From 87e2e891cbce316fb4a88b2a33712275629ead50 Mon Sep 17 00:00:00 2001 From: admin Date: Mon, 15 Jan 2024 23:38:24 +0000 Subject: [PATCH] Jenkins install build 1396. --- automated_tool_installation_log.tsv | 1 + requests/orthofinder_onlygroups@latest.yml | 4 - staging.gvl.org.au/annotation.yml | 92 +++---- staging.gvl.org.au/assembly.yml | 194 ++++++------- staging.gvl.org.au/bacterial_typing.yml | 6 +- staging.gvl.org.au/bb_tools.yml | 2 +- staging.gvl.org.au/bed.yml | 12 +- staging.gvl.org.au/blast.yml | 14 +- staging.gvl.org.au/chemicaltoolbox.yml | 58 ++-- staging.gvl.org.au/chip_seq.yml | 12 +- staging.gvl.org.au/collection_operations.yml | 6 +- staging.gvl.org.au/convert_formats.yml | 42 +-- staging.gvl.org.au/deeptools.yml | 114 ++++---- staging.gvl.org.au/dna_metabarcoding.yml | 10 +- staging.gvl.org.au/emboss.yml | 2 +- staging.gvl.org.au/epigenetics.yml | 6 +- staging.gvl.org.au/fastafastq.yml | 88 +++--- staging.gvl.org.au/fastq_quality_control.yml | 30 +- staging.gvl.org.au/filter_and_sort.yml | 6 +- staging.gvl.org.au/gemini_tools.yml | 26 +- staging.gvl.org.au/genome_editing.yml | 4 +- staging.gvl.org.au/get_data.yml | 30 +- staging.gvl.org.au/graphdisplay_data.yml | 48 ++-- staging.gvl.org.au/hca_single_cell.yml | 4 +- staging.gvl.org.au/hicexplorer.yml | 22 +- staging.gvl.org.au/imaging.yml | 50 ++-- staging.gvl.org.au/ivar.yml | 74 ++--- .../join_subtract_and_group.yml | 6 +- staging.gvl.org.au/machine_learning.yml | 50 ++-- staging.gvl.org.au/mapping.yml | 52 ++-- staging.gvl.org.au/metagenomic_analysis.yml | 88 +++--- staging.gvl.org.au/mothur.yml | 6 +- staging.gvl.org.au/multiple_alignments.yml | 52 ++-- staging.gvl.org.au/nanopore.yml | 42 +-- staging.gvl.org.au/none.yml | 48 ++-- staging.gvl.org.au/phylogenetics.yml | 92 ++++--- staging.gvl.org.au/picard.yml | 8 +- staging.gvl.org.au/proteomic_ai.yml | 10 +- staging.gvl.org.au/proteomics.yml | 158 +++++------ staging.gvl.org.au/rad_seq.yml | 80 +++--- staging.gvl.org.au/rna_seq.yml | 154 +++++------ staging.gvl.org.au/rseqc.yml | 2 +- staging.gvl.org.au/sambam.yml | 60 ++-- staging.gvl.org.au/send_data.yml | 8 +- staging.gvl.org.au/single_cell.yml | 56 ++-- staging.gvl.org.au/statistics.yml | 30 +- staging.gvl.org.au/text_manipulation.yml | 34 +-- staging.gvl.org.au/variant_calling.yml | 38 +-- staging.gvl.org.au/vcfbcf.yml | 256 +++++++++--------- usegalaxy.org.au/annotation.yml | 96 +++---- usegalaxy.org.au/assembly.yml | 198 +++++++------- usegalaxy.org.au/bacterial_typing.yml | 8 +- usegalaxy.org.au/bb_tools.yml | 2 +- usegalaxy.org.au/bed.yml | 12 +- usegalaxy.org.au/blast.yml | 10 +- usegalaxy.org.au/chemicaltoolbox.yml | 56 ++-- usegalaxy.org.au/chip_seq.yml | 10 +- usegalaxy.org.au/collection_operations.yml | 10 +- usegalaxy.org.au/convert_formats.yml | 34 +-- usegalaxy.org.au/deeptools.yml | 122 ++++----- usegalaxy.org.au/dna_metabarcoding.yml | 6 +- usegalaxy.org.au/emboss.yml | 2 +- usegalaxy.org.au/epigenetics.yml | 4 +- usegalaxy.org.au/fastafastq.yml | 70 ++--- usegalaxy.org.au/fastq_quality_control.yml | 34 +-- usegalaxy.org.au/filter_and_sort.yml | 6 +- usegalaxy.org.au/gemini_tools.yml | 34 +-- usegalaxy.org.au/genome_editing.yml | 4 +- usegalaxy.org.au/get_data.yml | 34 +-- usegalaxy.org.au/graphdisplay_data.yml | 50 ++-- usegalaxy.org.au/hca_single_cell.yml | 2 +- usegalaxy.org.au/hicexplorer.yml | 14 +- usegalaxy.org.au/imaging.yml | 50 ++-- usegalaxy.org.au/ivar.yml | 70 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 8 +- usegalaxy.org.au/machine_learning.yml | 48 ++-- usegalaxy.org.au/mapping.yml | 42 +-- usegalaxy.org.au/metagenomic_analysis.yml | 110 ++++---- usegalaxy.org.au/mothur.yml | 8 +- usegalaxy.org.au/multiple_alignments.yml | 48 ++-- usegalaxy.org.au/nanopore.yml | 30 +- usegalaxy.org.au/none.yml | 30 +- usegalaxy.org.au/phylogenetics.yml | 86 +++--- usegalaxy.org.au/picard.yml | 8 +- usegalaxy.org.au/proteomic_ai.yml | 8 +- usegalaxy.org.au/proteomics.yml | 150 +++++----- usegalaxy.org.au/rad_seq.yml | 62 ++--- usegalaxy.org.au/rna_seq.yml | 154 +++++------ usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 66 ++--- usegalaxy.org.au/send_data.yml | 4 +- usegalaxy.org.au/single_cell.yml | 50 ++-- usegalaxy.org.au/statistics.yml | 34 +-- usegalaxy.org.au/text_manipulation.yml | 32 +-- usegalaxy.org.au/variant_calling.yml | 32 +-- usegalaxy.org.au/vcfbcf.yml | 234 ++++++++-------- usegalaxy.org.au/viral_tools.yml | 2 +- 97 files changed, 2238 insertions(+), 2235 deletions(-) delete mode 100644 requests/orthofinder_onlygroups@latest.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 1b51df811..97d66ba01 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -6140,3 +6140,4 @@ Install 1388 15/01/24 11:12:44 pharokka True Tests failed iuc 2f40d2ccb0eb lates Install 1390 15/01/24 13:09:19 data_manager_pharokka True Shed-tools error iuc 50caca83e7c9 50caca83e7c9 Production Installation 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1390/install_log.txt Install 1392 15/01/24 13:12:47 data_manager_pharokka True Already Installed iuc 50caca83e7c9 50caca83e7c9 Production Installation None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1392/install_log.txt Install 1394 16/01/24 08:57:21 orthofinder_onlygroups True Tests failed iuc b3d25fae5389 latest Production Testing 0/0 2/9 Phylogenetics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1394/install_log.txt +Install 1396 16/01/24 09:38:04 orthofinder_onlygroups False Already Installed iuc b3d25fae5389 latest Production Installation 9/9 Phylogenetics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1396/install_log.txt diff --git a/requests/orthofinder_onlygroups@latest.yml b/requests/orthofinder_onlygroups@latest.yml deleted file mode 100644 index baffd8311..000000000 --- a/requests/orthofinder_onlygroups@latest.yml +++ /dev/null @@ -1,4 +0,0 @@ -tools: -- name: orthofinder_onlygroups - owner: iuc - tool_panel_section_label: Phylogenetics diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index efcdb7de3..fd342dcac 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -3,10 +3,10 @@ tools: owner: iuc revisions: - 4efdca267d51 - - 3f3e247c053d + - c2ef298da409 - 78c75f134c16 + - 3f3e247c053d - 6e9aea89e388 - - c2ef298da409 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,15 +36,15 @@ tools: - name: annotatemyids owner: iuc revisions: - - 133f36c29579 - cd2480f35935 - - f29602ae449e - - 1aae04680c4b - - b5d8e5475247 - - 44018dd6b447 + - 133f36c29579 - fe3ca740a485 + - 44018dd6b447 - 4f2967b27e67 + - 1aae04680c4b + - b5d8e5475247 - 3e1f6f6d557e + - f29602ae449e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -57,17 +57,17 @@ tools: - name: augustus_training owner: bgruening revisions: - - 7be22100e5e1 - dc027fa56d55 - 6519ebe25019 + - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - ca6d970d931c - - 28433faa6e42 - 09855551d713 + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -79,9 +79,9 @@ tools: - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - 8fd427007e93 - fe48aa4ccd5e + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -93,8 +93,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: cpat @@ -106,9 +106,9 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - - 63662ae295d6 - 9d1fbff733cf + - 63662ae295d6 + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -126,45 +126,45 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 582fd74dc2a1 + - 14f588312c56 - 9f2455341fac - - 756376aeb1ae - b6b5cd37f2a2 - - 14f588312c56 + - 756376aeb1ae - 3bbe70fef6df + - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 30fb23d4c31c - 1691af4a0d17 + - 0ffe5be70caf + - a230ea445788 + - 30fb23d4c31c - 73428a792541 - 989f7c061f35 - - a230ea445788 - - 0ffe5be70caf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - e94187d661df + - 563a19373357 - 494f0bb4a993 + - b69c46064ec7 - 5a5ae61da69c - 30f08d74024f - - b69c46064ec7 - - 563a19373357 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 2bba2ff070d9 + - 7abc5f6dd595 - d6c7106b7b2e + - f77d7b685bb3 - f31125bb85ea - 1bc5a03faf2e - - 7abc5f6dd595 - - f77d7b685bb3 + - 2bba2ff070d9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort @@ -172,10 +172,10 @@ tools: revisions: - d3af38b9c7e1 - 52af33194019 + - b3cf4684e9c7 - 54961e026fe4 - 520e30695ec3 - fed64e676186 - - b3cf4684e9c7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -187,8 +187,8 @@ 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 @@ -203,8 +203,8 @@ tools: revisions: - 602de62d995b - ef2ad746b589 - - 43798b4caee0 - 8b3e3657034e + - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -229,8 +229,8 @@ tools: - name: interproscan owner: bgruening revisions: - - 98cafcbd2578 - c55643c3d813 + - 98cafcbd2578 - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -256,16 +256,16 @@ tools: - name: maker owner: iuc revisions: - - d46d803ca6cc - 3c1a01127868 - 370c210d9541 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -289,11 +289,11 @@ tools: - name: prokka owner: crs4 revisions: - - 8a22554cdde2 - bf68eb663bc3 - eaee459f3d69 - - d643e3b03500 + - 8a22554cdde2 - a17498c603ec + - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -305,15 +305,15 @@ 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: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snap_training @@ -326,20 +326,20 @@ tools: owner: iuc revisions: - 5c7b70713fb5 + - cfcf33df7fc0 - 268d162b9c49 - - 5b80f544c67f - - 5a29ab10dba6 - - 68693743661e - 8f92c2b26e6d + - 68693743661e + - 5b80f544c67f - 9473cd297a76 - - cfcf33df7fc0 + - 5a29ab10dba6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - 2b3e65a4252f + - 09d6806c609e - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -352,8 +352,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -365,15 +365,15 @@ tools: - name: tbprofiler owner: iuc revisions: - - 37213cf56392 - - e1a9d6fd258d - - ac8250086ac3 - - 809dfc93d593 + - ba6f87115e13 - 2c68b0c38785 - - 200c378d85f3 - 45083d070fb8 - - ba6f87115e13 + - e1a9d6fd258d + - 200c378d85f3 + - 37213cf56392 + - ac8250086ac3 - 037a11682176 + - 809dfc93d593 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 7423e180f..1bc1f17a7 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,12 +2,12 @@ tools: - name: abyss owner: iuc revisions: - - fa5259cc561b - 890b794c997d - - 841084c5fc46 + - fa5259cc561b + - 7547fcab5d19 - 8f1b150a2487 + - 841084c5fc46 - 553bfe8bd0b5 - - 7547fcab5d19 - 0e93176640ac - a929ce596a34 tool_panel_section_label: Assembly @@ -15,11 +15,11 @@ tools: - name: bandage owner: iuc revisions: - - 94fe43e75ddc + - 067592b6b312 - ddddce450736 - b9e31c5c01c7 + - 94fe43e75ddc - b2860df42e16 - - 067592b6b312 - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -33,11 +33,11 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - - 3371c5bdc17a - 5258e18bbe23 + - 22286dab5aa1 - a7f16f24e9a1 - faee8629b460 + - 3371c5bdc17a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,30 +49,30 @@ tools: - name: busco owner: iuc revisions: + - 94170eee0ad8 + - f18f0b887c31 - bb935709506a - - 602fb8e63aa7 - - e4bd1e99bacf - - 5ecdeca79a0d + - cf13a1e03e5b + - 2a5b8b9936bf + - 0d243f458b53 - 1440ae06552f - - 2dd755c1c6ff + - 5ecdeca79a0d + - 41030a6c03b7 + - e824f5d958d0 - 46ae58b1d792 - 1e62c28ba91d - - 0d243f458b53 - - f18f0b887c31 - - e824f5d958d0 - - 2a5b8b9936bf + - 602fb8e63aa7 + - 2dd755c1c6ff - 4048d82f0c88 - - 94170eee0ad8 - - 41030a6c03b7 - - cf13a1e03e5b + - e4bd1e99bacf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - 5732f959936a - - 86f150c8019d - c5b7390290b1 + - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -85,36 +85,36 @@ tools: owner: bgruening revisions: - 276f5d8712d5 + - 8d4f03b5fe9d - e27815e82dd4 - 3ee0ef312022 - - 8d4f03b5fe9d - - 1ce9b1d72ec3 - cb8dfd28c16f + - 1ce9b1d72ec3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - 01210c4e9144 + - b2f674562a18 - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: + - 06bcf65179fb - 7348b69e5109 - 8b330a577046 - - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: + - 690c2caa367e + - 3fba9c77550a - 3ef480892a9f - 5127a713de83 - - 3fba9c77550a - - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -127,20 +127,20 @@ tools: owner: bgruening revisions: - ec9e21e9c71b - - 60024a528cbd - - 2061fb3b81b4 + - 41cea2aa2dce - da9d8bf98802 - - 366a11d316a7 + - 9ef6920c3089 - f3c89da3af16 - - 0ee0c3089254 - - 6505bd37670d - - 41cea2aa2dce - - 5bec28269d95 - 3f7be05a1597 + - 045c7c3d8e59 + - 60024a528cbd - 5f625c63b8bc - - 9ef6920c3089 + - 6505bd37670d - 71740308d412 - - 045c7c3d8e59 + - 2061fb3b81b4 + - 0ee0c3089254 + - 366a11d316a7 + - 5bec28269d95 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -159,38 +159,38 @@ tools: owner: iuc revisions: - 14ddfc8ffb93 + - 7518ee87b53d - a96f3ad4e0d8 - de387b2b2803 - - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 9d79beb19ac3 - 09c589057ee8 - 39edec572bae - f8113c25bc6b + - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - 51c2360aa807 - 29dabd8db6f2 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - e731ea24e48d - - 2ecf5a570907 - - 606b09cc9860 - f338e9942b27 - fd128c111ab0 + - e731ea24e48d - eb7a370f6588 + - 606b09cc9860 - 3ca2d2a9068c + - 2ecf5a570907 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -202,11 +202,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8dee0218ac7d - - a7b889b90140 - 73a3846701e1 - - 8b6d0d85252b + - a7b889b90140 - 80d1250bd5fd + - 8dee0218ac7d + - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -218,8 +218,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 7c2f5268d01c + - 64a1c751d99b - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -233,74 +233,74 @@ tools: owner: iuc revisions: - dfb8a4497339 + - d256a51a656b - 8fef980d48b5 - 511e5e3cd55e - - bbe19ef04a74 - 2b16ba799da9 - - d256a51a656b + - bbe19ef04a74 - 02831bf9e95f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: + - a315c25dc813 - 76d4cbefff85 - e9bd16ba5ebd - - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: + - 59db8ea8c845 + - 342a1d1fed7b - 3061c8b029e5 + - 6fcbee531de6 - 875d0f36d66f - 7594365c546b - - 342a1d1fed7b - - ebb0dcdb621a - - 72472698a2df - - 6fcbee531de6 - 675488238c96 - - 59db8ea8c845 + - 72472698a2df + - ebb0dcdb621a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - aa39b19ca11e - 78c533842eeb + - 39bed8de8017 - a199cd7ac344 - - d865b62f501c + - aa39b19ca11e - cd06929b224b - - 39bed8de8017 + - d865b62f501c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - 2b2a352488fa - - 3edba9afc9bc + - f8564b2d7f63 - 33b7d8481a76 - f11b994b7eb2 - - f8564b2d7f63 + - 3edba9afc9bc + - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - 53c2bc8c2ae3 - e122f9101584 - - 378e55aeeb25 - 1d06c8b38e77 + - 378e55aeeb25 - ef69617ecb42 - - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - ab5b7f6b7198 - 9a22227bb6d0 - - ba7b0f11e470 - f77f7a7f3b83 + - ab5b7f6b7198 + - ba7b0f11e470 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -312,13 +312,13 @@ tools: - name: shovill owner: iuc revisions: - - ee17a294d3a3 - f698c7604b3b - 865119fcb694 - - 83ead2be47b2 - - 196a599ec43d - - ad80238462c1 - d9f6a00b6db7 + - ad80238462c1 + - ee17a294d3a3 + - 196a599ec43d + - 83ead2be47b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot @@ -332,50 +332,50 @@ tools: - name: spades_biosyntheticspades owner: iuc revisions: - - 1fc82fe7ebef - 1bb12736175c + - 7490b213baa9 - 904bf932cf78 + - 1fc82fe7ebef - 051fd2db8a27 - - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - 34305b013402 - d6e617c4e338 - - ad8b536d1caa - fee85957cebe - - 34305b013402 - 808b3a0a6716 + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - 21da31ed41a1 - - e5a3b75a271f - b8002c3f7141 - 8d4b90bf9caf - 6b5a5842531e + - e5a3b75a271f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 86f66ab58e14 - f1532cb33c75 - - 9de69775f512 - - 2a10645aeadd - 328aa71f0f3c + - 86f66ab58e14 + - 2a10645aeadd + - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 340bc17f49cf - 1708851f8804 - e41dcb0e913b - 85fb02c43042 + - 340bc17f49cf - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -383,20 +383,20 @@ tools: owner: iuc revisions: - d159735a6a9f - - b3490b036c5a - - 249f6a28c751 - d5fb354f745d + - 249f6a28c751 - b65a43f70b99 + - b3490b036c5a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d2d1df21dfb9 - 33368fec3b70 - b7829778729f - - 7897763d14ec - dd7ad84f3943 + - 7897763d14ec + - d2d1df21dfb9 - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -404,8 +404,8 @@ tools: owner: iuc revisions: - 6f4c8ad6ea01 - - 189e837009c9 - 8f631679571f + - 189e837009c9 - ced385aa976d - 505a9833ab5d tool_panel_section_label: Assembly @@ -413,70 +413,70 @@ tools: - name: trycycler_consensus owner: iuc revisions: - - e59bee4565b3 - 356afed970b4 - - d40ed4eb0c0e + - e59bee4565b3 - 19bdfd1e6fe3 + - d40ed4eb0c0e - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - ebd801e712bc - - 6dd935e4984b - - b23249f81bc4 - 4688ae3b49b5 + - b23249f81bc4 + - 6dd935e4984b - 80a17897564d + - ebd801e712bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b64696992ee9 - 59bd28f6265d - - 937ea677d437 + - b64696992ee9 - b5e35a2ca4f3 + - 937ea677d437 - cb1e3db43020 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 2628f6790eda - - cb4768eeca3b - 383bb5ad32e2 - - 6015aa0303f2 - 05bd7504fdb2 + - 6015aa0303f2 + - cb4768eeca3b + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 8f9f06995f98 - e92675014ac9 - 9e3e80cc4ad4 - - 6e26c9afd301 - 0a3a602cd1e3 + - 8f9f06995f98 + - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 8d09f8be269e - - 08256557922f - 920677cd220f + - 8d09f8be269e - 5da9a0e2fb2d + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 0e2b4e3f9ca1 + - 82398ba86ba7 + - d81360ea69d8 - 4a53b89fa703 - 37d88f41c810 - - d81360ea69d8 - - 82398ba86ba7 + - 0e2b4e3f9ca1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index a67c8d8bf..53c611a36 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,8 +2,8 @@ tools: - name: integron_finder owner: iuc revisions: - - 4768f7f8e93f - 1ae00120dd24 + - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -24,8 +24,8 @@ tools: - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - - 17fcac7ddf54 - 24a7a95867b0 + - 17fcac7ddf54 + - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 93b7c3d31..05eb64807 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - a9c9d768b751 - 159b04e36791 - 204a131e47db + - a9c9d768b751 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index ccf586a82..4d85d9c43 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - dde39ba9c031 - - 0a5c785ac6db - - 87ee588b3d45 - - 589e7e57fd6d - - ce3c7f062223 - a1a923cd89e8 + - dde39ba9c031 + - 07e8b80f278c - b28e0cfa7ba1 + - 0a5c785ac6db - a8eabd2838f6 - - 07e8b80f278c + - 87ee588b3d45 - a68aa6c1204a - e19bebe96cd2 + - 589e7e57fd6d + - ce3c7f062223 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index e18944a38..995a4501c 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - 62c9df8382c2 - - 54f751e413f4 - f921014aba5a + - 62c9df8382c2 - e8ac2b53f262 + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,14 +23,14 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - d999e774072a - - 5edc472ec434 - - a52d2d93e595 + - e25d3acf6e68 - 6f386c5dc4fb + - 5edc472ec434 + - d999e774072a - 0e3cf9594bb7 - - 2889433c7ae1 - - e25d3acf6e68 - acf4e47b734c + - a52d2d93e595 + - 2889433c7ae1 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 5579b9750..82a783dc7 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 27ee142314a9 - - f4230f116196 - - c8cdde00b105 - - da6bd1975a71 + - 710301bc46fa - 6ca543ec1bf8 + - da6bd1975a71 - 095ad4d096d1 - - 710301bc46fa + - 27ee142314a9 + - c8cdde00b105 + - f4230f116196 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -80,8 +80,8 @@ 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 @@ -107,10 +107,10 @@ tools: owner: chemteam revisions: - bfb65cb551d8 - - 0fac8e2afc13 - - 79cfd9ead848 - 3b8a9d5ced85 - 88076940fa94 + - 0fac8e2afc13 + - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em @@ -118,8 +118,8 @@ tools: revisions: - b46d4b4d995c - f5d979cb4b54 - - 55918daa5651 - d532b7e5f64b + - 55918daa5651 - eb6564a60136 - 715cd0e87781 tool_panel_section_label: ChemicalToolBox @@ -127,18 +127,18 @@ tools: - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a - - f26afd1b7104 - 97872d87ba80 - - fdf2cc80adb5 - 5579659312e6 + - fdf2cc80adb5 + - d2f955aea23a + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - d1d0efda35c0 - 319a28774da9 + - d1d0efda35c0 - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -146,51 +146,51 @@ tools: owner: chemteam revisions: - 2c349b027a01 - - cac1886249a2 - - ed736e6eee39 - 4da9ee404eab + - ed736e6eee39 - 070e3ecc3fda + - cac1886249a2 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - 525ca7c8065f - da8753545526 - - 2e219a2d9327 + - c0c9a5024177 - 73008ef1f487 - - 525ca7c8065f - - 807aa4c9293d - d1f803b5943c + - 807aa4c9293d + - 2e219a2d9327 - f197e34c33a9 - - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 2c8ed1b52bf7 - 7568ae18908a - - 1809414a9454 - c4fbab8e03c5 - 61094e01eff9 + - 2c8ed1b52bf7 + - 1809414a9454 - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - d7ec25187599 - - 730ef07b90ae - - 79e8ab8f1e81 - ccfbd956a2d3 + - 730ef07b90ae - ba83f0923369 + - d7ec25187599 + - 79e8ab8f1e81 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 @@ -202,9 +202,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - - e6011617c748 - 1400d1977e7b + - e6011617c748 + - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction @@ -235,9 +235,9 @@ tools: owner: bgruening revisions: - d4c67ced6abc - - bf99565cec1f - - 9b48456a96fe - 85fad59f8168 + - 9b48456a96fe + - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 66ff86dec..314a5b170 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,8 +2,8 @@ tools: - name: diffbind owner: bgruening revisions: - - c97a786e8fb5 - fa56d93f7980 + - c97a786e8fb5 - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -22,17 +22,17 @@ 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: - - f5d67c722d67 + - 495a4173006f - 640d3af5d833 - 424aefbd7777 - - 495a4173006f + - f5d67c722d67 - 86e2413cf3f8 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -45,16 +45,16 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 - 4a14714649b4 