadc322b065 + - 4805fe3d8fda - 3b4b2121842f - e1461b5c52a0 + - dfadc322b065 + - 03627f24605f + - 65432c3abf6c - 074d44697036 - - 4805fe3d8fda tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 701d134358ad - 7dfca164d2e3 - 9cb929f21cfa - - 701d134358ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: + - 971e07ca4456 + - c27549b9aa1f - 426d707dfc47 - f4473557ffc7 - - c27549b9aa1f - - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: + - aa35ee7f3ab2 - cdaab621d454 - dbd9f2db9ed8 - - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -84,9 +84,9 @@ tools: - name: snippy owner: iuc revisions: - - 5bbf9eada9c2 - - fa016f1eea1a - d220115f882b + - fa016f1eea1a + - 5bbf9eada9c2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -122,17 +122,17 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 3b1e7c170b10 - 40f0591deda0 - ee4a90760848 + - 3b1e7c170b10 - e7aff4a85df5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - adc0645b945c - 4934c0ac6197 + - adc0645b945c - 02d81b994ef5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/vcfbcf.yml b/usegalaxy.org.au/vcfbcf.yml index 8990fc3fd..eefe03835 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ b/usegalaxy.org.au/vcfbcf.yml @@ -2,362 +2,362 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - b7ea370b8f5d - - 265fe0f9ea64 + - ebe5fc018e72 - 3f62d4939d54 - e075b1be5abb - - 8a2e296c07ef - - ebe5fc018e72 + - 265fe0f9ea64 - 6a88248893c4 + - 8a2e296c07ef + - b7ea370b8f5d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call owner: iuc revisions: + - c37b684e7f4e + - 0fba2c15b40d - b03984136ce4 + - 22637b1a55bf - f0d44631365f - 544cb432072b - - c37b684e7f4e - 21687e35f066 - - 0fba2c15b40d - - 22637b1a55bf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv owner: iuc revisions: + - 8627b2b383b4 + - 8ca3647c90fd - 0238f68ad641 - - 8408bffd5616 - 3a7084316a6e - 01d6b7d6365e - - 8ca3647c90fd - - bf1f4994f104 - - 8627b2b383b4 - 6d35a3780bfd + - 8408bffd5616 + - bf1f4994f104 tool_panel_section_label: VCF/BCF tool_shed_url: 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