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index d169b27e1..59e97c3c8 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,16 +2,16 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: + - 33151a38533a - 25136a2b0cfe - 830961c48e42 - - 33151a38533a - 90981f86000f tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,9 +25,9 @@ tools: - name: split_file_to_collection owner: bgruening revisions: + - 0046692724f9 - baabc30154cd - 6cbe2f30c2d7 - - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index edaa65245..4758e8349 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -8,37 +8,37 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 4a6ee918c13a - - f3a19509108a - - 6ef0b5664c69 - dad9da48a09a - - 0b3c3ad92827 - - 367b1ed91207 - - a3b86937ead6 - e3cbd2287f63 + - f3a19509108a + - 0b3c3ad92827 + - 4a6ee918c13a - 5e1240a87bcb + - 6ef0b5664c69 + - a3b86937ead6 + - 367b1ed91207 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - e177a8ea0bf1 + - bd46669113b9 + - 1b5fc03380d4 + - a4db66553a61 - 33c99804a32f - 584008e574b2 + - 54ccb7e1f49a - 72ed72122deb - - a4db66553a61 - - 1b5fc03380d4 - - bd46669113b9 - - 501c21cce614 + - e177a8ea0bf1 - e525f9ffb9ac - - 54ccb7e1f49a + - 501c21cce614 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 @@ -57,16 +57,16 @@ tools: - name: fastq_to_fasta owner: devteam revisions: - - 77b41c89d856 - 186b8d913e6c - 8979c288aefb + - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -78,8 +78,8 @@ 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 @@ -91,9 +91,9 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - - 154d00cbbf2d - 3e436657dcd0 + - 154d00cbbf2d + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -111,8 +111,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - 8190f6083c0d - f5c632894818 + - 8190f6083c0d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -132,11 +132,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 19e45916daf9 + - 26c6706bfb07 - 92ac8e086317 - b9b385097f13 + - 19e45916daf9 - 63769c4217a7 - - 26c6706bfb07 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 1743c7f05..29e59df90 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,13 +2,13 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - 268e91e540ee - 5f6d123679f4 - 29451af70c52 + - de72ba3ed6f2 - e821645ef8fc - a1ca9bccc7f2 - c929a006727f - - 268e91e540ee - - de72ba3ed6f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage @@ -16,95 +16,95 @@ tools: revisions: - 12af64f93288 - bb1e4f63e0e6 + - 0e143b4c3987 - 2d2cf5c1ea8a + - 5d11599b8a7d - 7a7fd0f5f15d - 0e49b109abc2 - - 0e143b4c3987 - - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 1d848bc4585f - - 7c1beb6d6eca + - 195e98217334 - 81b1e3e1fc6c - c06951d10364 - dc059492a995 - - 195e98217334 + - 1d848bc4585f + - 7c1beb6d6eca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 07418a30ed01 - - a67ac707496a - - bfff7454b59a - - 26e7304d6737 - 3d211717a775 - 71aa86af6762 + - 26e7304d6737 + - a67ac707496a + - 07418a30ed01 + - bfff7454b59a - 93eb012d9eed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - dd0b7398bb96 - 29fcfd36e90a - 2bc10a9ca58b - - b8858746dc1f - - dd0b7398bb96 - - 26983857c91a - 56d5b797ce84 + - 26983857c91a + - b8858746dc1f - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7e6bcd2e5128 + - 72bfafe3330b - 7ef978dc1b8a + - e6d0bff01239 - c3e012dfe21f + - 7e6bcd2e5128 - ee3a1b0f45f1 - - e6d0bff01239 - 9384cd033f30 - - 72bfafe3330b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - d9a637e83828 - 9470f29702f8 - - fd1275e01605 + - fb9cf9c97ec4 - b73e213add0c - 514fa53b5efb - - fb9cf9c97ec4 - - a60c359ec43c - 167788df3b46 + - a60c359ec43c + - fd1275e01605 + - d9a637e83828 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 5bffaa8354a1 - - e479c7ca5570 - ca0616bb2cdf - - 86febdcc4283 - - 2c37ce318bc3 + - e479c7ca5570 - c34d11ea4ba6 - a02cfa31e9cb + - 5bffaa8354a1 + - 2c37ce318bc3 + - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 192ef85c0b0b - - 1fcb7adc39b8 - - 69a8621ca2f0 - 78f405266706 + - 01fb6a7654e6 - 2d466b530754 + - 69a8621ca2f0 + - 192ef85c0b0b + - 1fcb7adc39b8 - 004aea905d4d - - 01fb6a7654e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary @@ -112,95 +112,95 @@ tools: revisions: - 9ecba5e225a6 - db940c262830 - - 3c9f0c486cca - - d580d6acd1df - - 2f9e4843f480 - - 137c4beed34b - 459cfa861f0b - d9ce4897dbb2 + - d580d6acd1df + - 3c9f0c486cca + - 137c4beed34b + - 2f9e4843f480 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - f264afa9fa6f - - fbe773640707 - 32e451def88c - - 2c66e43f1c86 + - fbe773640707 - fd408d755394 - bd7db9e2f2cb + - 2c66e43f1c86 + - f264afa9fa6f - bad3ca889618 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 7fda5607e777 - 4e12ea27f788 - - 3b9d990a0a0e - - 9368fbc49c8b - 7e361d147872 - - 56bce3c82278 - 231994413f89 + - 3b9d990a0a0e + - 56bce3c82278 + - 9368fbc49c8b + - 7fda5607e777 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 4431f39ede55 + - b1779366c8e9 - d9114ef1c8a5 - - c03c3384cd81 + - ce4ce3316f74 + - 4431f39ede55 - e65d16fb2724 - 94ca68515826 - - b1779366c8e9 - - ce4ce3316f74 + - c03c3384cd81 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 23f7c5f1fdaf - d57251071381 - 793665fff0f8 - 4ed32329e0ed - - b88ebb3672a1 - - 2da482e408b8 - f8fc4e5aff9d + - 23f7c5f1fdaf + - 2da482e408b8 + - b88ebb3672a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 25d830337d31 - - e4c7985d4585 - - 010e58e9d822 + - ba6efa77fb79 - c60570fa602f - a7849312d328 - - ba6efa77fb79 + - 010e58e9d822 + - 25d830337d31 - 512155688d98 - a4dfb122e52b + - e4c7985d4585 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 38e3f226248b + - 69264da0ce77 - c899e0ccff8c - - 443d9a9d6d11 - aa200e4f3939 - - 69264da0ce77 + - 443d9a9d6d11 - 4d678170d29b + - 38e3f226248b - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 10301d137111 - d806504e96d9 - - 6662b1a8d326 - a2d70c4fd406 - - c361b12d207a + - 6662b1a8d326 + - 10301d137111 - aac8444d6681 + - c361b12d207a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index 9fe82ea03..a875f1aa7 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -23,15 +23,15 @@ tools: - 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 @@ -44,8 +44,8 @@ tools: - name: obi_sort owner: iuc revisions: - - 12b9e285ca1c - e614dcabd870 + - 12b9e285ca1c tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat @@ -58,14 +58,14 @@ tools: - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 5f7003111e32 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - ec215ed98831 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index f664232e7..c72370b98 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - ce385837c160 - 832c20329690 - 63dd26468588 - dba489bfcd62 - - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index 343ffc844..1d62e8a20 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - d82648ad25a3 - 29bdbc353f20 - - 6da3972210ee + - d82648ad25a3 - 62f5fab76dfb + - 6da3972210ee 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: - - d6787bab7b11 - 183cb55b1729 + - d6787bab7b11 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index e0c08ac12..b94db23e4 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,22 +8,22 @@ tools: - name: cutadapt owner: lparsons revisions: + - 44e2cc14f75b + - 49370cb85f0f + - c4b82dce8335 - c053d4cad713 - - 093678460093 + - 48f587c13075 - 4e5056fefd88 - - c4b82dce8335 - 8665bcc8b847 - - 288f97432497 - - 49370cb85f0f - - 5915ea1ec9b1 + - de6cebe3c043 - 8c0175e03cee + - 660cffd8d92a + - 288f97432497 - 135b80fb1ac2 + - 093678460093 - c5e2e5902201 - - 44e2cc14f75b - e4691e1589d3 - - de6cebe3c043 - - 48f587c13075 - - 660cffd8d92a + - 5915ea1ec9b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -35,9 +35,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: - - 8889eb864cef - 9db07fd39f85 - f666895cbebd + - 8889eb864cef tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -49,15 +49,15 @@ 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 owner: devteam revisions: - - 717aee069681 - 25b8736c627a + - 717aee069681 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -77,8 +77,8 @@ tools: owner: devteam revisions: - 9457a20156db - - 859422bcb689 - 516b97a23d7e + - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -90,16 +90,16 @@ tools: - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - - ec0b5076173a - f81d4362b6c1 + - ec0b5076173a + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -111,10 +111,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 0dbb995c7d35 - - cd0874854f51 - - 9c620a950d3a - 56022eb50bbd + - 9c620a950d3a + - cd0874854f51 + - 0dbb995c7d35 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -140,36 +140,36 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 10b75444feae - 81a9090d6df3 + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - - 47e5dbc3e790 - 8611b80a14d6 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation 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 @@ -196,8 +196,8 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 249c8393f2d4 - e39cc71d3ed6 + - 249c8393f2d4 - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -224,15 +224,15 @@ tools: - 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 owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -244,10 +244,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 - d5e9e83cd3d8 - 567d5b3c52b1 - 09070cacefd8 + - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -259,8 +259,8 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 0b7ec11b3c7c - 4bedca26c133 + - 0b7ec11b3c7c - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -274,9 +274,9 @@ tools: owner: devteam revisions: - 90858c306551 + - bdf1ce174e39 - cb1e251cac37 - 736b8f6ee456 - - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -289,8 +289,8 @@ tools: owner: devteam revisions: - 421f0af4ee95 - - 7ce1891db6f5 - 07497255281e + - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -302,10 +302,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - - f984bb114520 - b29d37ca9e41 - 02f8a17a4ebd + - f984bb114520 + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -319,8 +319,8 @@ tools: revisions: - 0c2907307ba4 - 177f0621c266 - - e246088b6e34 - 6027ef51ef91 + - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -332,10 +332,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: + - 73194cdd4f57 - 61b4cedc8934 - - 377ac2829eac - 547e8d00f11c - - 73194cdd4f57 + - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -359,8 +359,8 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - b4c6f054210a + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -372,8 +372,8 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -405,8 +405,8 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - bf04bd405d5b - 71f649c23021 + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -418,11 +418,11 @@ tools: - name: umi_tools_count owner: iuc revisions: + - e654095ab143 + - a535cf1e5da4 - b557acca0b56 - 24013bf85a6f - - a535cf1e5da4 - 8250ea3a1501 - - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -440,12 +440,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: + - 9fa7803d1c51 - 6a675c3aa610 - - f3759eec3018 - 828dba98cdb4 - - 27ac32a22ad2 - - 9fa7803d1c51 + - f3759eec3018 - 7accf7407811 + - 27ac32a22ad2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 1626c8dad..bcd4bb309 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,27 +2,27 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c - e41385662e5e - - ce9cd02d5b88 - 7b4468117008 + - 64e9a6afdd0c + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - 3d0c7bdf12f5 - f2e8552cf1d0 - - e7b2202befea - 9da02be9c6cc - ff9530579d1f + - 3d0c7bdf12f5 + - e7b2202befea - 5ec9f6bceaee - 2b0c9d9fc6ca tool_panel_section_label: FASTQ Quality Control @@ -30,53 +30,53 @@ tools: - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - 18a51655db17 - - ad116ae3f4d9 - b6b54ba71bd8 + - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: + - 59003d0543cd - cc0fd298cc17 - 7306ec78632a - - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - a72af9de6bf5 - - 8880fb74ef56 - 1f296803dfa3 + - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: + - 5e33b465d8d5 - 9a913cdee30e - - 75c93c70d094 + - 3d93dd18d9f8 + - abfd8a6544d7 - bf675f34b056 - - 1c2db0054039 - b2f1f75d49c4 - - 5e33b465d8d5 - - 3d93dd18d9f8 + - 1c2db0054039 - f7985e0479b9 - - abfd8a6544d7 + - 75c93c70d094 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - 084bbd8ba7b8 + - cd7e644cae1d - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index d934ded82..54bbfa7ed 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 85ef5f5a0562 - - 141612f8c3e3 - 83a19df00eab + - 141612f8c3e3 + - 85ef5f5a0562 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 629d3793d..ab4426fe7 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -17,8 +17,8 @@ tools: owner: iuc revisions: - 8f53b238a360 - - f2f3bc622a16 - 0c8f7322f8fc + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -31,22 +31,22 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -94,51 +94,51 @@ tools: - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways 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: - - 86e46972e183 - 9e83673fa6d2 + - 86e46972e183 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - da74170c55c7 - 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: - - 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 @@ -158,8 +158,8 @@ tools: - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 8627a5283..8b48bb87e 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -9,15 +9,15 @@ tools: - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index cd440707a..13c43f534 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - 983bf725dfc2 - b39347891609 - - e9df53a75f3c + - 983bf725dfc2 - c1b437242fee + - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download @@ -19,23 +19,23 @@ tools: - name: sra_tools owner: iuc revisions: - - 83c7d564b128 + - c441583adae5 + - 69ebb7f46e45 + - 4df8de2d0e48 + - aad3885b3216 + - e08a7ad4378b + - 6591f049cf7e - 9a776b080193 - - e407b9da183a - 6ea73833cf67 - - e08a7ad4378b - - 4df8de2d0e48 - - 69ebb7f46e45 - - c441583adae5 + - 7068f48d0ef9 + - f5ea3ce9b9b0 + - 1790dcf3c32d - 653e89d73fc4 - 734abc7ac21d - - 4317d3cb6cba - - 1790dcf3c32d - - aad3885b3216 - - f5ea3ce9b9b0 - 5e6237d58b0c - - 7068f48d0ef9 - - 6591f049cf7e + - 4317d3cb6cba + - e407b9da183a + - 83c7d564b128 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept @@ -50,8 +50,8 @@ tools: - name: uniprot_rest_interface owner: bgruening revisions: - - af5eccf83605 - 054483e27a35 - bfdc6a7ffd3a + - af5eccf83605 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index d0ed8a4d1..ddcec5004 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,14 +2,14 @@ tools: - name: circos owner: iuc revisions: + - df7356989ac1 - 290a11559985 - - 7f13dc906cb9 - - fd59d783248a - 740057a5126d + - a64dc31ab7f2 + - 7f13dc906cb9 - c4bde687c846 - 4b519282a05b - - a64dc31ab7f2 - - df7356989ac1 + - fd59d783248a - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -35,8 +35,8 @@ tools: owner: devteam revisions: - 7cf5b1d072b5 - - f95284aa2946 - 867ab348287d + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -49,19 +49,19 @@ tools: owner: iuc revisions: - '566197475670' - - 53460afd5115 - ca7cb0eaad62 + - 53460afd5115 - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 10515715c940 + - da4c086cff5b - d3a9e32672ec - 3d059e9c2fba - 391a4cc45fea - - 10515715c940 - - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point @@ -69,9 +69,9 @@ tools: revisions: - d0fc8b746d57 - 5fe1dc76176e - - 299307abd804 - 1acf88921176 - 3b12bf9b4b87 + - 299307abd804 - e3a675da7fd0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -91,31 +91,31 @@ tools: - name: graphlan owner: iuc revisions: - - a490b70e46fc - 8f62f666dcb6 + - a490b70e46fc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram owner: devteam revisions: - - 6f134426c2b0 - cdb9e89e2970 + - 6f134426c2b0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse owner: iuc revisions: - - 667e17248bfe - - 836d1aa3e89a - - 112eb40ba6cf - a6e57ff585c0 - - 2bb2e07a7a21 + - 836d1aa3e89a - fd5dbf0f732e + - 112eb40ba6cf + - ca2def38369c - 4542035c1075 + - 2bb2e07a7a21 - 17359b808b01 - - ca2def38369c - - 1cfc579079a6 - 6cd09d7b5f37 + - 667e17248bfe + - 1cfc579079a6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -133,8 +133,8 @@ tools: - name: pathview owner: iuc revisions: - - fe154a7af404 - f1691de443a7 + - fe154a7af404 - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -147,8 +147,8 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 62e3a4e8c54c - 85da91bbdbfb + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -167,9 +167,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: + - 0a10fddd97d2 - 44c66e8d21e6 - 7c9417381ad5 - - 0a10fddd97d2 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -181,13 +181,13 @@ tools: - name: pygenometracks owner: iuc revisions: - - 4ac4e7083b7e - - a1abfa420d9d - - 59fd173ac850 - - 326a3db8d9d1 - 360df4999907 + - 59fd173ac850 - 14e7c35f3d00 - 2824d77cd8f8 + - a1abfa420d9d + - 4ac4e7083b7e + - 326a3db8d9d1 - 7dd841a32245 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 281318760..48e3e9ec5 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.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 @@ -173,8 +173,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - 767a675b5254 + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 4d7de725c..14d4b42fb 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,9 +2,9 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 29f66c353bcb - - 921a2da49a0c - 9edf8894a22d + - 921a2da49a0c + - 29f66c353bcb - ed2cca6b5de4 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu @@ -12,35 +12,35 @@ tools: owner: bgruening revisions: - d404277cc87a - - ec4b948dc6f0 - - 78fb5e286609 - 5746d61f0a91 + - 78fb5e286609 + - ec4b948dc6f0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 03dd3c16ae4e - - 9e357a8b2ec3 - - 977dc15add20 - 4d511437b1e5 + - 977dc15add20 + - 9e357a8b2ec3 + - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: + - 41dbf4d162a2 + - 3b5b54ed6392 - 0ba4f56a3613 - 77919cc3618e - - 3b5b54ed6392 - - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e + - 5308ca68ef3d - 9939786dd9c9 + - b63363075c2e - 7babd8a46fe0 - - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index b3b2f0a25..ebaa1e6f3 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,9 +2,9 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 3df9f0a4bf34 - 81f0cbca04a7 - 0c777d708acc - - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction @@ -17,22 +17,22 @@ tools: - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - e576b73a2e2f - 6ad1d3cfdea1 + - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - 77f7159d775a - 70316d792fc9 + - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - dba87c4b32d3 + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert @@ -54,9 +54,9 @@ tools: - name: count_objects owner: imgteam revisions: + - b58447a2eed2 - 5bf8eb50b280 - 664232d2a3f7 - - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler @@ -70,23 +70,23 @@ tools: - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - 670975e92458 - e7273daa5ae2 + - 670975e92458 - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - cdf8e3c57dae - df3ad3ba5c6f + - cdf8e3c57dae - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -101,41 +101,41 @@ tools: - name: cp_enhance_or_suppress_features owner: bgruening revisions: + - f2ed92b011a9 - 11f177b1a59e - bace5a93a97c - - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f24c370e5ea4 - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - ad271f78a87a - - 3245681b2f6d - 31d195bedf6d + - 3245681b2f6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - - 87d4d92d7487 - 993faa34333b + - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - ff1a86a87364 - - c09dcda1143f - 6100a22bf4f2 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -149,57 +149,57 @@ tools: - name: cp_measure_granularity owner: bgruening revisions: + - a1a961c46d4b - 2564f461de62 - ac5bea85a391 - - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - a32c3f810ade - - 91e03287f285 - 20dbb1f7ec7b + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 5499dc6f8ac1 - - b64af54c5c09 - 8536b1ae0254 + - b64af54c5c09 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - 6f4715b8540a - d3890df07463 - e972e07c7845 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - e52c75a28c4b - 980aed9e8fd5 - 407925835dd9 + - e52c75a28c4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: + - acf3aa487283 - d85f11570109 - 79e10d12d90a - - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - 80b200ae516b - 035a58c7f54a - b76841ee5560 - - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -211,16 +211,16 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 8083a87d2fdf - 3a3033222f61 - 48102a685037 + - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -247,7 +247,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index cb7a1df3e..ca1728265 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - a38934e303b9 - - f362150bef41 - - d6e72da3ec35 + - 3e4f434a69c6 + - 1069f6db0a0e - 78bbd17d0703 - e319b5b65879 - e4ee04da1c19 - 17f911830a8c - - 1069f6db0a0e - - 3e4f434a69c6 + - d6e72da3ec35 + - a38934e303b9 + - f362150bef41 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 1ef5b6e3e09d - - 8f8df367470d - - 0135f1d487a0 - - 9537184d421f - - f91cfb73d369 - 72ddd32392cd + - 2b95d5c04908 - c88553ec696e + - f91cfb73d369 + - 0135f1d487a0 + - 1ef5b6e3e09d + - 9537184d421f + - 8f8df367470d - 7fe36019c073 - - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 - - d7e79eb3bcb3 - 2cf4a1cafc16 + - ad0dc9f4c9e2 - fafb3d685fa9 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 9eaadf03e0df - - 8d36959b000d - - 28a6f1908fcc - - 8c05afb547fa - bd2a7d1316b9 - - 43aac8d29685 - ee29337f905c - - 7f1cfa4c0e32 - - 94df24c6bc00 - - 6a1515bb0687 + - 3d18f8c3c0f6 + - 8c05afb547fa - 69797fa273c3 + - 8d36959b000d + - 94df24c6bc00 + - 43aac8d29685 - ee2beb764a7b - - 3d18f8c3c0f6 + - 28a6f1908fcc + - 7f1cfa4c0e32 + - 6a1515bb0687 + - 9eaadf03e0df tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - c092052ed673 - - 0893a1dbb807 - - bcaa0d571ce2 + - 9f978da6528a + - cb903c9dc33d + - d37ede8589b2 - 8858fa037a15 + - 5d6ed46cc101 + - 0893a1dbb807 + - c092052ed673 - 5671e1d3d5ee - db536ad45f28 - 364f4ffec275 - - 9f978da6528a - - d37ede8589b2 - - 5d6ed46cc101 - - cb903c9dc33d - e3bb03cf207a + - bcaa0d571ce2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - c5c9f02b6167 - - f95f403841ad - - 12d66d0d05ac - - 49236b03e4fd - 38b91a3190cd - - 3b6a16d82c1b - - 230b05597996 - - e1a015876aa9 - - 045d6d00f606 - 584beffa972b + - 045d6d00f606 + - 3b6a16d82c1b + - f95f403841ad - ed28dd32141c + - e1a015876aa9 + - 230b05597996 + - 49236b03e4fd + - c5c9f02b6167 + - 12d66d0d05ac tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index ac34606e9..de5b70d1d 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: + - 17e3b698dd52 - 0f1724dd59d2 - f198773344e4 - - 17e3b698dd52 - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: + - ac092723240d - ba0c40780ecf - - 374cb875d38a - a513e3fbb4c5 + - 374cb875d38a - 22c2a1ac7ae3 - - ac092723240d tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index 5a0556b1a..6b89a991a 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,27 +2,27 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - 772e0e89fc68 - 522137aaa9c4 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 4d81e3e2fb63 - f22a9297440f + - 4d81e3e2fb63 - 8a794e6d3388 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - e1317b5502fa - - 2af1346e68c9 - f1b9a42d6809 - - b6ef6d0cb6b7 - 818f9b69d8a0 + - e1317b5502fa + - b6ef6d0cb6b7 + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex @@ -30,71 +30,71 @@ tools: revisions: - 8334dc98c48e - c80db5d6fd8c - - 05143043ca13 - 947c2eacccb8 - 1588f9076e32 + - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 29e4122c90de - - 9991c4ddde14 + - 25b46af53232 - 1552b8cb4a94 - 83228baae3c5 - - 25b46af53232 + - 9991c4ddde14 + - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 53616c8b0865 - - 1a53edc4b438 - - a07ab242b0b5 - f3dfa4bdf87e - - 060ca94ac049 + - 53616c8b0865 - 841a6cc5fc58 + - 060ca94ac049 + - a07ab242b0b5 + - 1a53edc4b438 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - dc4b5fd604a6 - 2fc89dcd41c8 - - d4808d5b83da - - 927586a18553 - 91c4e3331208 + - d4808d5b83da + - dc4b5fd604a6 - 40f4447733b2 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - e5a5ad882f1f - - c6ae57f774c6 - - 301e07345c93 - - 25ab6b4e376e - 7626ea9c2e1b + - 301e07345c93 - 36e8d6d5d01b + - 25ab6b4e376e + - e5a5ad882f1f + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 - - b7c3e9a3b954 + - 4ed102b922cb - f9639b488779 - 02d2be90dedb - - 4ed102b922cb + - b7c3e9a3b954 - 80852884053f + - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - - ec69cbe34b73 - 61634a87efc7 + - ec69cbe34b73 - caeb57858702 + - 14180f9c831e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 6744c2eab..7e74127a1 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - a6d65b0c67af - - 03e9b2fbc005 - 017aba02828d - cd659e8cc5fa + - 3ba8d4563129 - 749c918495f7 - - f6877ad76b00 + - a6d65b0c67af - 937aa69e715f + - 03e9b2fbc005 + - f6877ad76b00 - 17062a0decb7 - - 3ba8d4563129 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -22,18 +22,18 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 53646aaaafef - - 3fe632431b68 - - e188dc7a68e6 - - dfd8b7f78c37 - 64f11cf59c6e + - dfd8b7f78c37 + - e188dc7a68e6 + - 3fe632431b68 + - 53646aaaafef tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -45,43 +45,43 @@ tools: - name: lastz owner: devteam revisions: - - 2ff111fac1d7 - e7f19d6a9af8 - - 3e1ea2facca6 - - 60afcc2c1d05 - 37b497aa133f + - 60afcc2c1d05 + - 2ff111fac1d7 + - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 037c6e54df11 - f54f5baedfdd - - 09b53c1d4ab1 - - 8c6cd2650d1f - - 53c0b7a1a0c3 + - 11a0d50a54e6 + - 037c6e54df11 + - 77b2770508f6 - b3eab4b67562 - 6b1e195506a3 + - 09b53c1d4ab1 - 3f4d6399997b - - be1d967337e4 - c0c2d0941de8 - - 11a0d50a54e6 - - 77b2770508f6 + - 8c6cd2650d1f + - be1d967337e4 + - 53c0b7a1a0c3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 00fbfac99d39 + - 13022c3d3076 + - ec9cbd6b9a49 - 178bdbdb6d24 - - 1cd2511a396e - - 9ee34ba73ebf - - e403d27e8f24 - - 5ef7ec16b04f - 79b885ce78d7 - - ec9cbd6b9a49 - - 13022c3d3076 + - e403d27e8f24 - b8f5f6e87f5c + - 5ef7ec16b04f + - 1cd2511a396e + - 9ee34ba73ebf + - 00fbfac99d39 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index ed15e0f99..64a28567e 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -34,9 +34,9 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: + - 7c2100246a2f - 5b5a7af9fbb4 - 63f86089423e - - 7c2100246a2f - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -44,17 +44,17 @@ tools: owner: iuc revisions: - 1c35dadbe76f - - 18a502a9d287 - 96336c6a2bb7 + - 18a502a9d287 - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - addaf9d22850 - - f732237754fc - 34e55239e68b + - f732237754fc + - addaf9d22850 - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -62,8 +62,8 @@ tools: owner: iuc revisions: - 04c15826a0b8 - - 75403243703a - 8c202e741d68 + - 75403243703a - 0776d824d896 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -71,53 +71,53 @@ tools: owner: iuc revisions: - 8470de786d47 - - 43c99742158b - 1c9b3bcd4261 + - 43c99742158b - e96bbb9e24ea tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 5c865a382933 - - 1d75bd0595e2 - 306a40d4bb8f - 84743da21318 + - 1d75bd0595e2 + - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a - - 555ccac8a4c5 - 78faebd0879c + - 555ccac8a4c5 - 8daf4564ccda + - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - a58e4a43f49c - - d60df8727f59 - f947b4bb5107 - 7b8cb2b02978 + - d60df8727f59 + - a58e4a43f49c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 04144473e59e - 1bc3657cd694 - - 7f3b59dee073 - 7136e9ab70db - - 04144473e59e + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - d943081510da - - 9058d8943303 - 0a1224c4b781 + - 9058d8943303 - 19299bb1c6af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -132,23 +132,23 @@ tools: owner: iuc revisions: - dbf1798c0dcc - - c4db8c4de66f - 6501b5b33988 + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - fa35f1106d3e - 15dbb444df71 + - fa35f1106d3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - 6c84982ee6f7 - 6d364c65c946 + - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -160,8 +160,8 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - 6aad8ca3918b - e66ab198ec15 + - 6aad8ca3918b - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -169,8 +169,8 @@ tools: owner: iuc revisions: - b084117133af - - d77397f09da1 - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways @@ -190,51 +190,51 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 + - 79706f10d680 - e88b731dad59 + - 31c6d107e7a5 - c409a495841f - - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 172920f67a84 - - 094ad9c068af - - 71ea608ddfa3 - 714d5a28cc5c - d24841f5c3d2 + - 094ad9c068af + - 71ea608ddfa3 + - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - d7e9a3c41657 - - a293a742194f - - 12fb63b5f63f - 4137b492233e - a4d7148ccee4 + - 12fb63b5f63f + - a293a742194f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: + - 6fcb8ac37a3e - cf87759761eb - 97f7bb0851e7 + - 64bc7acc22a9 - 75bedfb2078b - e2c71b852aba - - 6fcb8ac37a3e - - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - c82508e76ad1 - 2d35528d2141 - 4033827c76b8 - 5e5a999ffaa9 - 080ea153677c + - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann @@ -309,9 +309,9 @@ tools: - name: kraken2 owner: iuc revisions: + - 4a9da2b6c2e3 - e674066930b2 - 328c607150ff - - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -337,8 +337,8 @@ tools: - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1902d3de4a4f + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -350,8 +350,8 @@ tools: - name: kraken owner: devteam revisions: - - aec58624706f - 8ba2174315aa + - aec58624706f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -389,18 +389,18 @@ tools: owner: iuc revisions: - e073891b2afc + - 4fd3b5d8706b - 2cff76cf35c6 - 0270541aaf46 - 27250f92a01a - - 4fd3b5d8706b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - 76bc4efa1aeb - eb50e7eca3dc + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -473,13 +473,13 @@ tools: - name: metaphlan owner: iuc revisions: + - a92a632c4d9b - 2131d7dca455 - - ff8f55893e7d - 6dee4abadccb - - a16313517e55 - 1a6cdf55390f - b89b0765695d - - a92a632c4d9b + - a16313517e55 + - ff8f55893e7d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -551,8 +551,8 @@ 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 @@ -570,8 +570,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 2e62e32d4f33 - 3bd5f5afb9b1 + - 2e62e32d4f33 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -601,13 +601,13 @@ tools: - name: staramr owner: nml revisions: + - 4d83eccf5f81 - be818ae858e4 - aeaa20b96ef2 - - 3b22de20bd4b - - 141afacabcfa - 2fd4d4c9c5c2 - - 4d83eccf5f81 + - 3b22de20bd4b - 4b9a8031ab74 + - 141afacabcfa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -637,8 +637,8 @@ tools: - name: vsearch owner: iuc revisions: - - 576963db5f1b - 9495df9dd6ef + - 576963db5f1b - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 9b6a140d4..3cbe17e3d 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 093449d18..d1fbe621c 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: + - 80f03df2e2ce + - 48c13389050d + - 94b8c6013083 + - 9baa871cb1d1 + - 9422c5a87ee2 - cd07731e4434 - - 2263989660f5 - - a74dbfee5a86 - - 6ae5a7b5a0a2 - 9eeb13a92d79 - - 9422c5a87ee2 - - 9baa871cb1d1 + - 6ae5a7b5a0a2 - 8b67dd48fec1 + - a74dbfee5a86 + - 2263989660f5 - bdfbaf0c10aa - - 48c13389050d - - 80f03df2e2ce - - 94b8c6013083 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 5abf2c2249aa - - f0af8936ed41 - be78f13134e2 + - '764845535798' - d7ce0ec78e51 - - bc3831dd65c1 - - f14193ec1f50 + - 3ff17bad4006 - aaa0d6a8b808 - - d390fe1567dc + - bc3831dd65c1 - 2e093badc689 - - '764845535798' - 4a60927aaca5 - - 3ff17bad4006 - - fc2e49f91e52 - c18157c68134 + - fc2e49f91e52 + - 5abf2c2249aa + - d390fe1567dc + - f14193ec1f50 + - f0af8936ed41 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -44,8 +44,8 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -64,19 +64,19 @@ tools: - name: mafft owner: rnateam revisions: - - f1a5908ea2cb - - 6f28e90db932 - c5908940967d - - f0d493f8f84f - - 15974dd17515 - a65296ffb4a0 + - 15974dd17515 + - f0d493f8f84f + - 6f28e90db932 + - f1a5908ea2cb tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -89,28 +89,28 @@ tools: - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - bcd65de9725b + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer 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.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index f378c2613..3c1c3d716 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,35 +8,35 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - - 79e9a869f40e - a7228a7ea146 - - fc8804320156 + - 79e9a869f40e + - cb34f00cc10f - 0e9e7fcdd543 + - fc8804320156 - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - d6cddc06aeae - - 18505fe2bdb1 - - fa11aa8103b2 - db25ec99c3ea + - fa11aa8103b2 + - 18505fe2bdb1 + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - edf6d4003fad - - 2bf63b38ee9b - - ec699520444c - - 19f3b583a9b3 - - 0f5f4a208660 - - eb746fa6f514 - cc36773a3681 + - eb746fa6f514 + - 19f3b583a9b3 + - edf6d4003fad - 222669c4afb6 - 43815fa60f3a + - 0f5f4a208660 + - ec699520444c + - 2bf63b38ee9b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -55,49 +55,49 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab + - 0f1c34698076 - 645159bcee2d + - a3c4fe6f49ab - edbb6c5028f5 - - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: + - 3b6f94fc7e1d - d219b6d8158a - 85a394edc247 - - 3b6f94fc7e1d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - 90a922f32523 - - be95355fef8d - a8d4be409446 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - d376944466bf - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - bec636361cfd - a3afc5f0a96c + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 5f76b20953e5 - 543cbeef3949 + - 5f76b20953e5 - 93d623d9979c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -117,8 +117,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - 5a82eb9e1b89 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -181,8 +181,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - ca22d8497db5 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 4bd2bfd1b..e52931f5c 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -14,8 +14,8 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 71186bb66ca2 - 4e85a3a5dbd1 + - 71186bb66ca2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts @@ -76,15 +76,15 @@ tools: revisions: - 2f27f3b86827 - e4b4837f06f5 - - ed1518ce2237 - edacc4bcd3cb + - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -96,16 +96,16 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 472dabcb03bf - 74af283d8ebd + - 472dabcb03bf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - - 5711fc06a63e - 48a42ca61006 + - 5711fc06a63e + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -118,8 +118,8 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - 81a286e4c5a2 - fcb8bdd124f4 + - 81a286e4c5a2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -145,8 +145,8 @@ 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 @@ -154,8 +154,8 @@ tools: revisions: - 27a6a256cd23 - b4b2b284230a - - 5bcf0e24f42c - 172815da3d41 + - 5bcf0e24f42c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -167,8 +167,8 @@ 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 @@ -180,16 +180,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - fea85c467896 - 19bbd19b74b3 + - fea85c467896 - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -213,9 +213,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 4ba60cb14cb0 - 0cb27ea69dc1 - 9c43baa60906 - - 4ba60cb14cb0 - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -228,18 +228,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 9d09724f2bf1 - aec831b54a5b - 0db22932bc39 + - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - 29c738066906 + - df30a2f1db55 - ed7a967cb11b + - 29c738066906 - 6e24e79d3d69 - - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -251,16 +251,16 @@ tools: - 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: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -272,17 +272,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - c520a52b5174 - d63c1442407f + - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 94a50db37d1a - 9946bc39c834 - 625fd9476402 + - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1033,16 +1033,16 @@ tools: - name: rdock_rbcavity owner: bgruening revisions: - - 744a777e9f90 - 7e5c2e4bc227 + - 744a777e9f90 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbdock owner: bgruening revisions: - - a22969b08177 - - e4b7d1507a75 - c362398df83b + - e4b7d1507a75 + - a22969b08177 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 67c633a27..c99f7d84d 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,87 +33,93 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - f73435dc282b - - 6a457678efcb - f04a1264e2a2 - - 3f59ebfbfe3d - - 8834daeb9892 + - cce7b18495e4 - 107d3ba7024a + - a6619171428e - 3b8b5bde0bd9 - 5a7c56a5cc08 - - cce7b18495e4 - - c78f3d7dd1db + - 3f59ebfbfe3d - 81e66674859e - - d7c7ef3353fe - - d033ffc1c161 + - 8834daeb9892 - 26de3a7b1cb9 - - a6619171428e - - '841557158611' + - d033ffc1c161 + - f73435dc282b + - 6a457678efcb - b89cac5156ec + - d7c7ef3353fe + - c78f3d7dd1db + - '841557158611' tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 88c4aa435ded - - 6a726db04d4b - - 6223845127ea - - 5fcd1ece3a6e + - 4755f52427c4 - b0af57c1a968 + - a185b079b095 + - 659517798cc4 + - e75442c7f4da + - 6223845127ea + - 88c4aa435ded - aa8cc71438cf + - 5b777002c2de - 6283babe736e - - 659517798cc4 - - 4755f52427c4 - - a185b079b095 + - 5fcd1ece3a6e - 7a2092844346 - - 02b8758214b0 - - 3b96e92e8ec3 - - 5b777002c2de - - e75442c7f4da + - 6a726db04d4b - df47d4845b62 + - 3b96e92e8ec3 + - 02b8758214b0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: + - b8476e82ac20 - 524d31add34a - f97743d52b87 - 9b892d7f82cc - d1c340a5664b - - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - feb40665d7cd - - 128ba8da994f + - daddf188c13f - 9e10ba792be2 + - 128ba8da994f + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: orthofinder_onlygroups + owner: iuc + revisions: + - b3d25fae5389 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 81804a978fc0 - - 5f8727ff21e7 - - b6abccb1f25b + - 03ed9524dcd1 + - 42a174224817 + - 3a43c3982401 + - b7e297c2ede6 + - 14ae456b8cc5 - 437e28791761 - - 7bb8726be37c + - 81804a978fc0 - 36912871ccdc + - 2fa9d4f1b48f + - abf6dbe8c9d7 + - 5f8727ff21e7 - ca337cce3888 - - 14ae456b8cc5 - - 9d61d3fa046c + - 7bb8726be37c - 2f1019071464 - - 3a43c3982401 - ca0d8cf80567 - - 2fa9d4f1b48f + - b6abccb1f25b - a2099fb98cdb - - 42a174224817 - - 03ed9524dcd1 - 83a69484cb87 - - b7e297c2ede6 - - abf6dbe8c9d7 + - 9d61d3fa046c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -126,22 +132,22 @@ tools: - name: raxml owner: iuc revisions: + - a4b71be30c3c - ba29b5e2a4be - - b1e68bbe4cef + - 73a469f7dc96 - 29ff6a849eac - ea30d3089354 - - 73a469f7dc96 - - a4b71be30c3c + - b1e68bbe4cef tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - f1ccc8a6eb05 - - 809e42326fc2 + - 15ac71df11a0 - 91887494eb97 - e88a7de55d6e - - 15ac71df11a0 + - f1ccc8a6eb05 + - 809e42326fc2 - dbe2b2204555 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index ad476603c..f69d94bc6 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - 1aac2a13842a - fc288950c3b7 - - 881d7645d1bf + - b502c227b5e6 - f6ced08779c4 + - f9242e01365a + - 1aac2a13842a - a1f0b3f4b781 - - b502c227b5e6 + - 881d7645d1bf - 7d34178f2812 - - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index 0c18f25c7..3f3ec9650 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,14 +2,14 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - 5b85006245f3 - d00e15139065 - - c0e71cb2bd1b - - e4a053d67e24 - 7fbec959cf2b + - c0e71cb2bd1b + - a58f7eb0df2c - 3bd420ec162d - - ca90d17ff51b - eb085b3dbaf8 - - a58f7eb0df2c + - 5b85006245f3 + - ca90d17ff51b + - e4a053d67e24 tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomics.yml b/staging.gvl.org.au/proteomics.yml index 6e5c36b8c..5ba7da24e 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,11 +2,11 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - f28ad96b76dc - - ece627528a78 - - b574b84afc4d - 277dc652246e + - f28ad96b76dc - b18329a8ac14 + - b574b84afc4d + - ece627528a78 - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -14,73 +14,73 @@ tools: owner: galaxyp revisions: - e215f71d7983 - - e988563cc6e5 - - b41107d8fe89 - bf06d196e23d + - b41107d8fe89 - 525f201b86c1 + - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 - - bb6397b94018 - 4fbffddde8cd + - bb6397b94018 + - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - - b8c79e70516d - f23d67e28cc8 + - b8c79e70516d - a8157342d9a3 + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 - - a95a82eb4d50 + - a69865da6f80 - 25b83cbd596a + - a95a82eb4d50 - 80600735685d - - a69865da6f80 + - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - f1897eb07081 - e0669b1854b1 + - 798da6bdff3d - ed9ed1e6cca2 - 611d80c0e29d - - 798da6bdff3d + - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - - 74b61bf5bc4b - 5a35e3a8d013 + - 74b61bf5bc4b + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - 82f6c2f4332d - - df2187f9013b - cc430977c8ff + - df2187f9013b + - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 1693b2126f30 - - 043f9c91f686 - - c5aa9fca18c6 - 10566783d718 + - c5aa9fca18c6 + - 1693b2126f30 - d2483487e077 + - 043f9c91f686 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -98,9 +98,9 @@ tools: - name: diann owner: galaxyp revisions: - - ae4dc0c041f9 - bf0728e000cd - 9fa3dbf06f17 + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -119,9 +119,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - - 0fa397f4f40b - 1c5cbf8f79ce + - 0fa397f4f40b + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -147,72 +147,72 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: + - e66f552a3c47 - 160538a890a6 - d286ff4600dd - - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: + - 4d17fcdeb8ff - e42225f8a659 - - 2133b0be850a + - f522c08e900c - 837224ad1694 - - 37d669de2828 - - 4d17fcdeb8ff + - 8934bc76bb52 + - 2133b0be850a + - 1f39c833f65f - 97a7f34fcb6a - - f522c08e900c + - 37d669de2828 - 7f432d87c82c - - 1f39c833f65f - - 8934bc76bb52 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 - - '860429737408' - a72ac2c7cc5b + - '860429737408' + - 0ed07016d668 - 85b8866f06d7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 4187b6df1a40 - - 352b37c66d97 - 1974224d63c2 + - 352b37c66d97 - 990b4560ead7 + - 4187b6df1a40 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 99450519d727 - - deaf035bbe9f - 4f359549383c + - deaf035bbe9f - a1daafbf5233 + - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - 40ca115438d2 - c1343e3389ca + - 40ca115438d2 - c7745841de24 - e79958768a2c tool_panel_section_label: Proteomics @@ -220,18 +220,18 @@ tools: - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 - da986f83631b - - b648e45fd3cf - d46d64e7964d + - d2eac53666f0 + - b648e45fd3cf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 944b43462104 - eb811f3018ea - 1199751329b0 + - 944b43462104 - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -251,9 +251,9 @@ tools: owner: galaxyp revisions: - 8212e342e482 - - b7034eff0db1 - 28434abe6c5c - 593839e1f2c3 + - b7034eff0db1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -266,9 +266,9 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 01dbaf6a57e0 - 4e77b8f12cd3 - 8960fb791701 + - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -281,58 +281,58 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 - - f7fef900f5b2 - c9eff69a7c62 + - 9cdf15d3cfc8 - 518b1730cf2a + - f7fef900f5b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - ca88bd28f116 - - dff6c756eee5 - 5e948629bc73 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 890025d6e426 - 658494a2cb00 + - 890025d6e426 - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - 9b7977080f6d - 6634cad7d797 + - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - 05d5e1ddc985 - - d6878d27f051 - 0bb5056cb775 + - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: + - febd569ad26f - 52ba9695e752 - 5ad830edc021 - - febd569ad26f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 27cba4c5fc42 - - 39e8fde08881 - 92352a475eed + - 39e8fde08881 + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector @@ -346,51 +346,51 @@ tools: - 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 owner: galaxyp revisions: + - c427a8628cbe - ca799a7246e7 - 382cde407f81 - - c427a8628cbe - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - b5d0905419da - - 39caaa778d2e - 8ddb7bab1138 + - 39caaa778d2e + - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 8d4db262964c - - 1c5f31b8d632 - 18f93351f8b6 - f817513840a9 + - 8d4db262964c + - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 5d9f175dff81 - 111c3a00136d + - 5d9f175dff81 - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - be74a8cd7d66 - 476b5e296979 - 0e52c85f3b15 + - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -404,22 +404,22 @@ tools: owner: galaxyp revisions: - c18d8efa4474 - - 2b2a7551a857 - a407b6790342 + - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - d0304fb829c0 - 4e66c4e73909 + - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - ee860980edc6 - 8098330f6d91 + - ee860980edc6 - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -461,15 +461,15 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 89254095cbf6 - 8b814eafce2c + - 89254095cbf6 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 @@ -497,10 +497,10 @@ tools: - name: openms_peptideindexer owner: galaxyp revisions: - - dd173849c3d8 - - 5182338d5e7c - e039cc5c7aed + - 5182338d5e7c - 539a3a4dcc9e + - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -532,36 +532,36 @@ 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: - - cb0378d2d487 - 5f49ffce52cb + - cb0378d2d487 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 1beff3ddce58 + - 943a34df6047 - 3ec27b4cee7c - - 3634c90301af - - 07ff622ec007 + - 1beff3ddce58 - 7fdd9119cc4f + - 07ff622ec007 - a72c48001f7c + - 3634c90301af - da885ca16cb2 - - 943a34df6047 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -615,10 +615,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 265c35540faa + - a371252a2cf6 - 1a5690a5eedc - 12692567c7f9 - - a371252a2cf6 + - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index 0225e6c37..001fa4b2b 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - e345aadf914f - 289b7d6b69a4 - - cd5f98911089 - - 2f1d464ebfd2 - 42201b90e3f4 + - cd5f98911089 + - e345aadf914f - 110a346daf36 + - 2f1d464ebfd2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,11 +19,11 @@ tools: - name: stacks2_cstacks owner: iuc revisions: + - c207119ba5f6 - 0cd2df8af811 - - 42d9087b4789 - - fcce77c09289 - 8501601a118d - - c207119ba5f6 + - fcce77c09289 + - 42d9087b4789 - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - 421c33b8bf17 - - ad5ab22ffe24 - - 405a212b32ab - 89eb29319bf4 - - 33486216eec0 + - ad5ab22ffe24 + - 421c33b8bf17 - 04db7fd6b238 + - 33486216eec0 + - 405a212b32ab tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - 7b72fde3d27e - 1d839ead7ad3 - - 7370bb65bad4 - - eb784fa07f80 - - fa51dc5e8386 + - 7b72fde3d27e - f6e91108b7b1 + - fa51dc5e8386 + - eb784fa07f80 + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - a3e86cd9cac7 - 8a55d29c8fcf - - 3d70c2996730 + - a3e86cd9cac7 - c9b77ced9a78 - 1544278c272e - d30e36c48c93 + - 3d70c2996730 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - 7b881f5f5ad5 - - 564c33e5c3e3 - - 887cf585cafc - - a5969aa9347e - e2db212d64ad + - 7b881f5f5ad5 - b242deb58952 + - a5969aa9347e + - 887cf585cafc + - 564c33e5c3e3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: + - e897c74a48bb - bd5ff77e2036 + - 9a171f9a450b - b4bab607eb05 - 8cff84759bf6 - - e897c74a48bb - - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: + - 5e10f396979e - 33f0793edf93 - - 887e0991eb24 - 4f65e343ecdf - - 6dafad990086 - adc7a7610d4f - - 5e10f396979e + - 887e0991eb24 + - 6dafad990086 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - c287418eb288 - 97575d01f06b - - 17d39bf0a63a - - 4e280b27a831 - - c5d7050e4ad7 - 43e3eeb2e0ec + - c5d7050e4ad7 + - 4e280b27a831 + - 17d39bf0a63a + - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - cd034465d4a4 - - d9bf483266a1 - 09b8edb56d80 - - 0b8c84a7fdb5 - - a819ec3b362d - 9586f08634c0 + - a819ec3b362d + - 0b8c84a7fdb5 + - d9bf483266a1 + - cd034465d4a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: + - bf0e43ab0416 - a4b4bd84f69e - - 69842dd5aa48 - a9c34a289493 - - 95351dd0fd3f - 2645575d1bf2 - - bf0e43ab0416 + - 95351dd0fd3f + - 69842dd5aa48 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: + - 8a35a3bc6752 - 912f904a6e1e - d1fda11e602f - - d033e1ccb386 - bb0475c884ff - - 8a35a3bc6752 - cfb504394ae1 + - d033e1ccb386 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - 95286af4139b - d504d945a655 + - d1fad35bdb4a 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.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 487800a82..dfc3e2f10 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,17 +2,17 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - 31f8063eedea + - cf01dd6c6b1f - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: + - 703a2cb3fb38 - 32e542c2a773 - 125d20cb23d7 - - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -71,8 +71,8 @@ tools: owner: devteam revisions: - 6a6717a5f421 - - cf747d1bd79a - 86285ddd4512 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -84,8 +84,8 @@ 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 @@ -109,10 +109,10 @@ tools: - name: describe_samples owner: iuc revisions: - - 3b36efd62b3e + - e3b16fd7dd08 - 8f0181aacb7a + - 3b36efd62b3e - 0693ccd171c4 - - e3b16fd7dd08 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -124,13 +124,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 24a09ca67621 - - 8fe98f7094de - - 6a3a025714d3 - - d027d1f4984e - 9a882d108833 - cd9874cb9019 - 0696db066a5b + - 24a09ca67621 + - 6a3a025714d3 + - 8fe98f7094de + - d027d1f4984e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -142,10 +142,10 @@ tools: - name: dexseq owner: iuc revisions: - - b47c006d90c5 - - 2872c633f07e - - df929f257179 - 62adf13b86ea + - df929f257179 + - 2872c633f07e + - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -157,17 +157,17 @@ tools: - name: edger owner: iuc revisions: - - f2843df56434 - 5bf899c13979 - - 334ce9b1bac5 - - df0c8d0a5992 - 0cb907a2a810 - - 070900306913 - - 555659de7321 - - a8305cf0c951 - 6e53e565fc6a - - 9bdff28ae1b1 + - 555659de7321 + - df0c8d0a5992 - 3d89af8a44f0 + - 070900306913 + - 334ce9b1bac5 + - f2843df56434 + - 9bdff28ae1b1 + - a8305cf0c951 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -198,17 +198,17 @@ tools: - name: featurecounts owner: iuc revisions: + - f3a5f075498f + - 6f66ae7c5f7a + - 38b6d12edc68 + - a37612abf7f9 - af814359d244 - f9d49f5cb597 - - 7db9d3ea71c9 - - f3a5f075498f - ea04b737afa0 - - a37612abf7f9 - - a56fbe2d6ba7 - - 6f66ae7c5f7a - 90d16db017d7 + - 7db9d3ea71c9 - e6a2a912677a - - 38b6d12edc68 + - a56fbe2d6ba7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -232,9 +232,9 @@ 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 @@ -252,13 +252,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 26371a1df031 + - d4b55e2beb12 - 6ab42baa56e9 + - 26371a1df031 - f4af63aaf57a - 3fb01a8c902d - 6c19daec423d - a86e80d3c09c - - d4b55e2beb12 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -298,8 +298,8 @@ tools: - 87c11c05d238 - 1c75aa5de15e - ce5d418183c5 - - 5ae5c312d718 - 01247aaf0a10 + - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -311,9 +311,9 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 - 4f9c4e6566e5 - c971db6f0fe5 + - 40985510cd98 - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -326,13 +326,13 @@ tools: - name: limma_voom owner: iuc revisions: - - 97e06a4c7c75 - - e827f9aae031 - - 58c35179ebf0 - - 708348a17fa1 - - 32511f586472 - d6f5fa4ee473 + - 32511f586472 - 0921444c832d + - 97e06a4c7c75 + - 708348a17fa1 + - 58c35179ebf0 + - e827f9aae031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -393,19 +393,19 @@ tools: - name: rgrnastar owner: iuc revisions: - - 99b17b74a8cd - - 4074fc1940e2 + - 7ed2edc1337f - e132e7d02a3e + - 4074fc1940e2 + - 0a563fd2f22e - 4df95e2d7f61 - - 79de45b5069b - 5ec75f5dae3c - - c772497b2c32 - - 3ea5a2a63fa2 - - 0a563fd2f22e - - 7ed2edc1337f - - b9e04854e2bb + - 79de45b5069b - c7c55b694974 + - b9e04854e2bb + - 3ea5a2a63fa2 + - c772497b2c32 - 980d2a2e1180 + - 99b17b74a8cd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -429,13 +429,13 @@ tools: - name: salmon owner: bgruening revisions: - - 49121db48873 - - cc05793bb896 - - e3d32471da11 - ebab418107f5 + - e3d32471da11 - 15cd64d7c58b - - 2c0ca397d302 - 53e9709776a0 + - 2c0ca397d302 + - cc05793bb896 + - 49121db48873 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -447,22 +447,22 @@ tools: - name: seurat owner: iuc revisions: - - 8c28affc7c48 - 56242ff81c84 - - c0fd285eb553 - fab6ff46e019 + - c0fd285eb553 + - 8c28affc7c48 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - ae618321f34a - - 76d290331481 - - 1ebd14235b92 - 258d696dbd7e + - 1ebd14235b92 - dd4df992d93d - - 914cfcba0ec8 + - 76d290331481 + - ae618321f34a - cef79931dda5 + - 914cfcba0ec8 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -498,10 +498,10 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 - c6334cb383ff - - ffd1300599a1 + - d0d4cef4f967 - 0db979fead3a + - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -513,10 +513,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - 74217fbfba4d + - ba3720d7e68b - bcc5f03f1900 + - 74217fbfba4d - d6a479fd4281 - - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -528,10 +528,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - c2b82a94493e - 2fb4ee002432 - 478f36effca1 - 56162e446004 + - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -543,9 +543,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - 3f4094b6a565 - 9ff3765e7172 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -557,10 +557,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e - - 34a018cbee9c - be3f26533209 + - 34a018cbee9c - 4687ecf0eb2d + - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -572,11 +572,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - c5fbddcac63a - 33406f5a445c - - 5192f657f305 - 65e7dea767ea - 05ab8d5e04a2 + - c5fbddcac63a + - 5192f657f305 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -588,10 +588,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: + - 1fdb25a8384d - 6f0fb35b799c - - a35cba31d904 - e406ac71165d - - 1fdb25a8384d + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -603,8 +603,8 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 - c2c039e421af + - 964b7efe2639 - 37a1129c89d2 - 7c7fbf13aadd tool_panel_section_label: RNA-seq @@ -618,10 +618,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 24e94d84adc9 - eafea3083352 - 1d689e4e1caf - 047c22569787 + - 24e94d84adc9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -633,10 +633,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: + - 9871104ea630 - 04bb8bb7c198 - - 1812dbc5bb7b - 3a4ac03d1266 - - 9871104ea630 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -648,15 +648,15 @@ tools: - name: trinity owner: iuc revisions: - - 8f1c3df4dd49 + - d2bc35f3d1c5 - c9cfec002f71 - - cee61b3fcf78 + - 8f1c3df4dd49 - 32b86cd8eb50 - - d84caa5a98ad - - 9fa24d5aac68 - - d2bc35f3d1c5 - db1f362cca3e + - d84caa5a98ad - 48636f857c4b + - cee61b3fcf78 + - 9fa24d5aac68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -668,10 +668,10 @@ tools: - name: trinotate owner: iuc revisions: - - 6fd16fad465d - - 9e61bc67866f - 4383070d29ed + - 6fd16fad465d - 2b093007fab9 + - 9e61bc67866f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index ee91e8906..b2c45c52e 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -3,7 +3,7 @@ tools: owner: nilesh revisions: - 1a052c827e88 - - 473382134e56 - 080fd5739bb4 + - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index 3e35c1cc0..c3b97cb78 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 88eedb4abea0 - 10184eaa85fc - a53efedba9e7 + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,9 +16,9 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - - 1dfd95ee241e - 108db6635177 + - 1dfd95ee241e + - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -55,9 +55,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: + - 5f8e69cc4c6e - 19ece8afbaab - e7fd6754d093 - - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -69,8 +69,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -109,17 +109,17 @@ tools: owner: devteam revisions: - 56c31114ad4a - - dc6ff68ea5e8 - 649a225999a5 + - dc6ff68ea5e8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - 9149ad20699a - - 12749212f61b - 6856f8a01905 - 46c6639921f1 + - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -131,10 +131,10 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 92ec40abcdcf - c89806670ab9 - - 33208952b99d - 06dc50b7b711 + - 92ec40abcdcf + - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -146,9 +146,9 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 720217c23995 - - b3d99709fe1a - 66e23b11feae + - b3d99709fe1a + - 720217c23995 - a8d69aee190e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -161,10 +161,10 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - db17d5321bad + - cc61ade70eb8 - fefd89ab563c - 22970df7a40e - - cc61ade70eb8 + - db17d5321bad - fe34990e5ce7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,10 +178,10 @@ tools: owner: devteam revisions: - 811fc2d75ad4 - - 88b8c2916784 - - 7def34e6cf4d - 7a6034296ae9 + - 7def34e6cf4d - fa5d3e61e429 + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -202,11 +202,11 @@ tools: - name: samtools_mpileup owner: devteam revisions: + - 329deb17a9f7 - 9da0311ab1dd - - b61f5d6a7f25 - - fa7ad9b89f4a - 583abf29fc8e - - 329deb17a9f7 + - fa7ad9b89f4a + - b61f5d6a7f25 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -218,8 +218,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -231,10 +231,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - d7b4851d1971 - - 30388d878f81 - bb8cfc6f6e0c - db000c6007a0 + - d7b4851d1971 + - 30388d878f81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -252,9 +252,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - b5c88b7b153e - 344fc91e1bfd - a4a10c7924d1 + - b5c88b7b153e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -281,10 +281,10 @@ tools: - name: samtools_split owner: devteam revisions: + - 135c85f4cfaf - 5d9ae78f34d3 - b7f7826ef1cd - bcedabb53ddf - - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -297,11 +297,11 @@ tools: owner: devteam revisions: - 1cc79f49b8d5 - - fed4aa48ba09 - - 3a0efe14891f - - 24c5d43cb545 - 5a08c09b9311 + - 24c5d43cb545 - 145f6d74ff5e + - fed4aa48ba09 + - 3a0efe14891f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -313,14 +313,14 @@ tools: - name: samtools_view owner: iuc revisions: - - 350bbc5c2ffd - - 5826298f6a73 - 0dbf49c414ae - - 6be888be75f9 + - 5826298f6a73 - b01db2684fa5 + - b72793637686 - bf328cec6a42 + - 350bbc5c2ffd - c370440f901e - - b72793637686 + - 6be888be75f9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.gvl.org.au/send_data.yml b/staging.gvl.org.au/send_data.yml index 0e45ba528..cdf82e037 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,11 +2,11 @@ tools: - name: ena_upload owner: iuc revisions: - - 480d9e9d156b - - d147d6455873 - - 4aab5ae907b6 - - 59bb6d34fca6 - 6f6537780379 + - 59bb6d34fca6 - a62c4a11a67d + - 4aab5ae907b6 + - d147d6455873 + - 480d9e9d156b tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index ac50726ad..fbbff41da 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -2,12 +2,12 @@ tools: - name: anndata_import owner: iuc revisions: + - 93dd15e13e6a - fb9e030ffae4 - - 00712416fdaa - 32e547223c9e - - cfc3f5a57dc6 + - 00712416fdaa - 55e35e9203cf - - 93dd15e13e6a + - cfc3f5a57dc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -19,12 +19,12 @@ tools: - name: anndata_inspect owner: iuc revisions: - - ee98d611afc6 - b9fac48532eb - - 038e32885fec - - 39e945f0b2c1 - 688357ad5e61 - 6f0d0c784f09 + - 038e32885fec + - 39e945f0b2c1 + - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -37,11 +37,11 @@ tools: owner: iuc revisions: - 9bd945a03d7b + - 3d748954434b - ed4996a16f7f - b85871dd69f9 - - 43cb7b5a6fe7 - d4af736e7b83 - - 3d748954434b + - 43cb7b5a6fe7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -53,10 +53,10 @@ tools: - name: dropletutils owner: iuc revisions: - - a9caad671439 - 2c1200fba922 - cdf4443d5625 - 8855361fcfc5 + - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -101,9 +101,9 @@ tools: - name: raceid_clustering owner: iuc revisions: + - 7e014059a88d - f911a64454fb - 0bff0ee0683a - - 7e014059a88d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -135,9 +135,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - a6821f856a1e - - df8e4e54d367 - 69018f285aa3 + - df8e4e54d367 + - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -149,9 +149,9 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - 2af7c5086a96 - c92d0f9338c5 - 44b935f2271b + - 2af7c5086a96 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -164,9 +164,9 @@ tools: owner: iuc revisions: - 6acb08931836 - - b2df381a6004 - aaa5da8e73a9 - 77b91b9bdf52 + - b2df381a6004 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -178,10 +178,10 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 3c86f71498bc - a97abb8cd15b - b409c2486353 - a03ff8633507 + - 3c86f71498bc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -193,11 +193,11 @@ tools: - name: scanpy_inspect owner: iuc revisions: + - 3081ff5c84a3 + - 6c145a6868cc - 5e9171dc8244 - - cc0deb593fc8 - c5d3684f7c4c - - 6c145a6868cc - - 3081ff5c84a3 + - cc0deb593fc8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -210,9 +210,9 @@ tools: owner: iuc revisions: - 94c19fb1281c - - a407e7f8bdc1 - 3bcd5445cd7a - ab55fe8030b6 + - a407e7f8bdc1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -224,10 +224,10 @@ tools: - name: scanpy_plot owner: iuc revisions: - - dbbe1ea8ecb1 - - 9b0cdb8cf6be - aa0c474463c2 + - dbbe1ea8ecb1 - 6adf98e782f3 + - 9b0cdb8cf6be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -239,10 +239,10 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - f2f6c703da06 - - bf2017df9837 - 458e8f43a775 + - bf2017df9837 - 215733a383f2 + - f2f6c703da06 - 73ab2ac53d06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -255,9 +255,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - fd808de478b1 - - b834074a9aff - 8f333f90d8d6 + - b834074a9aff + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -269,9 +269,9 @@ tools: - name: scater_filter owner: iuc revisions: - - b7ea9f09c02f - 652923ce664f - 7a365ec81b52 + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -284,8 +284,8 @@ tools: owner: iuc revisions: - 2e41b35b5bdd - - ef4c80837bc5 - 81e5bdff4853 + - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -297,9 +297,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: + - 46fc6751d746 - c99ba278dfa9 - 9e5c0bb18d08 - - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 597f36092..99d0111a9 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,32 +32,32 @@ tools: - name: datamash_ops owner: iuc revisions: - - 4c07ddedc198 - - 419027d822d6 - 2f3c6f2dcf39 + - 4c07ddedc198 - 562f3c677828 + - 419027d822d6 - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -121,10 +121,10 @@ tools: owner: bgruening revisions: - b1eda492f063 - - 4c4ec859c31a - 840f29aad145 - - aef56d0e7a61 + - 4c4ec859c31a - 7442b94d6a1e + - aef56d0e7a61 - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -132,31 +132,31 @@ tools: owner: bgruening revisions: - d0352e8b4c10 - - 9fda0b82f419 - - 375bbd555f4a - - 30d21a6041f6 - 07843f917990 + - 30d21a6041f6 + - 375bbd555f4a + - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - 4cc980df6265 - cd02bf168d23 - 7ae443e6217d - 2c58b83c9bad - - 4cc980df6265 - 8b1b2b91f8d0 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 4bbaf77573ef + - 7dd3fb35904f - ad7e0b4291ee - - bb9fc9d46ea4 - - e10e776f2109 + - 4bbaf77573ef - 1dd433d2c92c - - 7dd3fb35904f + - e10e776f2109 + - bb9fc9d46ea4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index 1d2246823..8ac50072b 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -21,21 +21,21 @@ 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: - 02026300aa45 - - 13b6f0007d9e - - 464b9305180e - - 6595517c2dd8 - - 9cd341095afd - 626658afe4cb - 6e8d94597139 - be25c075ed54 + - 6595517c2dd8 + - 464b9305180e + - 13b6f0007d9e + - 9cd341095afd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -72,10 +72,10 @@ tools: - name: filter_tabular owner: iuc revisions: - - 34d29339abab + - 9cc411a62277 - 37cde8134c6a - 557ec8d7087d - - 9cc411a62277 + - 34d29339abab tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -99,29 +99,29 @@ tools: - name: merge_cols owner: devteam revisions: - - f2aac0c5c60d - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f + - f2aac0c5c60d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - 33d61c89fb8d - - 623f3eb7aa48 - - 2e8f945f7285 - 83069b38aa85 - 1ea4e668bf73 - - 3a6b78c39dca + - 623f3eb7aa48 - cf34c344508d + - 2e8f945f7285 + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - 399da6b5ec21 - ae8c4b2488e7 - 503bcd6ebe4b - - 399da6b5ec21 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -133,8 +133,8 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - b722161a845a - f768f6183386 + - b722161a845a - bce29ec10b78 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -148,12 +148,12 @@ tools: - name: text_processing owner: bgruening revisions: + - f46f0e4f75c4 - 9ff72e942410 + - a6f147a050a2 + - ddf54b12c295 - 0a8c6b61f0f4 - d698c222f354 - 74a8bef53a00 - - a6f147a050a2 - - ddf54b12c295 - - f46f0e4f75c4 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index 90979a739..a06682aa4 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -2,9 +2,9 @@ tools: - name: breseq owner: iuc revisions: + - 82fb5e3bb93e - 85c57cc9b558 - 0d18a3ba2d1c - - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -16,29 +16,29 @@ tools: - name: freebayes owner: devteam revisions: - - ef2c525bd8cd - - 04fa42777df9 - 57def2d7c093 - - 156b60c1530f + - 04fa42777df9 + - ef2c525bd8cd - a5937157062f + - 156b60c1530f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 791f73caa0c8 + - e61c9ac190ad - 435b157bed6d - 09d6e4693887 - - e61c9ac190ad - - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: + - 3b4b2121842f - 65432c3abf6c - - dfadc322b065 - 074d44697036 - - 3b4b2121842f + - dfadc322b065 - 03627f24605f - e1461b5c52a0 - 4805fe3d8fda @@ -47,26 +47,26 @@ tools: - name: lofreq_filter owner: iuc revisions: - - 7dfca164d2e3 - 9cb929f21cfa + - 7dfca164d2e3 - 701d134358ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: + - 971e07ca4456 + - f4473557ffc7 - 426d707dfc47 - c27549b9aa1f - - f4473557ffc7 - - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - aa35ee7f3ab2 - - dbd9f2db9ed8 - cdaab621d454 + - dbd9f2db9ed8 + - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -84,11 +84,11 @@ tools: - name: snippy owner: iuc revisions: - - fa016f1eea1a + - c9a8ef2aa380 - 5bbf9eada9c2 - - d220115f882b - 9bccc8404a3c - - c9a8ef2aa380 + - fa016f1eea1a + - d220115f882b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -130,19 +130,19 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - 40f0591deda0 - ee4a90760848 - 3b1e7c170b10 - - 40f0591deda0 - - e7aff4a85df5 - 32f14a2723ec + - e7aff4a85df5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - adc0645b945c - 02d81b994ef5 - 4934c0ac6197 + - adc0645b945c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_somatic diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index e73ae9238..9dfca695f 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,13 +2,13 @@ tools: - name: bcftools_annotate owner: iuc revisions: + - e075b1be5abb + - 3f62d4939d54 - b7ea370b8f5d + - 6a88248893c4 - 8a2e296c07ef - 265fe0f9ea64 - ebe5fc018e72 - - 6a88248893c4 - - e075b1be5abb - - 3f62d4939d54 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 + - c37b684e7f4e - 21687e35f066 - 544cb432072b - - f0d44631365f - 22637b1a55bf - - c37b684e7f4e - b03984136ce4 + - 0fba2c15b40d + - f0d44631365f 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: - - 8ca3647c90fd + - bf1f4994f104 - 8627b2b383b4 - 6d35a3780bfd - - 3a7084316a6e - - 0238f68ad641 - - bf1f4994f104 - - 8408bffd5616 - 01d6b7d6365e + - 8ca3647c90fd + - 8408bffd5616 + - 0238f68ad641 + - 3a7084316a6e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -58,12 +58,12 @@ tools: owner: iuc revisions: - d144af39073a + - 6b6c992d3a14 - 08296952d12f - - f430a1ec7ee4 - 9b5abbf50d23 - - 6b6c992d3a14 - - 81426b3cf18b + - f430a1ec7ee4 - 03e0645395d2 + - 81426b3cf18b - 62ca6da715bf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -76,13 +76,13 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - d37e313a41be - 1829900b5dcd - - d3081540d175 - e522022137f6 + - 95c6f3f4c77f + - d3081540d175 + - d37e313a41be - 147de996e34f - 2363ef414c9b - - 95c6f3f4c77f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -94,13 +94,13 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 348cd212dbad - - cacc9970727a + - b14ff40958cb - 1137ce8efc1e - - 92c0aff8b53e - - 09f37afb3621 + - cacc9970727a - 9b29129fb491 - - b14ff40958cb + - 348cd212dbad + - 09f37afb3621 + - 92c0aff8b53e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -114,9 +114,9 @@ tools: revisions: - 55c0e906c14c - 367ba501b6eb - - 4935320a59a8 - - de68c11034f6 - 1f2183a23823 + - de68c11034f6 + - 4935320a59a8 - ecc9192912b8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -129,12 +129,12 @@ tools: - name: bcftools_csq owner: iuc revisions: + - f01b2c9506b9 - 64a8f7dae3ad - - 7cbf3c66d4ad - - 6c790a091c7c - 039ea3f1dea9 + - 6c790a091c7c + - 7cbf3c66d4ad - ae68ceb4cca3 - - f01b2c9506b9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -147,12 +147,12 @@ tools: owner: iuc revisions: - 33bd9301568c + - 277719af4dd7 - 656a916779fe + - cdb7b4927742 + - 6ea7170a016d - e7452697afd9 - 963a3635b2e1 - - 6ea7170a016d - - 277719af4dd7 - - cdb7b4927742 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: - - 26d97cdd5410 - - b7f0f59baa7e - - 501bfb078342 - a1213a0b7b66 - - a29a2f40b665 + - 501bfb078342 + - b7f0f59baa7e - 3eac729e66c9 + - a29a2f40b665 + - 26d97cdd5410 - 5a321fab1fe4 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 - - 63aabc920911 - - 5f27e814a119 - 97d19c008d15 - - c803c34361e0 + - 63aabc920911 - 81e4014fa809 + - 5f27e814a119 + - 768d04526638 - d7d1663559e9 - 709dd8291b83 + - c803c34361e0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -201,12 +201,12 @@ tools: - name: bcftools_merge owner: iuc revisions: - - 85ee7e6c4204 - b1eba148b35b - - 2215287d5cc9 - - b931e65638b8 + - 85ee7e6c4204 - 86296490704e - 7ba36babba2d + - 2215287d5cc9 + - b931e65638b8 - af163c712539 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -219,15 +219,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - cf06b44624c7 - - 9c711df3258d - - 37757ffb4c5f - - ce9396ddcb2b - 31ea13dfe5e6 - f506df85c652 - - 03191140c66a - - 4e1d23e5c691 - 5660b21a0dbd + - 37757ffb4c5f + - 4e1d23e5c691 + - ce9396ddcb2b + - 9c711df3258d + - cf06b44624c7 + - 03191140c66a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -239,12 +239,12 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 021693fdadaa - - 48291658fdf6 - - ebb2e12a6de1 - - a404f786a94c - 6deb4d549bc9 + - a404f786a94c - 19905c025d2a + - 48291658fdf6 + - 021693fdadaa + - ebb2e12a6de1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -256,13 +256,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 97e8145d7e30 - - 5ad5d4243987 + - 69d8b7567281 + - 71c78e0eea52 - be6b217710af - - c450406f722b + - 5ad5d4243987 - f7879f1e77f9 - - 71c78e0eea52 - - 69d8b7567281 + - 97e8145d7e30 + - c450406f722b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -274,13 +274,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: + - 2514e684f8a3 + - d31a2e310a52 + - 0fe007201caf + - 89720ec3d58e - 79f7a1acc2cd - cc7f9a4e186b - 52f9e4a660e3 - - 89720ec3d58e - - 0fe007201caf - - 2514e684f8a3 - - d31a2e310a52 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: - - 1411bef27a75 - 80e6e399ccd0 - - 026a989b7cee - - 75ddd081f608 - 230e424bde67 - - 99f4a81a47be - 0a62420cb9cd + - 75ddd081f608 + - 026a989b7cee + - 1411bef27a75 + - 99f4a81a47be 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: - - 5acfca5a76af - - c01be0ab9806 - ba20340426fe - - e493702b19eb - 5808f77b2bb6 - bca7ce81688f + - c01be0ab9806 - 444e6a756c35 + - 5acfca5a76af + - e493702b19eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -328,12 +328,12 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - f2482aa4862e - - d52b8947b269 - 12152af85697 - - 157ffcdd3fa7 - - 7fe09ad6a939 - 4d236c696844 + - 7fe09ad6a939 + - f2482aa4862e + - 157ffcdd3fa7 + - d52b8947b269 - 68fec03a63b7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -346,13 +346,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 0e5d11004815 - 8dbce095986c + - 0e5d11004815 - 29ba253e2e05 - - 8f2fc0ab30fb + - cbe39e530cbf - 27e2611639a9 + - 8f2fc0ab30fb - 6f8e223f78f3 - - cbe39e530cbf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -364,13 +364,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 88bb477f45f7 - - af36eb5418fe - - a8630d4fbaf8 + - e0a856def0b0 - 3ff5654b4e7d + - af36eb5418fe - a367a15c6de5 + - a8630d4fbaf8 - 9708e3086f32 - - e0a856def0b0 + - 88bb477f45f7 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: - - 31c096c6b156 - - 5c9729d54721 - - 6ce175385dd9 + - 03e30f06f15f - 96d0145c041a - - 2f4eef1f0d22 + - 5c9729d54721 - 4ed46189d6c6 - - 03e30f06f15f + - 31c096c6b156 + - 2f4eef1f0d22 + - 6ce175385dd9 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: - - 09f5e45a8212 - - a1aad8b559c6 + - 11af7fce71cf + - 40daf124be88 + - 46eb13bc2c73 - 2c4941386820 + - a1aad8b559c6 - 262bba5b90ef - - 46eb13bc2c73 - - 40daf124be88 - - 11af7fce71cf + - 09f5e45a8212 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: - - 882b2e649602 + - 743cd1472aeb - f272b8ba0983 + - 8cb121b6a1d2 + - 6cbb9c47795c + - 882b2e649602 - 0594ea1417c8 - - 12038f59c0f4 - 4b796b58938b - - 6cbb9c47795c - - 743cd1472aeb - - 8cb121b6a1d2 + - 12038f59c0f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -437,13 +437,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - 18cf9de1cf73 - - eccb508bb678 - - cced6715f926 - 238f78e38a8b - - dba06328556a + - eccb508bb678 - adee7e8b746f + - cced6715f926 + - 18cf9de1cf73 - 8c3ff4ef1190 + - dba06328556a 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: - - c9935c9e8a24 - - 9f36041495a3 - - e0ad88dec40d - 3ce32adc55b2 - - e53501abf992 + - 9f36041495a3 - f64e7ca2efd2 + - c9935c9e8a24 + - e53501abf992 - a850902cac64 + - e0ad88dec40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -475,11 +475,11 @@ tools: revisions: - 79489d5685dd - d43eb39b989e - - fd3539749127 - - 4db0695a6fc7 - - 8057cf55fa41 - d68c43202172 - b7be725976b6 + - fd3539749127 + - 8057cf55fa41 + - 4db0695a6fc7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -491,13 +491,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 1ccf0e7fb4f6 - - 6a636d58dfc2 - - b0d39ef600a7 + - 58091e1be01b - 5296d26b0373 - 78cd8b69da4c - - 58091e1be01b + - 1ccf0e7fb4f6 - bdc67eeb0bc9 + - 6a636d58dfc2 + - b0d39ef600a7 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: - - b641062a2587 - b17394940c7a - - a2f8dc22d7c0 - 4d3ce9dc1525 + - a2f8dc22d7c0 - baa8823f8073 - e8af591435d1 - '388983871932' + - b641062a2587 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -527,12 +527,12 @@ tools: - name: bcftools_view owner: iuc revisions: - - 59fa8742285e - - abc3ced31cd1 - d1f8f55f564d + - 59fa8742285e - 3a233c8eb814 - - 38d75661c235 - e6b5cbbf449b + - 38d75661c235 + - abc3ced31cd1 - 3ca3de4e5291 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -552,29 +552,29 @@ tools: - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives owner: devteam revisions: - - a8a4f94aa321 - 57a16b310fe8 + - a8a4f94aa321 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes owner: devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -587,8 +587,8 @@ tools: - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck @@ -615,44 +615,44 @@ tools: - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - 6b935ab36d7b - - eae7c08ebb6f - fa24bf0598f4 + - eae7c08ebb6f + - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten owner: devteam revisions: - - f285aa6bdcfb - b24e368ae7b1 + - f285aa6bdcfb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -672,8 +672,8 @@ tools: - name: vcfprimers owner: devteam revisions: - - d226a7327946 - 17096387c0e6 + - d226a7327946 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample @@ -686,15 +686,15 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 958b6484a7f1 - 2ba3b87f904f + - 958b6484a7f1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort owner: devteam revisions: - - 5b7120c66efc - dd44c3f416c3 + - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 25e27058a..f9f4825fa 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,10 +2,10 @@ tools: - name: abricate owner: iuc revisions: + - 4efdca267d51 + - 78c75f134c16 - 3f3e247c053d - c2ef298da409 - - 78c75f134c16 - - 4efdca267d51 - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -36,15 +36,15 @@ tools: - name: annotatemyids owner: iuc revisions: - - b5d8e5475247 + - f29602ae449e - 3e1f6f6d557e - - cd2480f35935 - - 133f36c29579 + - b5d8e5475247 - 4f2967b27e67 - - fe3ca740a485 - 1aae04680c4b - - f29602ae449e + - cd2480f35935 - 44018dd6b447 + - 133f36c29579 + - fe3ca740a485 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -57,9 +57,9 @@ tools: - name: augustus_training owner: bgruening revisions: + - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 - - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus @@ -79,8 +79,8 @@ tools: - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - 8fd427007e93 + - 7355bbf5e05f - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -106,9 +106,9 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf - - d9c3016f7283 - 63662ae295d6 + - d9c3016f7283 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -126,32 +126,32 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 9f2455341fac - - b6b5cd37f2a2 - - 756376aeb1ae - 3bbe70fef6df - - 14f588312c56 + - 756376aeb1ae - 582fd74dc2a1 + - b6b5cd37f2a2 + - 14f588312c56 + - 9f2455341fac tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 0ffe5be70caf - - 73428a792541 - 989f7c061f35 - 1691af4a0d17 + - 73428a792541 - a230ea445788 + - 0ffe5be70caf - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: + - e94187d661df + - 494f0bb4a993 - b69c46064ec7 - 5a5ae61da69c - - 494f0bb4a993 - - e94187d661df - 30f08d74024f - 563a19373357 tool_panel_section_label: Annotation @@ -159,11 +159,11 @@ tools: - name: funannotate_predict owner: iuc revisions: - - 1bc5a03faf2e - - f31125bb85ea - 7abc5f6dd595 + - 1bc5a03faf2e - f77d7b685bb3 - 2bba2ff070d9 + - f31125bb85ea - d6c7106b7b2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,11 +171,11 @@ tools: owner: iuc revisions: - fed64e676186 - - 54961e026fe4 + - d3af38b9c7e1 - 520e30695ec3 + - 54961e026fe4 - b3cf4684e9c7 - 52af33194019 - - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -187,8 +187,8 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 07d7991bf205 + - 2aea122fbd25 - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -201,10 +201,10 @@ tools: - name: goseq owner: iuc revisions: - - ef2ad746b589 - - 8b3e3657034e - 602de62d995b - 43798b4caee0 + - ef2ad746b589 + - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -229,9 +229,9 @@ tools: - name: interproscan owner: bgruening revisions: - - 98cafcbd2578 - - c55643c3d813 - 74810db257cc + - c55643c3d813 + - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -256,16 +256,16 @@ tools: - name: maker owner: iuc revisions: - - 3c1a01127868 - d46d803ca6cc + - 3c1a01127868 - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 033755194fe9 - 624606f7c996 + - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -289,10 +289,10 @@ tools: - name: prokka owner: crs4 revisions: + - 8a22554cdde2 - d643e3b03500 - - a17498c603ec - bf68eb663bc3 - - 8a22554cdde2 + - a17498c603ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -304,8 +304,8 @@ tools: - name: repeat_masker owner: bgruening revisions: - - 3f987772e283 - ba6d2c32f797 + - 3f987772e283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler @@ -324,29 +324,29 @@ tools: - name: snpeff owner: iuc revisions: - - cfcf33df7fc0 - - 5b80f544c67f - - 5c7b70713fb5 - - 9473cd297a76 + - 5a29ab10dba6 + - 68693743661e - 268d162b9c49 + - 5c7b70713fb5 - 8f92c2b26e6d - - 68693743661e - - 5a29ab10dba6 + - cfcf33df7fc0 + - 9473cd297a76 + - 5b80f544c67f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - 09d6806c609e - - 5fab4f81391d - 2b3e65a4252f + - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -358,22 +358,22 @@ tools: - name: tbprofiler owner: iuc revisions: - - 2c68b0c38785 - - ac8250086ac3 - - ba6f87115e13 - 809dfc93d593 - - e1a9d6fd258d - - 200c378d85f3 - 037a11682176 - - 45083d070fb8 + - 200c378d85f3 + - 2c68b0c38785 - 37213cf56392 + - e1a9d6fd258d + - 45083d070fb8 + - ba6f87115e13 + - ac8250086ac3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: trna_prediction diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index fbc372e7d..c0617e8d8 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,25 +2,25 @@ tools: - name: abyss owner: iuc revisions: - - 0e93176640ac - - 553bfe8bd0b5 - 841084c5fc46 - - a929ce596a34 + - 7547fcab5d19 - 890b794c997d - - 8f1b150a2487 - fa5259cc561b - - 7547fcab5d19 + - a929ce596a34 + - 0e93176640ac + - 8f1b150a2487 + - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 21e491ad532a - - 94fe43e75ddc - - ddddce450736 - b2860df42e16 + - 94fe43e75ddc - b9e31c5c01c7 + - ddddce450736 - 067592b6b312 + - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -33,11 +33,11 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - - faee8629b460 - 5258e18bbe23 - - a7f16f24e9a1 - 3371c5bdc17a + - faee8629b460 + - 22286dab5aa1 + - a7f16f24e9a1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,29 +49,29 @@ tools: - name: busco owner: iuc revisions: - - 2a5b8b9936bf - - e824f5d958d0 - - 46ae58b1d792 - - 0d243f458b53 + - 41030a6c03b7 + - cf13a1e03e5b - 1e62c28ba91d + - 46ae58b1d792 + - 4048d82f0c88 - 2dd755c1c6ff - - 5ecdeca79a0d - - bb935709506a - - 94170eee0ad8 + - e824f5d958d0 - 1440ae06552f - - cf13a1e03e5b - e4bd1e99bacf - - 41030a6c03b7 + - bb935709506a + - 2a5b8b9936bf + - 5ecdeca79a0d + - 0d243f458b53 - 602fb8e63aa7 - - 4048d82f0c88 + - 94170eee0ad8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 86f150c8019d - 5732f959936a - c5b7390290b1 - - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -83,37 +83,37 @@ tools: - name: flye owner: bgruening revisions: - - e27815e82dd4 - - 276f5d8712d5 - - cb8dfd28c16f - 1ce9b1d72ec3 + - 276f5d8712d5 - 8d4f03b5fe9d - 3ee0ef312022 + - cb8dfd28c16f + - e27815e82dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - 01210c4e9144 - b2f674562a18 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 7348b69e5109 - - 8b330a577046 - 06bcf65179fb + - 8b330a577046 + - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 3ef480892a9f - 3fba9c77550a - 690c2caa367e - 5127a713de83 + - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -125,21 +125,21 @@ tools: - name: hifiasm owner: bgruening revisions: - - 0ee0c3089254 - - 41cea2aa2dce - - 5f625c63b8bc - - 366a11d316a7 - - 71740308d412 + - f3c89da3af16 + - 60024a528cbd - ec9e21e9c71b + - 71740308d412 + - 5bec28269d95 + - 5f625c63b8bc + - 0ee0c3089254 + - 6505bd37670d + - 2061fb3b81b4 - 3f7be05a1597 - 9ef6920c3089 - - 045c7c3d8e59 - - 5bec28269d95 - - f3c89da3af16 - da9d8bf98802 - - 60024a528cbd - - 2061fb3b81b4 - - 6505bd37670d + - 045c7c3d8e59 + - 41cea2aa2dce + - 366a11d316a7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -157,18 +157,18 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - 14ddfc8ffb93 - de387b2b2803 - 7518ee87b53d + - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - f8113c25bc6b - - 9d79beb19ac3 - 39edec572bae + - 9d79beb19ac3 + - f8113c25bc6b - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -176,20 +176,20 @@ tools: owner: iuc revisions: - 29dabd8db6f2 - - eadfd71dde37 - 51c2360aa807 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 2ecf5a570907 - e731ea24e48d - - eb7a370f6588 - - fd128c111ab0 + - 2ecf5a570907 - 606b09cc9860 - f338e9942b27 + - fd128c111ab0 - 3ca2d2a9068c + - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -217,9 +217,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 7c2f5268d01c - 15200570e926 + - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -231,33 +231,33 @@ tools: - name: pretext_map owner: iuc revisions: - - 02831bf9e95f - - d256a51a656b - - dfb8a4497339 - bbe19ef04a74 - - 2b16ba799da9 + - 02831bf9e95f - 511e5e3cd55e + - dfb8a4497339 + - d256a51a656b - 8fef980d48b5 + - 2b16ba799da9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - a315c25dc813 - - e9bd16ba5ebd - 76d4cbefff85 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - 7594365c546b - - 59db8ea8c845 - - ebb0dcdb621a - - 6fcbee531de6 - - 342a1d1fed7b - 3061c8b029e5 + - 6fcbee531de6 - 72472698a2df + - ebb0dcdb621a + - 342a1d1fed7b + - 59db8ea8c845 - 875d0f36d66f - 675488238c96 tool_panel_section_label: Assembly @@ -265,41 +265,41 @@ tools: - name: racon owner: bgruening revisions: - - a199cd7ac344 - cd06929b224b - - d865b62f501c - - 39bed8de8017 - 78c533842eeb + - a199cd7ac344 + - d865b62f501c - aa39b19ca11e + - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - 2b2a352488fa - - f11b994b7eb2 - 33b7d8481a76 - - 3edba9afc9bc + - f11b994b7eb2 - f8564b2d7f63 + - 2b2a352488fa + - 3edba9afc9bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - 378e55aeeb25 - - 53c2bc8c2ae3 - - e122f9101584 - ef69617ecb42 + - e122f9101584 - 1d06c8b38e77 + - 53c2bc8c2ae3 + - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - 9a22227bb6d0 + - f77f7a7f3b83 - ab5b7f6b7198 - ba7b0f11e470 - - f77f7a7f3b83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -311,31 +311,31 @@ tools: - name: shovill owner: iuc revisions: + - ad80238462c1 - 83ead2be47b2 - - f698c7604b3b - - d9f6a00b6db7 - 865119fcb694 + - d9f6a00b6db7 + - f698c7604b3b - ee17a294d3a3 - 196a599ec43d - - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: + - 5a0ddb4dc3a4 - 5e0825476fb7 - 24e471d13fe9 - - 5a0ddb4dc3a4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - 7490b213baa9 - - 051fd2db8a27 - 904bf932cf78 - - 1fc82fe7ebef + - 051fd2db8a27 - 1bb12736175c + - 1fc82fe7ebef tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades @@ -351,9 +351,9 @@ tools: - name: spades_metaplasmidspades owner: iuc revisions: + - 21da31ed41a1 - b8002c3f7141 - 6b5a5842531e - - 21da31ed41a1 - 8d4b90bf9caf - e5a3b75a271f tool_panel_section_label: Assembly @@ -361,80 +361,80 @@ tools: - name: spades_metaviralspades owner: iuc revisions: + - 9de69775f512 - 328aa71f0f3c - - f1532cb33c75 - - 86f66ab58e14 - 2a10645aeadd - - 9de69775f512 + - 86f66ab58e14 + - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 6aad515a5270 - - 85fb02c43042 - 340bc17f49cf + - 85fb02c43042 - e41dcb0e913b - 1708851f8804 + - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - d159735a6a9f - b65a43f70b99 - b3490b036c5a - - 249f6a28c751 - - d159735a6a9f - d5fb354f745d + - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - b7829778729f + - 7897763d14ec - 9006e5836729 - - dd7ad84f3943 - 33368fec3b70 - - 7897763d14ec - d2d1df21dfb9 + - dd7ad84f3943 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - 505a9833ab5d - - 6f4c8ad6ea01 - - 8f631679571f - 189e837009c9 + - 6f4c8ad6ea01 - ced385aa976d + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - - 9ded6109434a - - 356afed970b4 - 19bdfd1e6fe3 + - d40ed4eb0c0e - e59bee4565b3 + - 356afed970b4 + - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 80a17897564d + - 4688ae3b49b5 + - 6dd935e4984b - b23249f81bc4 + - 80a17897564d - ebd801e712bc - - 6dd935e4984b - - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - b64696992ee9 - - 937ea677d437 - cb1e3db43020 + - 937ea677d437 - 59bd28f6265d - b5e35a2ca4f3 tool_panel_section_label: Assembly @@ -442,38 +442,38 @@ tools: - name: trycycler_subsample owner: iuc revisions: + - 6015aa0303f2 - cb4768eeca3b - 383bb5ad32e2 - - 6015aa0303f2 - - 2628f6790eda - 05bd7504fdb2 + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - e92675014ac9 - - 9e3e80cc4ad4 - 0a3a602cd1e3 - - 6e26c9afd301 + - 9e3e80cc4ad4 - 8f9f06995f98 + - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 8d09f8be269e - 5da9a0e2fb2d + - 8d09f8be269e - 920677cd220f + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 82398ba86ba7 - - 37d88f41c810 - 4a53b89fa703 + - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index 13d9c2d3f..bd3562396 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,24 +2,24 @@ tools: - name: integron_finder owner: iuc revisions: - - 4768f7f8e93f - 1ae00120dd24 + - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - 8e8dc9a1e3e5 - - 1f5641a52664 - - ded48b36f3b7 - 31812e7a1315 + - ded48b36f3b7 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: + - 17fcac7ddf54 - 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 70adf3e9d..26700f340 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -3,7 +3,7 @@ tools: owner: iuc revisions: - 204a131e47db - - 159b04e36791 - 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 42a92364d..a9822b853 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -3,15 +3,15 @@ tools: owner: iuc revisions: - 0a5c785ac6db - - a1a923cd89e8 + - a68aa6c1204a - e19bebe96cd2 - dde39ba9c031 - - a68aa6c1204a - - b28e0cfa7ba1 - - ce3c7f062223 + - a8eabd2838f6 - 87ee588b3d45 - - 589e7e57fd6d + - a1a923cd89e8 + - b28e0cfa7ba1 - 07e8b80f278c - - a8eabd2838f6 + - 589e7e57fd6d + - ce3c7f062223 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 ece6fb70a..3a46bb36b 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -10,21 +10,21 @@ tools: revisions: - f921014aba5a - 62c9df8382c2 - - 54f751e413f4 - e8ac2b53f262 + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - 2889433c7ae1 - - a52d2d93e595 + - e25d3acf6e68 - 0e3cf9594bb7 + - d999e774072a - acf4e47b734c - - 6f386c5dc4fb + - a52d2d93e595 - 5edc472ec434 - - d999e774072a - - e25d3acf6e68 + - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 6baf5dcf2..d7d90728a 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -2,11 +2,11 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 27ee142314a9 + - da6bd1975a71 - 6ca543ec1bf8 - - 710301bc46fa + - 27ee142314a9 - 095ad4d096d1 - - da6bd1975a71 + - 710301bc46fa - f4230f116196 - c8cdde00b105 tool_panel_section_label: ChemicalToolBox @@ -80,8 +80,8 @@ 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 @@ -106,47 +106,47 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 3b8a9d5ced85 + - 0fac8e2afc13 + - bfb65cb551d8 - 88076940fa94 - 79cfd9ead848 - - bfb65cb551d8 - - 0fac8e2afc13 + - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - f5d979cb4b54 - - eb6564a60136 - - d532b7e5f64b - 55918daa5651 + - d532b7e5f64b - 715cd0e87781 + - f5d979cb4b54 - b46d4b4d995c + - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a - - fdf2cc80adb5 - - 5579659312e6 - dae135dfd519 + - 5579659312e6 - f26afd1b7104 + - fdf2cc80adb5 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: + - d1d0efda35c0 - bc31d02be922 - 319a28774da9 - - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 4da9ee404eab - 070e3ecc3fda + - 4da9ee404eab - 2c349b027a01 - ed736e6eee39 - cac1886249a2 @@ -155,42 +155,42 @@ tools: - name: gmx_sim owner: chemteam revisions: - - 807aa4c9293d - - da8753545526 - c0c9a5024177 - 2e219a2d9327 - - d1f803b5943c - - f197e34c33a9 - - 73008ef1f487 + - da8753545526 - 525ca7c8065f + - 73008ef1f487 + - 807aa4c9293d + - f197e34c33a9 + - d1f803b5943c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - 2c8ed1b52bf7 - - 7568ae18908a - - 27ea4e1a3f95 - - 61094e01eff9 - c4fbab8e03c5 + - 61094e01eff9 + - 27ea4e1a3f95 + - 7568ae18908a - 1809414a9454 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: + - ccfbd956a2d3 - 79e8ab8f1e81 + - ba83f0923369 - 730ef07b90ae - - ccfbd956a2d3 - d7ec25187599 - - ba83f0923369 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 @@ -234,10 +234,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - - 9b48456a96fe - bf99565cec1f + - 85fad59f8168 - d4c67ced6abc + - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 5ea7ed273..e8bd01e13 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - fa56d93f7980 - - c97a786e8fb5 - 163688bb8f73 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -16,18 +16,18 @@ 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: + - 424aefbd7777 - 640d3af5d833 - - f5d67c722d67 - 495a4173006f + - f5d67c722d67 - 86e2413cf3f8 - - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator @@ -40,7 +40,7 @@ tools: - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 4d3dcf5b5..518e729a3 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - 705ebd286b57 - cd6da887a5f4 + - 705ebd286b57 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 33151a38533a - - 25136a2b0cfe - 90981f86000f + - 33151a38533a - 830961c48e42 + - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -26,14 +26,14 @@ tools: owner: bgruening revisions: - 0046692724f9 - - baabc30154cd - 6cbe2f30c2d7 + - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index a10d6337b..757ac9b06 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -8,30 +8,30 @@ tools: - name: biom_add_metadata owner: iuc revisions: + - 4a6ee918c13a + - 367b1ed91207 + - e3cbd2287f63 + - 5e1240a87bcb - dad9da48a09a - 0b3c3ad92827 - - 5e1240a87bcb - - e3cbd2287f63 - - 367b1ed91207 - - 4a6ee918c13a - - 6ef0b5664c69 - a3b86937ead6 + - 6ef0b5664c69 - f3a19509108a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 1b5fc03380d4 - - 33c99804a32f - - e177a8ea0bf1 - - e525f9ffb9ac - 54ccb7e1f49a - - bd46669113b9 - - 501c21cce614 - - a4db66553a61 - 584008e574b2 + - 501c21cce614 - 72ed72122deb + - e525f9ffb9ac + - a4db66553a61 + - e177a8ea0bf1 + - 1b5fc03380d4 + - bd46669113b9 + - 33c99804a32f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -49,8 +49,8 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta @@ -64,8 +64,8 @@ tools: - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa @@ -124,11 +124,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 19e45916daf9 - - 26c6706bfb07 - - 92ac8e086317 - b9b385097f13 + - 92ac8e086317 - 63769c4217a7 + - 19e45916daf9 + - 26c6706bfb07 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 89f463a9e..ba80330d8 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,205 +2,205 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 268e91e540ee - - 5f6d123679f4 - 29451af70c52 - - c929a006727f - - a1ca9bccc7f2 - e821645ef8fc + - c929a006727f - de72ba3ed6f2 + - 268e91e540ee + - 5f6d123679f4 + - a1ca9bccc7f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 2d2cf5c1ea8a - - bb1e4f63e0e6 + - 5d11599b8a7d + - 0e49b109abc2 - 12af64f93288 + - 2d2cf5c1ea8a - 0e143b4c3987 - - 0e49b109abc2 - - 5d11599b8a7d + - bb1e4f63e0e6 - 7a7fd0f5f15d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 7c1beb6d6eca - 1d848bc4585f + - 195e98217334 - c06951d10364 - 81b1e3e1fc6c + - 7c1beb6d6eca - dc059492a995 - - 195e98217334 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: + - a67ac707496a + - 93eb012d9eed - bfff7454b59a - - 07418a30ed01 - 26e7304d6737 - - 93eb012d9eed - - a67ac707496a - 3d211717a775 + - 07418a30ed01 - 71aa86af6762 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - dd0b7398bb96 + - b8858746dc1f - 56d5b797ce84 - - 29fcfd36e90a - - 5be24eba848d - 26983857c91a - 2bc10a9ca58b - - dd0b7398bb96 - - b8858746dc1f + - 29fcfd36e90a + - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7e6bcd2e5128 - - c3e012dfe21f - - 7ef978dc1b8a - 72bfafe3330b + - e6d0bff01239 + - c3e012dfe21f + - 7e6bcd2e5128 - ee3a1b0f45f1 - 9384cd033f30 - - e6d0bff01239 + - 7ef978dc1b8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - d9a637e83828 - - 514fa53b5efb - fd1275e01605 - 167788df3b46 - - fb9cf9c97ec4 - - b73e213add0c + - d9a637e83828 - a60c359ec43c - 9470f29702f8 + - fb9cf9c97ec4 + - b73e213add0c + - 514fa53b5efb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: + - a02cfa31e9cb - ca0616bb2cdf - - 86febdcc4283 - 2c37ce318bc3 + - 5bffaa8354a1 - c34d11ea4ba6 - - a02cfa31e9cb - e479c7ca5570 - - 5bffaa8354a1 + - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 192ef85c0b0b + - 78f405266706 - 2d466b530754 + - 01fb6a7654e6 + - 004aea905d4d - 1fcb7adc39b8 - 69a8621ca2f0 - - 78f405266706 - - 004aea905d4d - - 01fb6a7654e6 + - 192ef85c0b0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 3c9f0c486cca - 137c4beed34b - - 459cfa861f0b - - 2f9e4843f480 - d9ce4897dbb2 - - db940c262830 - - d580d6acd1df - 9ecba5e225a6 + - 3c9f0c486cca + - 2f9e4843f480 + - d580d6acd1df + - 459cfa861f0b + - db940c262830 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: + - fd408d755394 - 32e451def88c - - bd7db9e2f2cb - bad3ca889618 - - fbe773640707 - - 2c66e43f1c86 - - fd408d755394 + - bd7db9e2f2cb - f264afa9fa6f + - 2c66e43f1c86 + - fbe773640707 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 7fda5607e777 - 56bce3c82278 - 9368fbc49c8b - - 3b9d990a0a0e - 7e361d147872 - - 7fda5607e777 - - 4e12ea27f788 + - 3b9d990a0a0e - 231994413f89 + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: + - b1779366c8e9 + - c03c3384cd81 + - e65d16fb2724 + - d9114ef1c8a5 - 94ca68515826 - 4431f39ede55 - ce4ce3316f74 - - d9114ef1c8a5 - - b1779366c8e9 - - e65d16fb2724 - - c03c3384cd81 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - d57251071381 - - 793665fff0f8 - b88ebb3672a1 - - f8fc4e5aff9d - 4ed32329e0ed - 23f7c5f1fdaf - 2da482e408b8 + - f8fc4e5aff9d + - 793665fff0f8 + - d57251071381 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - ba6efa77fb79 - 512155688d98 - - 010e58e9d822 - - c60570fa602f - a4dfb122e52b - - 25d830337d31 - - ba6efa77fb79 - - a7849312d328 + - c60570fa602f - e4c7985d4585 + - 010e58e9d822 + - a7849312d328 + - 25d830337d31 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 443d9a9d6d11 - 69264da0ce77 + - 00d869ea03a1 - aa200e4f3939 + - 443d9a9d6d11 + - c899e0ccff8c - 4d678170d29b - 38e3f226248b - - 00d869ea03a1 - - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - aac8444d6681 + - d806504e96d9 - a2d70c4fd406 - 10301d137111 - 6662b1a8d326 - - aac8444d6681 - - d806504e96d9 - c361b12d207a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index 905857a5b..d11d5e1a0 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -2,8 +2,8 @@ tools: - name: obi_annotate owner: iuc revisions: - - f82cefbbcea5 - 3021b9f5809f + - f82cefbbcea5 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean @@ -23,8 +23,8 @@ tools: - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - fe7ec8a3d35e + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 3bf57dadf7cd - 76e69de726b2 + - 3bf57dadf7cd tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index caecd371d..58b655034 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 - dba489bfcd62 - ce385837c160 - 832c20329690 - - 63dd26468588 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 685df40a5..85a3f9836 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: + - d82648ad25a3 - 62f5fab76dfb - - 6da3972210ee - 29bdbc353f20 - - d82648ad25a3 + - 6da3972210ee tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 92c2d738a..4beed0354 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,30 +8,30 @@ tools: - name: cutadapt owner: lparsons revisions: - - 135b80fb1ac2 - - c053d4cad713 - - 4e5056fefd88 - 48f587c13075 - - 288f97432497 + - de6cebe3c043 - c4b82dce8335 - - 8665bcc8b847 - e4691e1589d3 - - de6cebe3c043 - - 093678460093 - - 44e2cc14f75b - 660cffd8d92a + - 8665bcc8b847 - c5e2e5902201 - 5915ea1ec9b1 - - 8c0175e03cee + - 4e5056fefd88 + - 288f97432497 + - 44e2cc14f75b + - c053d4cad713 - 49370cb85f0f + - 135b80fb1ac2 + - 093678460093 + - 8c0175e03cee tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: + - 9db07fd39f85 - 8889eb864cef - f666895cbebd - - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -71,26 +71,26 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - f81d4362b6c1 - ec0b5076173a + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: + - 0dbb995c7d35 - 9c620a950d3a - 56022eb50bbd - - 0dbb995c7d35 - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - dbf9c561ef29 - 65b93b623c77 - 1d8fe9bc4cb0 + - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -124,8 +124,8 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -138,8 +138,8 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 2ccb8dcabddc - 3e396e702cea + - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -153,23 +153,23 @@ tools: owner: devteam revisions: - 35e38452bb3f - - e39cc71d3ed6 - 249c8393f2d4 + - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - 74db4cffab1f - - 045f0e1043f7 - 54053ea6c77e + - 045f0e1043f7 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 @@ -190,58 +190,58 @@ tools: revisions: - d5e9e83cd3d8 - 09070cacefd8 - - 567d5b3c52b1 - 529bccd5e4a1 + - 567d5b3c52b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: + - 4bedca26c133 - 8abdedf55101 - 0b7ec11b3c7c - - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - bdf1ce174e39 - 736b8f6ee456 - 90858c306551 + - bdf1ce174e39 - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 07497255281e - 7ce1891db6f5 + - 07497255281e - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 + - f984bb114520 - b29d37ca9e41 - 02f8a17a4ebd - - f984bb114520 + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: + - 6027ef51ef91 - e246088b6e34 - 177f0621c266 - - 6027ef51ef91 - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 377ac2829eac - 73194cdd4f57 + - 377ac2829eac - 61b4cedc8934 - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ @@ -255,29 +255,29 @@ tools: - name: pear owner: iuc revisions: - - b4c6f054210a - 2f804526f5fd + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -290,11 +290,11 @@ tools: - name: umi_tools_count owner: iuc revisions: + - 8250ea3a1501 - b557acca0b56 - a535cf1e5da4 - e654095ab143 - 24013bf85a6f - - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -306,11 +306,11 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 7accf7407811 - - 27ac32a22ad2 - - f3759eec3018 - - 6a675c3aa610 - 828dba98cdb4 + - f3759eec3018 + - 27ac32a22ad2 + - 7accf7407811 - 9fa7803d1c51 + - 6a675c3aa610 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 c51d924f6..b014e8ba0 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c - - e41385662e5e - 7b4468117008 + - e41385662e5e - ce9cd02d5b88 + - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,65 +18,65 @@ tools: - name: fastqc owner: devteam revisions: - - 3d0c7bdf12f5 - f2e8552cf1d0 - - 5ec9f6bceaee + - ff9530579d1f - e7b2202befea + - 5ec9f6bceaee - 9da02be9c6cc - 2b0c9d9fc6ca - - ff9530579d1f + - 3d0c7bdf12f5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - - ad116ae3f4d9 - b6b54ba71bd8 + - ad116ae3f4d9 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 59003d0543cd - 7306ec78632a + - 59003d0543cd - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 8880fb74ef56 - - 1f296803dfa3 - a72af9de6bf5 + - 1f296803dfa3 + - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 1c2db0054039 + - 3d93dd18d9f8 + - bf675f34b056 - 5e33b465d8d5 - c1a4b5f3b432 + - 1c2db0054039 + - abfd8a6544d7 - 9a913cdee30e - - 75c93c70d094 - - bf675f34b056 - b2f1f75d49c4 - - 3d93dd18d9f8 - - abfd8a6544d7 + - 75c93c70d094 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - cd7e644cae1d + - 084bbd8ba7b8 - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 3b6522396..85c239a05 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 141612f8c3e3 - - 85ef5f5a0562 - 83a19df00eab + - 85ef5f5a0562 + - 141612f8c3e3 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index c2054cb65..e86d2178c 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -2,30 +2,30 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - 8f53b238a360 - - f2f3bc622a16 - 0c8f7322f8fc + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -38,8 +38,8 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -79,66 +79,66 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 2550239feed5 - 184aa4e686e2 + - 2550239feed5 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - b2c25142267e - cf61daf064fe + - b2c25142267e - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - da74170c55c7 - - 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: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -158,14 +158,14 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 8b48bb87e..ba4164156 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,8 +2,8 @@ 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 @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index dd5d3f734..76e7bd594 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,56 +2,56 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - b39347891609 - c1b437242fee - - e9df53a75f3c - 983bf725dfc2 - - b39347891609 + - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - 1c58de56d587 - - e063168e0a81 - 28587613264f + - e063168e0a81 + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - 69ebb7f46e45 - - 6ea73833cf67 - - aad3885b3216 - - 4df8de2d0e48 + - c441583adae5 - 9a776b080193 - - f5ea3ce9b9b0 - - 1790dcf3c32d - - 734abc7ac21d + - 6591f049cf7e - 83c7d564b128 - - c441583adae5 - - e407b9da183a + - aad3885b3216 + - 6ea73833cf67 - 5e6237d58b0c - - 6591f049cf7e + - 4df8de2d0e48 + - 4317d3cb6cba + - 734abc7ac21d - 653e89d73fc4 + - f5ea3ce9b9b0 + - 1790dcf3c32d - e08a7ad4378b - - 4317d3cb6cba - 7068f48d0ef9 + - e407b9da183a tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 34758ab8aaa4 - 75b3b3d0adbf - - 7863f1abcdda - 9aaa46d45472 - - 34758ab8aaa4 + - 7863f1abcdda tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 054483e27a35 - bfdc6a7ffd3a - af5eccf83605 + - 054483e27a35 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 1020ec4bd..689ce6b85 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 290a11559985 - - c4bde687c846 - 7f13dc906cb9 - - 4b519282a05b - - ae9994cf526f - 740057a5126d - - fd59d783248a + - c4bde687c846 + - 290a11559985 - a64dc31ab7f2 + - 4b519282a05b + - fd59d783248a - df7356989ac1 + - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -43,18 +43,18 @@ tools: owner: iuc revisions: - 53460afd5115 - - '566197475670' - ca7cb0eaad62 + - '566197475670' - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 391a4cc45fea + - d3a9e32672ec - 3d059e9c2fba - 10515715c940 - - d3a9e32672ec - - 391a4cc45fea - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -63,10 +63,10 @@ tools: revisions: - e3a675da7fd0 - 3b12bf9b4b87 - - 5fe1dc76176e - d0fc8b746d57 - 299307abd804 - 1acf88921176 + - 5fe1dc76176e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -78,8 +78,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - cf1df6b2220a + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -99,15 +99,15 @@ tools: owner: iuc revisions: - a6e57ff585c0 - - 6cd09d7b5f37 - - 4542035c1075 - - fd5dbf0f732e + - 667e17248bfe + - 2bb2e07a7a21 - ca2def38369c - - 836d1aa3e89a - 1cfc579079a6 - - 2bb2e07a7a21 + - 4542035c1075 + - 6cd09d7b5f37 + - fd5dbf0f732e - 112eb40ba6cf - - 667e17248bfe + - 836d1aa3e89a - 17359b808b01 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -126,9 +126,9 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - fe154a7af404 - 03c13085aecc + - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -140,15 +140,15 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - 62e3a4e8c54c + - 85da91bbdbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -160,9 +160,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 - 0a10fddd97d2 - 7c9417381ad5 + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -174,22 +174,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 4ac4e7083b7e + - 14e7c35f3d00 - 7dd841a32245 - 59fd173ac850 + - 4ac4e7083b7e - 2824d77cd8f8 - - 14e7c35f3d00 - 360df4999907 - - 326a3db8d9d1 - a1abfa420d9d + - 326a3db8d9d1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 83c573f2e73c - - 73b8cb5bddcd - 44608d0193ed + - 73b8cb5bddcd + - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 84644b2ba..a0fc89ef5 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index b8bc117eb..83120f572 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,45 +2,45 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 9edf8894a22d + - 29f66c353bcb - ed2cca6b5de4 - 921a2da49a0c - - 29f66c353bcb + - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - 78fb5e286609 - d404277cc87a - ec4b948dc6f0 - - 78fb5e286609 - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 977dc15add20 - 9e357a8b2ec3 - - 4d511437b1e5 - 03dd3c16ae4e - - 977dc15add20 + - 4d511437b1e5 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 77919cc3618e - - 3b5b54ed6392 - 0ba4f56a3613 - 41dbf4d162a2 + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e - 5308ca68ef3d - 9939786dd9c9 - 7babd8a46fe0 + - b63363075c2e 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 4242a2d8c..23966173c 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -10,8 +10,8 @@ tools: - name: 2d_feature_extraction owner: imgteam revisions: - - 0a53256b48c6 - 5791a7f65275 + - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features @@ -31,17 +31,17 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - dba87c4b32d3 + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - 85edbb7a436b - - f3360fbeda64 - 10eed33aa9b2 - b07f4839ca77 + - f3360fbeda64 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -54,16 +54,16 @@ tools: - name: count_objects owner: imgteam revisions: - - 5bf8eb50b280 - 664232d2a3f7 - b58447a2eed2 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - eb6c08714244 - 0e4dccaafef5 + - eb6c08714244 - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -77,9 +77,9 @@ tools: - name: cp_common owner: bgruening revisions: - - 670975e92458 - e7273daa5ae2 - 6070780813d9 + - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image @@ -102,71 +102,71 @@ tools: owner: bgruening revisions: - f2ed92b011a9 - - 11f177b1a59e - bace5a93a97c + - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f24c370e5ea4 - - d0178bdcd00e - f8fa0f6718a3 + - d0178bdcd00e + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - 3245681b2f6d - - ad271f78a87a - 31d195bedf6d + - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 87d4d92d7487 - b6eec6087271 + - 87d4d92d7487 - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - c09dcda1143f - - 6100a22bf4f2 - ff1a86a87364 + - 6100a22bf4f2 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: + - 667a513e67e4 - 3a05117669cf - b178453ea8d1 - - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - 2564f461de62 - a1a961c46d4b + - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 91e03287f285 - a32c3f810ade - 20dbb1f7ec7b + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 8536b1ae0254 - 5499dc6f8ac1 + - 8536b1ae0254 - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -181,48 +181,48 @@ tools: - name: cp_measure_object_intensity owner: bgruening revisions: - - 407925835dd9 - e52c75a28c4b + - 407925835dd9 - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - 79e10d12d90a - acf3aa487283 - d85f11570109 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - b76841ee5560 - - 035a58c7f54a - 80b200ae516b + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines owner: bgruening revisions: - - b44b081bcf37 - 91560258e972 + - b44b081bcf37 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - - 8083a87d2fdf - 3a3033222f61 + - 8083a87d2fdf + - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: + - 4ecf93628f97 - 33f4fa1413fb - 27edbb90ab2b - - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -234,8 +234,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index f964c2b4c..ba9d44b86 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -3,87 +3,87 @@ tools: owner: iuc revisions: - 78bbd17d0703 - - d6e72da3ec35 - - a38934e303b9 + - 3e4f434a69c6 + - f362150bef41 - e319b5b65879 + - e4ee04da1c19 + - a38934e303b9 - 1069f6db0a0e + - d6e72da3ec35 - 17f911830a8c - - e4ee04da1c19 - - 3e4f434a69c6 - - f362150bef41 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: + - 1ef5b6e3e09d - f91cfb73d369 - - 0135f1d487a0 - - 8f8df367470d - 72ddd32392cd - - 2b95d5c04908 - - 1ef5b6e3e09d - - 7fe36019c073 - - 9537184d421f + - 0135f1d487a0 - c88553ec696e + - 9537184d421f + - 7fe36019c073 + - 2b95d5c04908 + - 8f8df367470d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 - d7e79eb3bcb3 - fafb3d685fa9 - ad0dc9f4c9e2 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 3d18f8c3c0f6 + - 43aac8d29685 + - 8c05afb547fa - 6a1515bb0687 + - 94df24c6bc00 + - ee29337f905c + - 69797fa273c3 + - 28a6f1908fcc + - bd2a7d1316b9 - 7f1cfa4c0e32 - 9eaadf03e0df - - 94df24c6bc00 - - 43aac8d29685 - 8d36959b000d - - 8c05afb547fa - - 28a6f1908fcc + - 3d18f8c3c0f6 - ee2beb764a7b - - ee29337f905c - - bd2a7d1316b9 - - 69797fa273c3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5d6ed46cc101 - - 9f978da6528a - - 364f4ffec275 - d37ede8589b2 - - db536ad45f28 - - bcaa0d571ce2 - - 5671e1d3d5ee - - e3bb03cf207a + - 364f4ffec275 - c092052ed673 - - cb903c9dc33d - - 0893a1dbb807 + - db536ad45f28 + - 5d6ed46cc101 - 8858fa037a15 + - 0893a1dbb807 + - cb903c9dc33d + - e3bb03cf207a + - 9f978da6528a + - 5671e1d3d5ee + - bcaa0d571ce2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 230b05597996 + - 584beffa972b - f95f403841ad - - c5c9f02b6167 + - 38b91a3190cd - 3b6a16d82c1b - - 584beffa972b - - ed28dd32141c + - c5c9f02b6167 + - 045d6d00f606 + - 230b05597996 - e1a015876aa9 + - ed28dd32141c - 12d66d0d05ac - - 045d6d00f606 - - 38b91a3190cd - 49236b03e4fd 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 107dfea4c..d34b9f7d1 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: + - b8a457820315 + - 17e3b698dd52 - 0f1724dd59d2 - 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: - - ac092723240d - ba0c40780ecf - 374cb875d38a - - 22c2a1ac7ae3 + - ac092723240d - a513e3fbb4c5 + - 22c2a1ac7ae3 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 36b2fb579..695f57054 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,9 +2,9 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 772e0e89fc68 - - 66d7efc06000 - 522137aaa9c4 + - 66d7efc06000 + - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config @@ -18,83 +18,83 @@ tools: - name: keras_train_and_eval owner: bgruening revisions: - - 2af1346e68c9 + - e1317b5502fa - f1b9a42d6809 - 818f9b69d8a0 - - e1317b5502fa + - 2af1346e68c9 - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 05143043ca13 - 1588f9076e32 - - 8334dc98c48e - - 947c2eacccb8 + - 05143043ca13 - c80db5d6fd8c + - 947c2eacccb8 + - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - - 9991c4ddde14 - 25b46af53232 - 83228baae3c5 + - 9991c4ddde14 + - 1552b8cb4a94 - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 060ca94ac049 - - 53616c8b0865 - - 841a6cc5fc58 + - 1a53edc4b438 - a07ab242b0b5 - f3dfa4bdf87e - - 1a53edc4b438 + - 53616c8b0865 + - 060ca94ac049 + - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 40f4447733b2 - - 2fc89dcd41c8 - dc4b5fd604a6 - - 91c4e3331208 - d4808d5b83da + - 40f4447733b2 + - 91c4e3331208 - 927586a18553 + - 2fc89dcd41c8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 25ab6b4e376e - 36e8d6d5d01b - - e5a5ad882f1f - 7626ea9c2e1b + - 25ab6b4e376e - c6ae57f774c6 + - e5a5ad882f1f - 301e07345c93 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 4ed102b922cb + - 0630258dcf35 - 80852884053f - - 02d2be90dedb - - b7c3e9a3b954 - f9639b488779 - - 0630258dcf35 + - b7c3e9a3b954 + - 4ed102b922cb + - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - ec69cbe34b73 - - 14180f9c831e - caeb57858702 - 61634a87efc7 + - 14180f9c831e + - ec69cbe34b73 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 22fadf8dd..81e4b7b39 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - a6d65b0c67af - - 937aa69e715f - - 749c918495f7 - - 017aba02828d - - f6877ad76b00 - - cd659e8cc5fa - - 3ba8d4563129 - 03e9b2fbc005 + - 017aba02828d - 17062a0decb7 + - 3ba8d4563129 + - 749c918495f7 + - cd659e8cc5fa + - 937aa69e715f + - a6d65b0c67af + - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -29,11 +29,11 @@ tools: - name: bwa owner: devteam revisions: + - e188dc7a68e6 - dfd8b7f78c37 - - 64f11cf59c6e - 53646aaaafef + - 64f11cf59c6e - 3fe632431b68 - - e188dc7a68e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -47,40 +47,40 @@ tools: revisions: - 60afcc2c1d05 - 3e1ea2facca6 - - 2ff111fac1d7 - e7f19d6a9af8 - 37b497aa133f + - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 8c6cd2650d1f + - 09b53c1d4ab1 + - 77b2770508f6 + - 11a0d50a54e6 - c0c2d0941de8 - - 53c0b7a1a0c3 + - 037c6e54df11 - b3eab4b67562 + - 3f4d6399997b - f54f5baedfdd - - 11a0d50a54e6 - 6b1e195506a3 - - 77b2770508f6 - - 8c6cd2650d1f - - 037c6e54df11 - - 09b53c1d4ab1 - be1d967337e4 - - 3f4d6399997b + - 53c0b7a1a0c3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - 00fbfac99d39 - - 79b885ce78d7 - 13022c3d3076 - - ec9cbd6b9a49 - - b8f5f6e87f5c + - 79b885ce78d7 + - 1cd2511a396e - 178bdbdb6d24 - e403d27e8f24 - - 1cd2511a396e + - b8f5f6e87f5c - 9ee34ba73ebf + - ec9cbd6b9a49 - 5ef7ec16b04f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 6be9607d5..1bfef999a 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: - - 0094893f5001 - 18676df0cb3a + - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -22,71 +22,71 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: + - 63f86089423e + - 76d3d2b10738 - 5b5a7af9fbb4 - 7c2100246a2f - - 76d3d2b10738 - - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: + - 84fd33a60b35 - 96336c6a2bb7 - 1c35dadbe76f - 18a502a9d287 - - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - f732237754fc - 34e55239e68b - - a9f4a217dcd6 - addaf9d22850 + - f732237754fc + - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 8c202e741d68 + - 75403243703a - 04c15826a0b8 - 0776d824d896 - - 75403243703a - - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - - 8470de786d47 - - 43c99742158b - e96bbb9e24ea + - 43c99742158b + - 8470de786d47 + - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 84743da21318 - 306a40d4bb8f - 5c865a382933 - - 84743da21318 - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a + - 8daf4564ccda - 555ccac8a4c5 + - ac72310b038a - 78faebd0879c - - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - 7b8cb2b02978 + - f947b4bb5107 - d60df8727f59 - a58e4a43f49c tool_panel_section_label: Metagenomic Analysis @@ -94,17 +94,17 @@ tools: - name: dada2_removebimeradenovo owner: iuc revisions: - - 7f3b59dee073 - 7136e9ab70db - 1bc3657cd694 - 04144473e59e + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af - d943081510da + - 19299bb1c6af - 9058d8943303 - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis @@ -119,24 +119,24 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - c4db8c4de66f - 6501b5b33988 - dbf1798c0dcc + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - fa35f1106d3e - 15dbb444df71 + - fa35f1106d3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - 6d364c65c946 - 6c84982ee6f7 + - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -148,25 +148,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - e66ab198ec15 - 6aad8ca3918b - bd7a9c6efb10 - - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - b084117133af - - d77397f09da1 - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: + - 7f208f1eb64f - cad93abecac9 - 9704f1a3b32d - - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -188,50 +188,50 @@ tools: owner: iuc revisions: - 714d5a28cc5c - - 172920f67a84 - 094ad9c068af - - d24841f5c3d2 - 71ea608ddfa3 + - d24841f5c3d2 + - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - - a293a742194f - 12fb63b5f63f - - 4137b492233e - a4d7148ccee4 + - a293a742194f + - 4137b492233e + - d7e9a3c41657 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: + - 97f7bb0851e7 - 6fcb8ac37a3e - - cf87759761eb - 64bc7acc22a9 - - e2c71b852aba - - 97f7bb0851e7 - 75bedfb2078b + - e2c71b852aba + - cf87759761eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - - 4033827c76b8 - 080ea153677c - - 2d35528d2141 + - 5e5a999ffaa9 - c82508e76ad1 + - 2d35528d2141 + - 4033827c76b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: + - 6b7622dda516 + - 95bf7479d53c - fc6c328c292f - 2cd76b089570 - - 95bf7479d53c - - 6b7622dda516 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -299,8 +299,8 @@ tools: - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -312,15 +312,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 3d6570bffdb1 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1902d3de4a4f - 6c09bed3444f + - 1902d3de4a4f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -332,8 +332,8 @@ tools: - name: kraken owner: devteam revisions: - - aec58624706f - 8ba2174315aa + - aec58624706f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -345,8 +345,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: mash_sketch @@ -370,10 +370,10 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 4fd3b5d8706b + - 27250f92a01a - 2cff76cf35c6 + - 4fd3b5d8706b - 0270541aaf46 - - 27250f92a01a - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -381,8 +381,8 @@ tools: owner: iuc revisions: - 76bc4efa1aeb - - eb50e7eca3dc - 708abf08a626 + - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -448,20 +448,20 @@ 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: - - b89b0765695d - - 6dee4abadccb - 1a6cdf55390f - a16313517e55 - - a92a632c4d9b + - b89b0765695d + - 6dee4abadccb - 2131d7dca455 - ff8f55893e7d + - a92a632c4d9b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -552,8 +552,8 @@ 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 @@ -571,20 +571,20 @@ tools: - name: staramr owner: nml revisions: - - 141afacabcfa - - 4b9a8031ab74 - 2fd4d4c9c5c2 + - 141afacabcfa - 4d83eccf5f81 - - 3b22de20bd4b - - be818ae858e4 - aeaa20b96ef2 + - 4b9a8031ab74 + - be818ae858e4 + - 3b22de20bd4b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 576963db5f1b - - 9495df9dd6ef - b3c7199d8786 + - 9495df9dd6ef + - 576963db5f1b 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 3c78b5286..ddf17d6df 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - de3cfb122105 - 12e856482d26 + - de3cfb122105 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - ab12df91b47f - 4e9136c2c4c3 + - ab12df91b47f tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 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 047d0d9f9..a9effd174 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: + - 9422c5a87ee2 - 8b67dd48fec1 - - 2263989660f5 + - 9baa871cb1d1 - cd07731e4434 - 94b8c6013083 - - 80f03df2e2ce - - 48c13389050d - 6ae5a7b5a0a2 - a74dbfee5a86 + - 80f03df2e2ce + - 2263989660f5 + - 48c13389050d - bdfbaf0c10aa - - 9422c5a87ee2 - - 9baa871cb1d1 - 9eeb13a92d79 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: + - f0af8936ed41 + - be78f13134e2 + - f14193ec1f50 + - 5abf2c2249aa + - aaa0d6a8b808 - '764845535798' - - 3ff17bad4006 - fc2e49f91e52 - - 5abf2c2249aa + - 2e093badc689 + - 3ff17bad4006 + - d7ce0ec78e51 - bc3831dd65c1 - - be78f13134e2 - - f0af8936ed41 - - f14193ec1f50 - - d390fe1567dc - 4a60927aaca5 - - 2e093badc689 - c18157c68134 - - aaa0d6a8b808 - - d7ce0ec78e51 + - d390fe1567dc tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -44,15 +44,15 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -64,26 +64,26 @@ tools: - name: mafft owner: rnateam revisions: - - 6f28e90db932 - - c5908940967d - 15974dd17515 + - f0d493f8f84f + - c5908940967d - f1a5908ea2cb + - 6f28e90db932 - a65296ffb4a0 - - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - c9685bc0407c - 60698466facd + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer @@ -96,21 +96,21 @@ tools: - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - ebe3b0f84de9 + - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 636b049e6141 - e18267f90096 + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 5d1134bd6..06cc653e6 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,12 +2,12 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - 79e9a869f40e - - a7228a7ea146 - - 0e9e7fcdd543 - - 72b5e9dda577 - fc8804320156 + - 72b5e9dda577 + - 0e9e7fcdd543 + - a7228a7ea146 + - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus @@ -22,13 +22,13 @@ tools: - name: medaka_variant owner: iuc revisions: - - eb746fa6f514 - 19f3b583a9b3 + - eb746fa6f514 + - cc36773a3681 - 43815fa60f3a - - edf6d4003fad - - 222669c4afb6 - 0f5f4a208660 - - cc36773a3681 + - 222669c4afb6 + - edf6d4003fad - 2bf63b38ee9b - ec699520444c tool_panel_section_label: Nanopore @@ -49,18 +49,18 @@ tools: - name: nanoplot owner: iuc revisions: + - 645159bcee2d + - a3c4fe6f49ab - edbb6c5028f5 - 0f1c34698076 - - a3c4fe6f49ab - - 645159bcee2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: + - 85a394edc247 - d219b6d8158a - 3b6f94fc7e1d - - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation @@ -90,16 +90,16 @@ tools: - name: porechop owner: iuc revisions: - - 5f76b20953e5 - 93d623d9979c - 543cbeef3949 + - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - 28d7819c312f + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -144,8 +144,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -175,8 +175,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - ca22d8497db5 - 64a83664b814 + - ca22d8497db5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 301a98191..57372d7ef 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -20,17 +20,17 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - d74850cf4e42 - 3e73c97f025d + - d74850cf4e42 - adfd6bf710bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 9dd107db92c2 - 83da94c0e4a6 - 1586b111d2a3 + - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -72,8 +72,8 @@ tools: owner: iuc revisions: - 5711fc06a63e - - 38ccd4589990 - 48a42ca61006 + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -86,8 +86,8 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -113,16 +113,16 @@ 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: + - 52b6a4d98009 - 172815da3d41 - b4b2b284230a - - 52b6a4d98009 - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -135,8 +135,8 @@ 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 @@ -182,9 +182,9 @@ tools: owner: iuc revisions: - 9c43baa60906 + - 4ba60cb14cb0 - 0cb27ea69dc1 - 5fe20c915fa6 - - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -196,18 +196,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - - 0db22932bc39 - 9d09724f2bf1 + - 0db22932bc39 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - ed7a967cb11b - - 29c738066906 - df30a2f1db55 - 6e24e79d3d69 + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -219,16 +219,16 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 1865e693d8b2 + - ad90c2da4f38 - 3e4d45aca422 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -240,8 +240,8 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - 64deddb6a8ec + - c520a52b5174 - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -743,8 +743,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - d64562a4ebb3 - 544f6d2329ac + - d64562a4ebb3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 4ece24f3b..782581e8c 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,62 +33,62 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 5a7c56a5cc08 - - 26de3a7b1cb9 - - 8834daeb9892 + - '841557158611' + - c78f3d7dd1db - d033ffc1c161 - - 107d3ba7024a - - a6619171428e - cce7b18495e4 - - '841557158611' + - 107d3ba7024a + - f73435dc282b - d7c7ef3353fe - - b89cac5156ec - - 81e66674859e - - c78f3d7dd1db + - a6619171428e + - 26de3a7b1cb9 - 6a457678efcb - - f73435dc282b - - f04a1264e2a2 - - 3b8b5bde0bd9 + - 81e66674859e - 3f59ebfbfe3d + - 8834daeb9892 + - 3b8b5bde0bd9 + - 5a7c56a5cc08 + - b89cac5156ec + - f04a1264e2a2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 659517798cc4 + - 4755f52427c4 - 5fcd1ece3a6e + - b0af57c1a968 + - 3b96e92e8ec3 + - 5b777002c2de - e75442c7f4da - 6283babe736e - - 88c4aa435ded - - 7a2092844346 - - 5b777002c2de - - 3b96e92e8ec3 - - df47d4845b62 - - b0af57c1a968 + - 6a726db04d4b - 6223845127ea - - aa8cc71438cf + - df47d4845b62 + - 7a2092844346 - 02b8758214b0 - - 4755f52427c4 - a185b079b095 - - 6a726db04d4b + - 659517798cc4 + - 88c4aa435ded + - aa8cc71438cf tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 9b892d7f82cc - b8476e82ac20 + - 9b892d7f82cc + - f97743d52b87 - d1c340a5664b - c1d53e95327f - - f97743d52b87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: + - 128ba8da994f - feb40665d7cd - 9e10ba792be2 - - 128ba8da994f - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -101,53 +101,53 @@ tools: - name: pangolin owner: iuc revisions: - - 42a174224817 + - ca0d8cf80567 + - 9d61d3fa046c - b6abccb1f25b - - 83a69484cb87 - - 5f8727ff21e7 - - b7e297c2ede6 - - 36912871ccdc - 14ae456b8cc5 - - 9d61d3fa046c + - 2fa9d4f1b48f + - 03ed9524dcd1 + - 42a174224817 + - 437e28791761 - a2099fb98cdb - - 3a43c3982401 + - b7e297c2ede6 + - 5f8727ff21e7 - 2f1019071464 - - 7bb8726be37c - - 437e28791761 - - 03ed9524dcd1 - - abf6dbe8c9d7 - - ca0d8cf80567 - 81804a978fc0 + - 36912871ccdc - ca337cce3888 - - 2fa9d4f1b48f + - 7bb8726be37c + - 83a69484cb87 + - abf6dbe8c9d7 + - 3a43c3982401 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: raxml owner: iuc revisions: - - ea30d3089354 - a4b71be30c3c - 29ff6a849eac - 73a469f7dc96 - - ba29b5e2a4be - b1e68bbe4cef + - ea30d3089354 + - ba29b5e2a4be tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - 91887494eb97 + - dbe2b2204555 - e88a7de55d6e - - 809e42326fc2 - 15ac71df11a0 - f1ccc8a6eb05 - - dbe2b2204555 + - 809e42326fc2 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 879bb8546..b7d574319 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - 1aac2a13842a - - fc288950c3b7 - b502c227b5e6 - 7d34178f2812 + - 881d7645d1bf + - a1f0b3f4b781 + - fc288950c3b7 - f6ced08779c4 - f9242e01365a - - a1f0b3f4b781 - - 881d7645d1bf + - 1aac2a13842a 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 335bc07b4..0faf4dfec 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,14 +2,14 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - 7fbec959cf2b - eb085b3dbaf8 + - d00e15139065 + - c0e71cb2bd1b - ca90d17ff51b + - 5b85006245f3 - 3bd420ec162d - - c0e71cb2bd1b - - d00e15139065 - a58f7eb0df2c - - 5b85006245f3 - - 7fbec959cf2b - e4a053d67e24 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 59e77d2c3..eb74f53e8 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,57 +2,57 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - b574b84afc4d + - 277dc652246e - b18329a8ac14 - - f28ad96b76dc - ece627528a78 - - 277dc652246e + - b574b84afc4d - 0a18ac48ac53 + - f28ad96b76dc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - e988563cc6e5 - e215f71d7983 - - 525f201b86c1 - bf06d196e23d + - e988563cc6e5 - b41107d8fe89 + - 525f201b86c1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - bb6397b94018 - 4fbffddde8cd - 8da3511c9467 + - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - b8c79e70516d + - f23d67e28cc8 - 528fb09022be - a8157342d9a3 - - f23d67e28cc8 - - b8c79e70516d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 25b83cbd596a + - 80600735685d + - a95a82eb4d50 - a69865da6f80 + - 25b83cbd596a - 59e85306eae5 - - a95a82eb4d50 - - 80600735685d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - f1897eb07081 - - 611d80c0e29d - e0669b1854b1 + - 611d80c0e29d - 798da6bdff3d - ed9ed1e6cca2 tool_panel_section_label: Proteomics @@ -60,27 +60,27 @@ tools: - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 - a7fb9b395ddf + - 5a35e3a8d013 - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - df2187f9013b - 82f6c2f4332d - cc430977c8ff - - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 10566783d718 - 1693b2126f30 + - c5aa9fca18c6 + - 10566783d718 - 043f9c91f686 - d2483487e077 - - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -119,9 +119,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - 1c5cbf8f79ce - 0fa397f4f40b + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -134,8 +134,8 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -148,15 +148,15 @@ tools: owner: galaxyp revisions: - 160538a890a6 - - d286ff4600dd - e66f552a3c47 + - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -169,25 +169,25 @@ tools: - name: maxquant owner: galaxyp revisions: - - 37d669de2828 - - 97a7f34fcb6a - - 837224ad1694 - - 7f432d87c82c - e42225f8a659 - 8934bc76bb52 - - f522c08e900c + - 837224ad1694 - 2133b0be850a - 1f39c833f65f + - 7f432d87c82c - 4d17fcdeb8ff + - 97a7f34fcb6a + - f522c08e900c + - 37d669de2828 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - - 0ed07016d668 - '860429737408' - 85b8866f06d7 + - a72ac2c7cc5b + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand @@ -195,44 +195,44 @@ tools: revisions: - 4187b6df1a40 - 352b37c66d97 - - 1974224d63c2 - 990b4560ead7 + - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: + - 4f359549383c - a1daafbf5233 - - 99450519d727 - deaf035bbe9f - - 4f359549383c + - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - e79958768a2c - 40ca115438d2 - - c7745841de24 - c1343e3389ca + - c7745841de24 + - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - d46d64e7964d - - b648e45fd3cf - - da986f83631b - d2eac53666f0 + - da986f83631b + - b648e45fd3cf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: + - 1199751329b0 - 9bf325045235 - - eb811f3018ea - 944b43462104 - - 1199751329b0 + - eb811f3018ea tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -250,56 +250,56 @@ tools: - name: msstats owner: galaxyp revisions: - - b7034eff0db1 - - 28434abe6c5c - - 8212e342e482 - 593839e1f2c3 + - 8212e342e482 + - 28434abe6c5c + - b7034eff0db1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - bd1535813cfe - a5e394b36d87 + - bd1535813cfe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - 8960fb791701 - 4e77b8f12cd3 + - 8960fb791701 - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - 25529df60a81 + - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: + - 518b1730cf2a - c9eff69a7c62 - f7fef900f5b2 - 9cdf15d3cfc8 - - 518b1730cf2a 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 - 658494a2cb00 + - 41859bbdc16e - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -307,23 +307,23 @@ tools: owner: galaxyp revisions: - 9b7977080f6d - - 6634cad7d797 - 5ad0b5bf1deb + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 05d5e1ddc985 - d6878d27f051 - 0bb5056cb775 + - 05d5e1ddc985 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - febd569ad26f + - 5ad830edc021 - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -331,15 +331,15 @@ tools: owner: galaxyp revisions: - 92352a475eed - - 27cba4c5fc42 - 39e8fde08881 + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 9e26f5c770f8 - d413dc49d650 + - 9e26f5c770f8 - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -347,15 +347,15 @@ tools: owner: galaxyp revisions: - c28f13cab67a - - 8a04ed1c1d1b - 3720e349ba2a + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - ca799a7246e7 - c427a8628cbe + - ca799a7246e7 - c55dddc5844a - 382cde407f81 tool_panel_section_label: Proteomics @@ -363,41 +363,41 @@ tools: - name: openms_idmapper owner: galaxyp revisions: + - b5d0905419da - 39caaa778d2e - 8ddb7bab1138 - - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 18f93351f8b6 - f817513840a9 - - 8d4db262964c + - 18f93351f8b6 - 1c5f31b8d632 + - 8d4db262964c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 111c3a00136d - - c69f69d7867a - 5d9f175dff81 + - c69f69d7867a + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 476b5e296979 - be74a8cd7d66 - 0e52c85f3b15 + - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - e133b5c8878f - 9866e1170611 + - e133b5c8878f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter @@ -418,9 +418,9 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: + - bf32e0bcf554 - ee860980edc6 - 8098330f6d91 - - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer @@ -433,29 +433,29 @@ tools: - 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 owner: galaxyp revisions: - - 1bf940c18d93 - e8f64a7dc470 + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 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 @@ -475,8 +475,8 @@ tools: - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 18826fb8e5db - 6e8cc5ed2a9b + - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -489,25 +489,25 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - 5ae104d0da6e - decc397c3b7e - 3d8d4ada5405 + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - 539a3a4dcc9e + - 5182338d5e7c - dd173849c3d8 - e039cc5c7aed - - 5182338d5e7c - - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - 8a45fd5a608a + - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter @@ -532,16 +532,16 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - 7f6a1f27553e - c8b225c69a7f - fb52e95a370c + - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate @@ -554,14 +554,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: + - 943a34df6047 + - da885ca16cb2 + - 3634c90301af - 3ec27b4cee7c - 7fdd9119cc4f - 07ff622ec007 - - 943a34df6047 - - 3634c90301af - a72c48001f7c - 1beff3ddce58 - - da885ca16cb2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -615,10 +615,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: + - 12692567c7f9 - 265c35540faa - a371252a2cf6 - 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 0ef1d1466..c2ee9d410 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,43 +2,43 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 2f1d464ebfd2 - - cd5f98911089 - 42201b90e3f4 - - 289b7d6b69a4 - e345aadf914f + - cd5f98911089 + - 2f1d464ebfd2 - 110a346daf36 + - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 42d9087b4789 + - 8501601a118d + - 0cd2df8af811 - c207119ba5f6 - - 0345dbaaa79b - fcce77c09289 - - 0cd2df8af811 - - 8501601a118d + - 0345dbaaa79b + - 42d9087b4789 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - ad5ab22ffe24 - - 33486216eec0 - 405a212b32ab - - 04db7fd6b238 + - 33486216eec0 - 89eb29319bf4 - 421c33b8bf17 + - 04db7fd6b238 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - fa51dc5e8386 - - eb784fa07f80 - 7370bb65bad4 + - fa51dc5e8386 - f6e91108b7b1 + - eb784fa07f80 - 7b72fde3d27e - 1d839ead7ad3 tool_panel_section_label: RAD-seq @@ -47,22 +47,22 @@ tools: owner: iuc revisions: - 1544278c272e - - 8a55d29c8fcf - - c9b77ced9a78 - 3d70c2996730 - - a3e86cd9cac7 + - c9b77ced9a78 - d30e36c48c93 + - 8a55d29c8fcf + - a3e86cd9cac7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - a5969aa9347e - - b242deb58952 - - 7b881f5f5ad5 - - 564c33e5c3e3 - e2db212d64ad + - 7b881f5f5ad5 - 887cf585cafc + - 564c33e5c3e3 + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -70,30 +70,30 @@ tools: revisions: - e897c74a48bb - 8cff84759bf6 - - 9a171f9a450b - b4bab607eb05 - bd5ff77e2036 + - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 887e0991eb24 - - 33f0793edf93 - - 6dafad990086 - 5e10f396979e - - adc7a7610d4f + - 6dafad990086 + - 887e0991eb24 - 4f65e343ecdf + - adc7a7610d4f + - 33f0793edf93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - 43e3eeb2e0ec - - c5d7050e4ad7 - - c287418eb288 - 97575d01f06b + - c5d7050e4ad7 - 17d39bf0a63a + - c287418eb288 - 4e280b27a831 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -102,31 +102,31 @@ tools: revisions: - 0b8c84a7fdb5 - 9586f08634c0 - - d9bf483266a1 - 09b8edb56d80 - cd034465d4a4 - a819ec3b362d + - d9bf483266a1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - a4b4bd84f69e + - 2645575d1bf2 + - bf0e43ab0416 - 69842dd5aa48 - a9c34a289493 - - bf0e43ab0416 - 95351dd0fd3f - - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - bb0475c884ff - d1fda11e602f + - bb0475c884ff - 912f904a6e1e - - cfb504394ae1 - d033e1ccb386 + - cfb504394ae1 - 8a35a3bc6752 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: + - d1fad35bdb4a - d504d945a655 - 95286af4139b - - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 519b1841a..ad9b99d89 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,17 +2,17 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 2d4e3aff9dc7 - cf01dd6c6b1f - 31f8063eedea + - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - - 125d20cb23d7 - 32e542c2a773 + - 125d20cb23d7 + - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -31,8 +31,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: circexplorer @@ -57,16 +57,16 @@ tools: - name: cufflinks owner: devteam revisions: - - d080005cffe1 - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - cf747d1bd79a - - 86285ddd4512 - 6a6717a5f421 + - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -97,47 +97,47 @@ tools: - name: describe_samples owner: iuc revisions: + - 3b36efd62b3e + - 0693ccd171c4 - 8f0181aacb7a - e3b16fd7dd08 - - 0693ccd171c4 - - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: + - cd9874cb9019 - d027d1f4984e - - 0696db066a5b - 9a882d108833 - - 6a3a025714d3 - - cd9874cb9019 + - 0696db066a5b - 8fe98f7094de - 24a09ca67621 + - 6a3a025714d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: + - b47c006d90c5 + - df929f257179 - 2872c633f07e - 62adf13b86ea - - df929f257179 - - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: + - 5bf899c13979 - df0c8d0a5992 - - 6e53e565fc6a + - 0cb907a2a810 + - f2843df56434 + - 334ce9b1bac5 - 555659de7321 + - a8305cf0c951 - 3d89af8a44f0 - - 070900306913 - - 5bf899c13979 - 9bdff28ae1b1 - - a8305cf0c951 - - 334ce9b1bac5 - - f2843df56434 - - 0cb907a2a810 + - 6e53e565fc6a + - 070900306913 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -156,17 +156,17 @@ tools: - name: featurecounts owner: iuc revisions: - - 90d16db017d7 - a37612abf7f9 - - e6a2a912677a - - ea04b737afa0 - f3a5f075498f - - 7db9d3ea71c9 - - f9d49f5cb597 - a56fbe2d6ba7 - af814359d244 - - 6f66ae7c5f7a + - e6a2a912677a - 38b6d12edc68 + - ea04b737afa0 + - 6f66ae7c5f7a + - f9d49f5cb597 + - 90d16db017d7 + - 7db9d3ea71c9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -184,9 +184,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - - f99dd58de04f - 0f710191a66d + - f99dd58de04f + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -198,20 +198,20 @@ tools: - name: hisat2 owner: iuc revisions: + - 26371a1df031 - a86e80d3c09c - - 3fb01a8c902d - - 6c19daec423d - d4b55e2beb12 - - 26371a1df031 - f4af63aaf57a - 6ab42baa56e9 + - 3fb01a8c902d + - 6c19daec423d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -223,32 +223,32 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 - - 01247aaf0a10 - 1c75aa5de15e - ce5d418183c5 + - 01247aaf0a10 + - 87c11c05d238 - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: + - c971db6f0fe5 - 40985510cd98 - 10c98fab6c5a - - c971db6f0fe5 - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 58c35179ebf0 - - 708348a17fa1 + - e827f9aae031 - d6f5fa4ee473 - - 32511f586472 + - 708348a17fa1 - 0921444c832d + - 58c35179ebf0 - 97e06a4c7c75 - - e827f9aae031 + - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -297,19 +297,19 @@ tools: - name: rgrnastar owner: iuc revisions: - - c7c55b694974 - - 3ea5a2a63fa2 - - 4df95e2d7f61 - - 7ed2edc1337f - - c772497b2c32 - - 0a563fd2f22e - - 5ec75f5dae3c + - 99b17b74a8cd - 980d2a2e1180 + - 0a563fd2f22e - b9e04854e2bb - 79de45b5069b - - 99b17b74a8cd + - 5ec75f5dae3c + - 3ea5a2a63fa2 - 4074fc1940e2 - e132e7d02a3e + - 7ed2edc1337f + - c772497b2c32 + - 4df95e2d7f61 + - c7c55b694974 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -321,34 +321,34 @@ tools: - name: salmon owner: bgruening revisions: - - cc05793bb896 - 15cd64d7c58b - - 49121db48873 + - e3d32471da11 + - cc05793bb896 - 2c0ca397d302 - ebab418107f5 + - 49121db48873 - 53e9709776a0 - - e3d32471da11 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - fab6ff46e019 + - 56242ff81c84 - c0fd285eb553 + - fab6ff46e019 - 8c28affc7c48 - - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - dd4df992d93d - - 76d290331481 - - cef79931dda5 + - 258d696dbd7e - ae618321f34a + - dd4df992d93d - 1ebd14235b92 - - 258d696dbd7e - 914cfcba0ec8 + - cef79931dda5 + - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -378,62 +378,62 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 + - ffd1300599a1 - 0db979fead3a - c6334cb383ff - - ffd1300599a1 + - d0d4cef4f967 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - bcc5f03f1900 - ba3720d7e68b - 74217fbfba4d - d6a479fd4281 - - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - c2b82a94493e - 2fb4ee002432 + - 478f36effca1 - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: + - fab23c3b5258 - 3f4094b6a565 - 9ff3765e7172 - - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: + - 34a018cbee9c + - be3f26533209 - 4687ecf0eb2d - 870ac06dff8e - - be3f26533209 - - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 05ab8d5e04a2 - - 65e7dea767ea + - c5fbddcac63a - 33406f5a445c + - 65e7dea767ea - 5192f657f305 - - c5fbddcac63a + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - e406ac71165d - 6f0fb35b799c + - e406ac71165d - 1fdb25a8384d - a35cba31d904 tool_panel_section_label: RNA-seq @@ -441,17 +441,17 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - 964b7efe2639 - - c2c039e421af - 7c7fbf13aadd + - c2c039e421af + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - eafea3083352 - 24e94d84adc9 + - eafea3083352 - 047c22569787 - 1d689e4e1caf tool_panel_section_label: RNA-seq @@ -459,24 +459,24 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - - 04bb8bb7c198 - 9871104ea630 + - 04bb8bb7c198 - 3a4ac03d1266 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - 9fa24d5aac68 - - 48636f857c4b - - db1f362cca3e - - cee61b3fcf78 + - d84caa5a98ad - c9cfec002f71 - 32b86cd8eb50 - 8f1c3df4dd49 - - d84caa5a98ad + - 9fa24d5aac68 - d2bc35f3d1c5 + - db1f362cca3e + - 48636f857c4b + - cee61b3fcf78 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index dfa03fca7..b2c45c52e 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: + - 1a052c827e88 - 080fd5739bb4 - 473382134e56 - - 1a052c827e88 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index f09733b68..7a3eb7a94 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,17 +2,17 @@ tools: - name: bam_to_sam owner: devteam revisions: - - a53efedba9e7 - 88eedb4abea0 + - a53efedba9e7 - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 1dfd95ee241e - - 108db6635177 - cb20f99fd45b + - 108db6635177 + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -42,9 +42,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: + - 5f8e69cc4c6e - 19ece8afbaab - e7fd6754d093 - - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -68,8 +68,8 @@ tools: - name: sam_pileup owner: devteam revisions: - - 890d97772e2a - a3b4ad6858ff + - 890d97772e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -95,67 +95,67 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - - 6856f8a01905 - 12749212f61b - 46c6639921f1 + - 6856f8a01905 + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - c89806670ab9 - - 92ec40abcdcf - 06dc50b7b711 + - 92ec40abcdcf - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx owner: iuc revisions: - - 66e23b11feae + - 720217c23995 - b3d99709fe1a - a8d69aee190e - - 720217c23995 + - 66e23b11feae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - 22970df7a40e - - db17d5321bad - fefd89ab563c - - fe34990e5ce7 - cc61ade70eb8 + - 22970df7a40e + - fe34990e5ce7 + - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - - 811fc2d75ad4 - 7a6034296ae9 - - 88b8c2916784 - 7def34e6cf4d + - 811fc2d75ad4 + - fa5d3e61e429 + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 36677f429310 - 740ce0a18f0d - b40e2d865d52 - 65a38e8c8e2a + - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - 329deb17a9f7 - - 9da0311ab1dd + - 8da515fbc1bf - b61f5d6a7f25 + - 9da0311ab1dd - 583abf29fc8e - - 8da515fbc1bf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -168,10 +168,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - 30388d878f81 - - db000c6007a0 - d7b4851d1971 + - 30388d878f81 - bb8cfc6f6e0c + - db000c6007a0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -183,50 +183,50 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - a4a10c7924d1 - - 344fc91e1bfd - b5c88b7b153e + - 344fc91e1bfd + - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c + - cab3f8d35989 - 6c2c1836728b + - e613c1ad4c4c - a577ea614bed - - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd - 5d9ae78f34d3 - 135c85f4cfaf + - b7f7826ef1cd - bcedabb53ddf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 24c5d43cb545 - 5a08c09b9311 - 3a0efe14891f - - 145f6d74ff5e - fed4aa48ba09 - 1cc79f49b8d5 + - 145f6d74ff5e + - 24c5d43cb545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - 6be888be75f9 - - 350bbc5c2ffd - - 5826298f6a73 - b72793637686 - - 0dbf49c414ae + - 350bbc5c2ffd - c370440f901e - - b01db2684fa5 + - 0dbf49c414ae + - 6be888be75f9 - bf328cec6a42 + - 5826298f6a73 + - b01db2684fa5 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 010b92f07..d5afbad0a 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,11 +2,11 @@ tools: - name: ena_upload owner: iuc revisions: - - d147d6455873 - a62c4a11a67d - - 59bb6d34fca6 - 480d9e9d156b - 6f6537780379 + - 59bb6d34fca6 + - d147d6455873 - 4aab5ae907b6 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 92202c8bc..650a2acf2 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -2,43 +2,43 @@ tools: - name: anndata_import owner: iuc revisions: - - 55e35e9203cf - - 93dd15e13e6a - - cfc3f5a57dc6 - - fb9e030ffae4 - 32e547223c9e + - cfc3f5a57dc6 - 00712416fdaa + - 93dd15e13e6a + - fb9e030ffae4 + - 55e35e9203cf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: + - 688357ad5e61 - 038e32885fec - - 6f0d0c784f09 - - b9fac48532eb - 39e945f0b2c1 - ee98d611afc6 - - 688357ad5e61 + - b9fac48532eb + - 6f0d0c784f09 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: + - ed4996a16f7f + - 43cb7b5a6fe7 + - 9bd945a03d7b - b85871dd69f9 - d4af736e7b83 - - 9bd945a03d7b - 3d748954434b - - ed4996a16f7f - - 43cb7b5a6fe7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils owner: iuc revisions: + - cdf4443d5625 - a9caad671439 - 2c1200fba922 - 8855361fcfc5 - - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -64,8 +64,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - 7705cc75ac18 - 8c64a2da3869 + - 7705cc75ac18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -84,8 +84,8 @@ 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 @@ -106,9 +106,9 @@ tools: owner: iuc revisions: - 6acb08931836 - - aaa5da8e73a9 - b2df381a6004 - 77b91b9bdf52 + - aaa5da8e73a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -123,17 +123,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: + - 6bd82ed14acd - 5e9171dc8244 - - 3081ff5c84a3 - c5d3684f7c4c - - 6bd82ed14acd + - 3081ff5c84a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - a407e7f8bdc1 - 94c19fb1281c + - a407e7f8bdc1 - 3bcd5445cd7a - ab55fe8030b6 tool_panel_section_label: Single-cell @@ -141,51 +141,51 @@ tools: - name: scanpy_plot owner: iuc revisions: + - 6adf98e782f3 - aa0c474463c2 - dbbe1ea8ecb1 - 9b0cdb8cf6be - - 6adf98e782f3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 215733a383f2 - f2f6c703da06 - - 73ab2ac53d06 - bf2017df9837 - 458e8f43a775 + - 215733a383f2 + - 73ab2ac53d06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - fd808de478b1 - - 8f333f90d8d6 - b834074a9aff + - 8f333f90d8d6 + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: - - 652923ce664f - 7a365ec81b52 - b7ea9f09c02f + - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter owner: iuc revisions: - - 81e5bdff4853 - 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 - 46fc6751d746 - c99ba278dfa9 + - 9e5c0bb18d08 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 680fbbbac..be4b4a39c 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,39 +32,39 @@ tools: - name: datamash_ops owner: iuc revisions: - - 419027d822d6 - - 746e8e4bf929 - 562f3c677828 - 2f3c6f2dcf39 + - 419027d822d6 - 4c07ddedc198 + - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - e01e8a9a82f4 - 8564f6927b87 + - e01e8a9a82f4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e + - b1eda492f063 + - 4c4ec859c31a - aef56d0e7a61 - 9c3e1d3235c8 - - b1eda492f063 - 840f29aad145 - - 4c4ec859c31a + - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 9fda0b82f419 - 30d21a6041f6 - - d0352e8b4c10 - 07843f917990 - 375bbd555f4a + - d0352e8b4c10 + - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - cd02bf168d23 - - 4cc980df6265 + - 7ae443e6217d - 2c58b83c9bad + - 4cc980df6265 - 8b1b2b91f8d0 - - 7ae443e6217d + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: + - 4bbaf77573ef - bb9fc9d46ea4 + - 1dd433d2c92c - 7dd3fb35904f - - 4bbaf77573ef - - ad7e0b4291ee - e10e776f2109 - - 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 9a6a16d17..7f0608665 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -8,8 +8,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -21,20 +21,20 @@ 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 + - 464b9305180e - 6595517c2dd8 - - 6e8d94597139 + - be25c075ed54 - 9cd341095afd - - 464b9305180e - - 13b6f0007d9e - 02026300aa45 + - 13b6f0007d9e + - 6e8d94597139 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -71,8 +71,8 @@ tools: - name: filter_tabular owner: iuc revisions: - - 9cc411a62277 - 557ec8d7087d + - 9cc411a62277 - 34d29339abab - 37cde8134c6a tool_panel_section_label: Text Manipulation @@ -105,21 +105,21 @@ tools: - name: query_tabular owner: iuc revisions: - - 33d61c89fb8d - - 83069b38aa85 - 2e8f945f7285 - - 1ea4e668bf73 - 3a6b78c39dca - 623f3eb7aa48 + - 33d61c89fb8d + - 1ea4e668bf73 - cf34c344508d + - 83069b38aa85 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 @@ -131,9 +131,9 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - f768f6183386 - - bce29ec10b78 - b722161a845a + - bce29ec10b78 + - f768f6183386 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -147,10 +147,10 @@ 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- name: vcfannotategenotypes owner: devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -405,8 +405,8 @@ tools: - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck @@ -419,8 +419,8 @@ 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 @@ -455,22 +455,22 @@ tools: - name: vcfflatten owner: devteam revisions: - - b24e368ae7b1 - f285aa6bdcfb + - b24e368ae7b1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -483,15 +483,15 @@ tools: - name: vcfleftalign owner: devteam revisions: - - d2406f98a782 - 29f9b782727e + - d2406f98a782 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers owner: devteam revisions: - - d226a7327946 - 17096387c0e6 + - d226a7327946 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample @@ -504,15 +504,15 @@ tools: - 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_isec diff --git a/usegalaxy.org.au/viral_tools.yml b/usegalaxy.org.au/viral_tools.yml index 15250eab7..06370d956 100644 --- a/usegalaxy.org.au/viral_tools.yml +++ b/usegalaxy.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 9def47f3c1e4 - 18aad692772a + - 9def47f3c1e4 tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu