diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index ea6588f54..ce7954c57 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -8246,3 +8246,4 @@ Update 224 18/12/24 03:26:51 quast False Tests failed iuc a3b35edea53a a3b35edea Update 224 18/12/24 03:39:45 uniprotxml_downloader False Installed galaxyp 4ddc8da62671 4ddc8da62671 9/9 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_224/install_log.txt Update 224 18/12/24 03:40:28 volcanoplot False Installed iuc 99ace6c1ff57 99ace6c1ff57 Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_224/install_log.txt Install 1714 20/12/24 00:07:24 ncbi_fcs_gx True Tests failed iuc 32d058f3462a 32d058f3462a Staging Testing 1/2 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1714/install_log.txt +Install 1716 20/12/24 03:02:03 ncbi_fcs_gx True Installed iuc 32d058f3462a 32d058f3462a FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1716/install_log.txt diff --git a/requests/ncbi_fcs_gx@32d058f3462a.yml b/requests/ncbi_fcs_gx@32d058f3462a.yml deleted file mode 100644 index 19546f627..000000000 --- a/requests/ncbi_fcs_gx@32d058f3462a.yml +++ /dev/null @@ -1,7 +0,0 @@ -tools: -- name: ncbi_fcs_gx - owner: iuc - revisions: - - 32d058f3462a - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index e995442a5..031f92832 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 78c75f134c16 - - c2ef298da409 - - 3f3e247c053d - 6e9aea89e388 - 4efdca267d51 + - c2ef298da409 + - 78c75f134c16 + - 3f3e247c053d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -19,8 +19,8 @@ tools: - name: aegean_gaeval owner: iuc revisions: - - 1dd7adc21b6d - 8dc7512c9dc9 + - 1dd7adc21b6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus @@ -33,67 +33,67 @@ tools: - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - fe3ca740a485 - - 1aae04680c4b + - a79ee60b6926 - 133f36c29579 - - 44018dd6b447 - - f29602ae449e - 3e1f6f6d557e - - cd2480f35935 + - 1aae04680c4b - 4f2967b27e67 - - a79ee60b6926 + - f29602ae449e + - 44018dd6b447 + - fe3ca740a485 - b5d8e5475247 + - cd2480f35935 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - - dc027fa56d55 + - 6519ebe25019 + - f1e653756174 - aada0deea587 + - dc027fa56d55 - 7be22100e5e1 - - f1e653756174 - - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - bd0e53f3a891 - - ca6d970d931c - - 28433faa6e42 - 0fc0f9cf035a + - ca6d970d931c - 09855551d713 + - bd0e53f3a891 + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - 92eee5f31117 - - da5f1924bb2e - d77802fe76f7 - 728dacaf08a9 + - 92eee5f31117 + - da5f1924bb2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - 8fd427007e93 - - fe48aa4ccd5e - 7355bbf5e05f + - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -118,17 +118,17 @@ tools: - name: cpat owner: bgruening revisions: - - 1ac12c0cc7a0 - - 8e9e228c54c4 - 7ccc6234b54e + - 8e9e228c54c4 + - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -158,61 +158,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 9c15ca7e764e - - 582fd74dc2a1 + - 3bbe70fef6df - 9f2455341fac + - 9c15ca7e764e - b6b5cd37f2a2 + - 582fd74dc2a1 - 756376aeb1ae - - 3bbe70fef6df - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 1691af4a0d17 - 73428a792541 - - 8e1ace8f77c6 - 989f7c061f35 - a230ea445788 - 0ffe5be70caf + - 8e1ace8f77c6 - 30fb23d4c31c + - 1691af4a0d17 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - - 563a19373357 - 5a5ae61da69c - - 57c6718cbfcc - e94187d661df - - 0418d28136de + - 57c6718cbfcc + - 494f0bb4a993 + - 563a19373357 - 30f08d74024f + - 0418d28136de tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 4b96ced19f75 - - f77d7b685bb3 - d6c7106b7b2e + - 2bba2ff070d9 + - 1bc5a03faf2e + - 4b96ced19f75 - f31125bb85ea + - f77d7b685bb3 - 7abc5f6dd595 - - 1bc5a03faf2e - - 2bba2ff070d9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - b3cf4684e9c7 + - fed64e676186 + - 54961e026fe4 + - 52af33194019 - d77fdcca400e - d3af38b9c7e1 - - 54961e026fe4 - 520e30695ec3 - - fed64e676186 - - b3cf4684e9c7 - - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -239,9 +239,9 @@ tools: owner: iuc revisions: - 602de62d995b + - ef2ad746b589 - 8b3e3657034e - 43798b4caee0 - - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -265,16 +265,16 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - c55643c3d813 - - 74810db257cc - 98cafcbd2578 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -292,26 +292,26 @@ tools: - name: maker_map_ids owner: iuc revisions: - - 326f9c294b09 - e906fa778440 + - 326f9c294b09 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - - 370c210d9541 - - 3c1a01127868 - d46d803ca6cc + - 3c1a01127868 + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 033755194fe9 - - b815ec682418 - - c8ac28e8ac44 - e95d52d295d7 - 624606f7c996 + - c8ac28e8ac44 + - 033755194fe9 + - b815ec682418 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -353,11 +353,11 @@ tools: - name: prokka owner: crs4 revisions: + - d643e3b03500 - a17498c603ec + - 8a22554cdde2 - eaee459f3d69 - - d643e3b03500 - bf68eb663bc3 - - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -369,15 +369,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -401,15 +401,15 @@ tools: - name: snpeff owner: iuc revisions: + - 5c7b70713fb5 + - 5a29ab10dba6 + - 68693743661e - 8f92c2b26e6d - - 6322be79bd8e - c7275bd8b4d6 + - 6322be79bd8e + - 268d162b9c49 - 5b80f544c67f - cfcf33df7fc0 - - 268d162b9c49 - - 5a29ab10dba6 - - 5c7b70713fb5 - - 68693743661e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -429,8 +429,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -443,24 +443,24 @@ tools: owner: iuc revisions: - d03af1c7002c - - 37213cf56392 - - 45083d070fb8 - - ba6f87115e13 - - e1a9d6fd258d - 51dd22484644 + - 809dfc93d593 + - e1a9d6fd258d + - 45083d070fb8 + - 4839e590cb26 - ac8250086ac3 + - 37213cf56392 + - 200c378d85f3 - 037a11682176 + - ba6f87115e13 - 8cb134b8c1a5 - - 809dfc93d593 - - 200c378d85f3 - - 4839e590cb26 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 4064ccd27..bae1618f0 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,28 +2,28 @@ tools: - name: abyss owner: iuc revisions: - - 8f1b150a2487 - - a929ce596a34 - 0124fce4654a - - 0e93176640ac - - db9b10824c61 - 553bfe8bd0b5 - - 841084c5fc46 - - fa5259cc561b + - 8f1b150a2487 + - db9b10824c61 + - 0e93176640ac - d6d5ccc2c581 - 7547fcab5d19 + - fa5259cc561b - 890b794c997d + - 841084c5fc46 + - a929ce596a34 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - 067592b6b312 - b2860df42e16 - ddddce450736 - - 067592b6b312 + - b9e31c5c01c7 - 94fe43e75ddc - 21e491ad532a - - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -36,41 +36,41 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 5258e18bbe23 - - 3371c5bdc17a - faee8629b460 + - 3371c5bdc17a - 22286dab5aa1 - a7f16f24e9a1 + - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - '392811378515' - 53dd00a4ab68 + - '392811378515' tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 94170eee0ad8 + - cf13a1e03e5b + - f18f0b887c31 + - 602fb8e63aa7 - 41030a6c03b7 + - 46ae58b1d792 + - 1440ae06552f + - 5ecdeca79a0d - bb935709506a + - e824f5d958d0 - 0d243f458b53 + - e4bd1e99bacf - 2babe6d5c561 - - 1e62c28ba91d - - 46ae58b1d792 - - e824f5d958d0 - 2dd755c1c6ff - - 5ecdeca79a0d - 4048d82f0c88 - - f18f0b887c31 - - ea8146ee148f - - 1440ae06552f - - cf13a1e03e5b - - e4bd1e99bacf - - 602fb8e63aa7 + - 1e62c28ba91d - e5c372c91e46 + - ea8146ee148f + - 94170eee0ad8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu @@ -90,46 +90,46 @@ tools: - name: flye owner: bgruening revisions: - - cb8dfd28c16f - - cd11366d92cf - - 3e4f8642c77e - - 1f0769f0b56b + - 276f5d8712d5 - 8d4f03b5fe9d - - 291923e6f276 + - 1ce9b1d72ec3 - e27815e82dd4 - - 276f5d8712d5 + - 291923e6f276 + - 1f0769f0b56b + - 3e4f8642c77e - 3ee0ef312022 - - 1ce9b1d72ec3 + - cd11366d92cf + - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - 460fad600dce - 01210c4e9144 - 3169a38c2656 - b2f674562a18 - - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 8b330a577046 - 7348b69e5109 - - 06bcf65179fb + - 8b330a577046 - ba88bc5a6446 + - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - f4a3eff8ab85 - - 3ef480892a9f - 6ec1b853c8fd - - 3fba9c77550a + - f4a3eff8ab85 - 5127a713de83 - - 690c2caa367e - 764f2516d837 + - 690c2caa367e + - 3fba9c77550a + - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -141,24 +141,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - 60024a528cbd - - 6505bd37670d - - 71740308d412 - - 5f625c63b8bc - - 0ee0c3089254 - - 284a1cb82b61 - - ec9e21e9c71b - da9d8bf98802 - - 2061fb3b81b4 - - df25d4fb79b7 + - 71740308d412 - 366a11d316a7 - - 5bec28269d95 - 41cea2aa2dce + - 60024a528cbd - 9ef6920c3089 - - 3f7be05a1597 - - 5161f204ba63 - f3c89da3af16 + - ec9e21e9c71b + - 5f625c63b8bc + - 6505bd37670d + - 3f7be05a1597 + - 284a1cb82b61 - 045c7c3d8e59 + - 5161f204ba63 + - df25d4fb79b7 + - 5bec28269d95 + - 0ee0c3089254 + - 2061fb3b81b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -177,42 +177,42 @@ tools: owner: iuc revisions: - 14ddfc8ffb93 - - a96f3ad4e0d8 - de387b2b2803 - 7518ee87b53d + - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - f8113c25bc6b - - d7edbc9c3a07 - eb7b00ec347d + - d7edbc9c3a07 + - f8113c25bc6b - 09c589057ee8 - - 9d79beb19ac3 - 39edec572bae + - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: + - 51c2360aa807 - eadfd71dde37 - 29dabd8db6f2 - - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 606b09cc9860 - - f338e9942b27 - - 3ca2d2a9068c - - 99ecfdafc64f - fd128c111ab0 - - f369ef5f210b - e731ea24e48d - - 2ecf5a570907 - eb7a370f6588 + - 606b09cc9860 + - f338e9942b27 + - 2ecf5a570907 + - f369ef5f210b + - 99ecfdafc64f + - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -224,11 +224,11 @@ tools: - name: miniasm owner: iuc revisions: + - a7b889b90140 + - b799a615995d - 73a3846701e1 - 8b6d0d85252b - - a7b889b90140 - 8dee0218ac7d - - b799a615995d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -246,8 +246,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 15200570e926 - 7c2f5268d01c + - 15200570e926 - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -260,13 +260,13 @@ tools: - name: pretext_map owner: iuc revisions: + - c6cec5ab35c1 - bbe19ef04a74 + - dfb8a4497339 + - 8fef980d48b5 - 02831bf9e95f - d256a51a656b - 2b16ba799da9 - - 8fef980d48b5 - - dfb8a4497339 - - c6cec5ab35c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups @@ -280,25 +280,25 @@ tools: - name: quast owner: iuc revisions: + - 675488238c96 - 6fcbee531de6 - - 7594365c546b - - 72472698a2df - 875d0f36d66f - 3061c8b029e5 - - 675488238c96 + - 342a1d1fed7b + - 72472698a2df - 59db8ea8c845 - ebb0dcdb621a - - 342a1d1fed7b + - 7594365c546b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - - aa39b19ca11e - d865b62f501c - - 78c533842eeb - a199cd7ac344 + - 78c533842eeb + - aa39b19ca11e + - cd06929b224b - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -317,31 +317,31 @@ tools: - name: raven owner: iuc revisions: - - 2b2a352488fa - - 3edba9afc9bc - - 5c55448d0f33 - f8564b2d7f63 + - 3edba9afc9bc - f11b994b7eb2 - 33b7d8481a76 + - 2b2a352488fa + - 5c55448d0f33 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - f73ab5187eed - 8e66f695d859 + - f73ab5187eed tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - 5fc94b3a4704 - - 28189050e437 - 1d06c8b38e77 + - 28189050e437 - e122f9101584 - 53c2bc8c2ae3 - - ef69617ecb42 - 378e55aeeb25 + - ef69617ecb42 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -353,45 +353,45 @@ tools: - name: shovill owner: iuc revisions: - - 196a599ec43d - d9f6a00b6db7 - - ad80238462c1 - - 83ead2be47b2 - 865119fcb694 - - f698c7604b3b + - 83ead2be47b2 - ee17a294d3a3 + - 196a599ec43d + - f698c7604b3b + - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - 015283de3004 + - 24e471d13fe9 - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 604782a8a53a - - c33a476f4001 - 051fd2db8a27 - 904bf932cf78 - - 1bb12736175c + - 604782a8a53a - 1fc82fe7ebef - 7490b213baa9 + - 1bb12736175c + - c33a476f4001 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 655fa188c3cc - 34305b013402 - - d6e617c4e338 - - 808b3a0a6716 + - 655fa188c3cc + - fee85957cebe - 9678993ca5bd + - 808b3a0a6716 + - d6e617c4e338 - ad8b536d1caa - - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades @@ -399,34 +399,34 @@ tools: revisions: - b8002c3f7141 - e5a3b75a271f - - 037f9927c4ff - - 7e27faaad80e - - 21da31ed41a1 - 6b5a5842531e + - 7e27faaad80e + - 037f9927c4ff - 8d4b90bf9caf + - 21da31ed41a1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: + - 5b26685e5d3b + - 328aa71f0f3c - f1532cb33c75 - - 7922870efcca - 2a10645aeadd - - 328aa71f0f3c - - 5b26685e5d3b - 9de69775f512 + - 7922870efcca - 86f66ab58e14 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 85fb02c43042 - 8cc856b935ee - - 340bc17f49cf - e41dcb0e913b - - 6aad515a5270 + - 85fb02c43042 + - 340bc17f49cf - 1708851f8804 + - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades @@ -434,99 +434,99 @@ tools: revisions: - b3490b036c5a - d159735a6a9f - - b65a43f70b99 - d5fb354f745d - de1260f8a300 - 249f6a28c751 - 6357b127161e + - b65a43f70b99 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 7897763d14ec - - 33368fec3b70 - dd7ad84f3943 + - d2d1df21dfb9 + - d5887ace0dd4 - 9006e5836729 - a90db5dbaaf3 + - 33368fec3b70 + - 7897763d14ec - b7829778729f - - d5887ace0dd4 - - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 0368ac680e70 - ced385aa976d - - 6f4c8ad6ea01 - 505a9833ab5d - - 8f631679571f + - 6f4c8ad6ea01 - 189e837009c9 + - 0368ac680e70 + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - 9ded6109434a + - a7ed21de23fe + - 356afed970b4 - e59bee4565b3 - 19bdfd1e6fe3 - d40ed4eb0c0e - - 356afed970b4 - - a7ed21de23fe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - ebd801e712bc - - 80a17897564d - - 7673a6c920b2 - b23249f81bc4 - 4688ae3b49b5 + - ebd801e712bc + - 7673a6c920b2 - 6dd935e4984b + - 80a17897564d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - ed312479d9eb + - b64696992ee9 - b5e35a2ca4f3 - - 937ea677d437 - cb1e3db43020 + - 937ea677d437 - 59bd28f6265d - - b64696992ee9 - - ed312479d9eb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - 05bd7504fdb2 + - b9b0246a2be3 + - 383bb5ad32e2 - cb4768eeca3b - 2628f6790eda - 6015aa0303f2 - - 383bb5ad32e2 - - b9b0246a2be3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 3e44ef016b45 - e92675014ac9 + - e022dff952df + - 6e26c9afd301 + - 9e3e80cc4ad4 + - 3e44ef016b45 - 0a3a602cd1e3 - 8f9f06995f98 - - 9e3e80cc4ad4 - - 6e26c9afd301 - - e022dff952df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 08256557922f - 5da9a0e2fb2d - 920677cd220f - - 08256557922f - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -534,9 +534,9 @@ tools: owner: simon-gladman revisions: - 82398ba86ba7 - - 0e2b4e3f9ca1 - d81360ea69d8 - 4a53b89fa703 + - 0e2b4e3f9ca1 - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 7ca51e8ab..05fc24e6e 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: + - 392f100eebcd - 1ae00120dd24 - 4768f7f8e93f - bfd290fe1588 - - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,8 +17,8 @@ tools: - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - 1f5641a52664 + - 8e8dc9a1e3e5 - 31812e7a1315 - ded48b36f3b7 tool_panel_section_label: Bacterial Typing @@ -26,8 +26,8 @@ tools: - name: sistr_cmd owner: nml revisions: + - 5c8ff92e38a9 - 24a7a95867b0 - 17fcac7ddf54 - - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index da65b51cd..46b7e6773 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,14 +2,14 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - d58c27d2c5a7 - - 204a131e47db + - d1f62024a08b - a9c9d768b751 + - 1c427e24fb79 - 0840ba83860c - - 159b04e36791 - 7beb76ffbc0f - - 1c427e24fb79 - - d1f62024a08b + - 204a131e47db + - d58c27d2c5a7 + - 159b04e36791 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 9f02f0775..d570d59d2 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - ce3c7f062223 - - 07e8b80f278c - 589e7e57fd6d - - a1a923cd89e8 - - a68aa6c1204a - - b28e0cfa7ba1 - - dde39ba9c031 - e19bebe96cd2 - - 64e2edfe7a2c - - 0a5c785ac6db + - 07e8b80f278c - a8eabd2838f6 + - b28e0cfa7ba1 + - a1a923cd89e8 + - 0a5c785ac6db - 87ee588b3d45 + - 64e2edfe7a2c + - dde39ba9c031 + - a68aa6c1204a + - 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 ba5b8104f..eb6e18bb9 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -9,9 +9,9 @@ tools: owner: bgruening revisions: - f921014aba5a - - 62c9df8382c2 - - 54f751e413f4 - e8ac2b53f262 + - 54f751e413f4 + - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 6f386c5dc4fb - - 5edc472ec434 - - d999e774072a - 0e3cf9594bb7 - - 2889433c7ae1 - e25d3acf6e68 - - acf4e47b734c + - d999e774072a + - 5edc472ec434 - a52d2d93e595 - cbf3f518b668 + - 2889433c7ae1 + - acf4e47b734c + - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus @@ -43,8 +43,8 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 29806bdf9..055210f50 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - f4230f116196 - - 27ee142314a9 - - c8cdde00b105 - - 710301bc46fa - 095ad4d096d1 - - da6bd1975a71 + - 710301bc46fa - 6ca543ec1bf8 + - da6bd1975a71 + - 27ee142314a9 + - f4230f116196 + - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -111,8 +111,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -130,39 +130,39 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 88076940fa94 - 3b8a9d5ced85 - - 79cfd9ead848 - bfb65cb551d8 + - 79cfd9ead848 - 0fac8e2afc13 - - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - 55918daa5651 - 715cd0e87781 - d532b7e5f64b - - 55918daa5651 - - b46d4b4d995c - f5d979cb4b54 - eb6564a60136 + - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 97872d87ba80 - - d2f955aea23a - - fdf2cc80adb5 - - 5579659312e6 - f26afd1b7104 + - 5579659312e6 + - fdf2cc80adb5 + - d2f955aea23a + - 97872d87ba80 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - 319a28774da9 - d1d0efda35c0 + - 319a28774da9 - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -170,23 +170,23 @@ tools: owner: chemteam revisions: - 4da9ee404eab - - ed736e6eee39 - 070e3ecc3fda - - cac1886249a2 - 2c349b027a01 + - cac1886249a2 + - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 73008ef1f487 - - d1f803b5943c - - 807aa4c9293d - - 525ca7c8065f - 2e219a2d9327 + - c0c9a5024177 - f197e34c33a9 + - 73008ef1f487 + - 525ca7c8065f + - 807aa4c9293d - da8753545526 - - c0c9a5024177 + - d1f803b5943c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate @@ -196,8 +196,8 @@ tools: - 1809414a9454 - 2c8ed1b52bf7 - c4fbab8e03c5 - - 7568ae18908a - 27ea4e1a3f95 + - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,18 +209,18 @@ tools: - name: md_converter owner: chemteam revisions: - - 79e8ab8f1e81 - - 730ef07b90ae - d7ec25187599 - - ccfbd956a2d3 + - 730ef07b90ae - ba83f0923369 + - 79e8ab8f1e81 + - ccfbd956a2d3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - e6011617c748 - 1400d1977e7b - 4242b4d68e9c - b59c91adeac1 - - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -340,8 +340,8 @@ tools: owner: bgruening revisions: - 85fad59f8168 - - bf99565cec1f - d4c67ced6abc + - bf99565cec1f - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 606e3ec3a..66f84f082 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: - - c97a786e8fb5 - fa56d93f7980 - 163688bb8f73 - f907216064f6 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -23,18 +23,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 11cf21ee4242 - 4124781932db + - 11cf21ee4242 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 640d3af5d833 - - f5d67c722d67 - - 495a4173006f - 86e2413cf3f8 + - 495a4173006f + - f5d67c722d67 - 424aefbd7777 + - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -54,8 +54,8 @@ tools: owner: devteam revisions: - 74c9214cc8e6 - - 5c2cc3b58c7d - 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 574184099..0780e0f99 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 90981f86000f - 25136a2b0cfe - - 33151a38533a - 830961c48e42 + - 33151a38533a + - 90981f86000f tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - baabc30154cd - - 2dae863c8f42 - 0046692724f9 - 6cbe2f30c2d7 + - 2dae863c8f42 + - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index d71e05733..248e454ff 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -2,9 +2,9 @@ tools: - name: agat owner: bgruening revisions: - - d6ede73082da - - abba05ead5d7 - e7449b2c14bf + - abba05ead5d7 + - d6ede73082da tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -17,38 +17,38 @@ tools: owner: iuc revisions: - 4a6ee918c13a + - ab9350a8ab4d + - 5e1240a87bcb + - a3b86937ead6 + - 6ef0b5664c69 + - 3b6f97e7094c - f3a19509108a - 0b3c3ad92827 - - 3b6f97e7094c - 367b1ed91207 - - 6ef0b5664c69 - - a3b86937ead6 - - ab9350a8ab4d - e3cbd2287f63 - - 5e1240a87bcb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 091bb5922a82 + - d4d4e9febf5c - 584008e574b2 - - e525f9ffb9ac - - 501c21cce614 - e177a8ea0bf1 - - 1b5fc03380d4 - - d4d4e9febf5c - - 33c99804a32f - - 54ccb7e1f49a - bd46669113b9 + - 54ccb7e1f49a + - 501c21cce614 + - 091bb5922a82 + - 33c99804a32f - 72ed72122deb + - 1b5fc03380d4 + - e525f9ffb9ac tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - 11c3eb512633 - a0d092f27fdf + - 11c3eb512633 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -60,24 +60,24 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 77b41c89d856 - 186b8d913e6c - 8979c288aefb + - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 43807a65369f - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa + - 43807a65369f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -89,8 +89,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -102,9 +102,9 @@ tools: - name: gffread owner: devteam revisions: - - 3e436657dcd0 - - 154d00cbbf2d - 4dea02886337 + - 154d00cbbf2d + - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -136,26 +136,26 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0b4e36026794 - 0a7799698fe5 + - 0b4e36026794 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - - 78fb18899c99 - 68f57cc8fad0 + - 78fb18899c99 - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 26c6706bfb07 - - b9b385097f13 - 19e45916daf9 + - 26c6706bfb07 - 63769c4217a7 - 92ac8e086317 + - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -169,15 +169,15 @@ tools: owner: iuc revisions: - e9bbe2f71784 - - 3c6f9e8a4c17 - 8067dfa00ed2 + - 3c6f9e8a4c17 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - fa49730d1d4b - 98704d357ede + - fa49730d1d4b - a2f83a375bf2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 1cd59d72d..fba917d78 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,182 +2,182 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 268e91e540ee - - a1ca9bccc7f2 + - e821645ef8fc - de72ba3ed6f2 - c929a006727f - 5f6d123679f4 + - 268e91e540ee + - a1ca9bccc7f2 - 29451af70c52 - - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 12af64f93288 - - 2d2cf5c1ea8a - - 7a7fd0f5f15d - 0e143b4c3987 - - 5d11599b8a7d + - 7a7fd0f5f15d - bb1e4f63e0e6 - 0e49b109abc2 + - 2d2cf5c1ea8a + - 12af64f93288 + - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 81b1e3e1fc6c - c06951d10364 - - dc059492a995 - 1d848bc4585f - 195e98217334 - 7c1beb6d6eca + - 81b1e3e1fc6c + - dc059492a995 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 71aa86af6762 + - 26e7304d6737 + - 93eb012d9eed - bfff7454b59a - - a67ac707496a - 3d211717a775 - 07418a30ed01 - - 26e7304d6737 - - 93eb012d9eed + - a67ac707496a + - 71aa86af6762 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 56d5b797ce84 - - b8858746dc1f + - 26983857c91a - dd0b7398bb96 + - 56d5b797ce84 - 2bc10a9ca58b - - 29fcfd36e90a - - 26983857c91a - 5be24eba848d + - b8858746dc1f + - 29fcfd36e90a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - e6d0bff01239 - - 72bfafe3330b + - ee3a1b0f45f1 - 7ef978dc1b8a - - c3e012dfe21f + - e6d0bff01239 - 7e6bcd2e5128 - 9384cd033f30 - - ee3a1b0f45f1 + - c3e012dfe21f + - 72bfafe3330b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - 514fa53b5efb - - b73e213add0c - 167788df3b46 - - 9470f29702f8 + - b73e213add0c + - 514fa53b5efb - fd1275e01605 - - a60c359ec43c - d9a637e83828 - fb9cf9c97ec4 + - a60c359ec43c + - 9470f29702f8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: + - 5bffaa8354a1 - a02cfa31e9cb - - e479c7ca5570 - - c34d11ea4ba6 + - 2c37ce318bc3 - ca0616bb2cdf + - e479c7ca5570 - 86febdcc4283 - - 2c37ce318bc3 - - 5bffaa8354a1 + - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - 78f405266706 - - 69a8621ca2f0 - - 01fb6a7654e6 - 004aea905d4d + - 192ef85c0b0b - 2d466b530754 - 1fcb7adc39b8 - - 192ef85c0b0b + - 01fb6a7654e6 + - 69a8621ca2f0 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 2f9e4843f480 - d9ce4897dbb2 + - d580d6acd1df + - 9ecba5e225a6 - 459cfa861f0b - - 2f9e4843f480 - - 137c4beed34b - 3c9f0c486cca - db940c262830 - - 9ecba5e225a6 - - d580d6acd1df + - 137c4beed34b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fbe773640707 - fd408d755394 - - bd7db9e2f2cb + - fbe773640707 + - f264afa9fa6f - 32e451def88c + - bd7db9e2f2cb - bad3ca889618 - - f264afa9fa6f - 2c66e43f1c86 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 56bce3c82278 - - 7fda5607e777 - - 9368fbc49c8b - 4e12ea27f788 - - 3b9d990a0a0e - - 231994413f89 - 7e361d147872 + - 231994413f89 + - 9368fbc49c8b + - 7fda5607e777 + - 3b9d990a0a0e + - 56bce3c82278 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - b1779366c8e9 - - 94ca68515826 - - e65d16fb2724 - - 4431f39ede55 - - c03c3384cd81 - d9114ef1c8a5 + - 94ca68515826 - ce4ce3316f74 + - c03c3384cd81 + - 4431f39ede55 + - e65d16fb2724 + - b1779366c8e9 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 793665fff0f8 - 23f7c5f1fdaf - - d57251071381 - f8fc4e5aff9d - 2da482e408b8 - - b88ebb3672a1 - 4ed32329e0ed - - 793665fff0f8 + - b88ebb3672a1 + - d57251071381 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a4dfb122e52b - - c60570fa602f + - ba6efa77fb79 - 010e58e9d822 - 25d830337d31 + - a4dfb122e52b - 512155688d98 - - ba6efa77fb79 - e4c7985d4585 + - c60570fa602f - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -185,22 +185,22 @@ tools: owner: bgruening revisions: - 00d869ea03a1 - - 69264da0ce77 - 443d9a9d6d11 - - 4d678170d29b - 38e3f226248b - - aa200e4f3939 + - 69264da0ce77 + - 4d678170d29b - c899e0ccff8c + - aa200e4f3939 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - 6662b1a8d326 + - c361b12d207a + - d806504e96d9 - 10301d137111 - a2d70c4fd406 - - 6662b1a8d326 - aac8444d6681 - - d806504e96d9 - - 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 741f56294..c1e165269 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -2,15 +2,15 @@ tools: - name: obi_annotate owner: iuc revisions: - - 3021b9f5809f - d50dc96e3ce9 + - 3021b9f5809f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean owner: iuc revisions: - - 08d873cdd5f6 - 7d16de45c021 + - 08d873cdd5f6 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -30,15 +30,15 @@ tools: - name: obi_illumina_pairend owner: iuc revisions: - - 8cb6bd511879 - 94f412098ac8 + - 8cb6bd511879 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 91a1ed0b486f - 76e69de726b2 + - 91a1ed0b486f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 5f4544915893 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index 682da2752..a3d84dd92 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - d82648ad25a3 - 6da3972210ee - - 29bdbc353f20 - cf1322aeb137 - 62f5fab76dfb + - d82648ad25a3 + - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 5e574dc09..f4648155a 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - b1c926deaa2d + - 135b80fb1ac2 + - 660cffd8d92a + - de6cebe3c043 + - 49370cb85f0f + - c053d4cad713 - 8665bcc8b847 - - 4e5056fefd88 - - 8c0175e03cee + - c5e2e5902201 - c4b82dce8335 - - e4691e1589d3 - - 288f97432497 - - 48f587c13075 - - 49370cb85f0f - - 64172f1c1202 - - 660cffd8d92a - 5915ea1ec9b1 - - c5e2e5902201 + - 8c0175e03cee + - e4691e1589d3 - 44e2cc14f75b - - 093678460093 - fe74900d6dc7 - - c053d4cad713 - - 135b80fb1ac2 - - de6cebe3c043 - 5eb7e84243f2 + - b1c926deaa2d + - 64172f1c1202 + - 093678460093 + - 4e5056fefd88 + - 48f587c13075 + - 288f97432497 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -46,8 +46,8 @@ tools: owner: devteam revisions: - f666895cbebd - - 8889eb864cef - 9db07fd39f85 + - 8889eb864cef tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -86,16 +86,16 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - e626b3ff9922 - 8cacfcf96a52 + - e626b3ff9922 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 9457a20156db - - 859422bcb689 - 516b97a23d7e + - 859422bcb689 + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -114,9 +114,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a - - f773e98b26cf - f81d4362b6c1 + - f773e98b26cf + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -128,10 +128,10 @@ tools: - name: fasta_stats owner: iuc revisions: + - 9c620a950d3a - 0dbb995c7d35 - cd0874854f51 - 56022eb50bbd - - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -143,14 +143,14 @@ tools: - name: fastp owner: iuc revisions: - - 65b93b623c77 - - d60c3f704da0 - dbfc505896e9 - a626e8c0e1ba - - ecb9f4854617 - - 1d8fe9bc4cb0 - c59d48774d03 + - 65b93b623c77 + - ecb9f4854617 - dbf9c561ef29 + - 1d8fe9bc4cb0 + - d60c3f704da0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -162,9 +162,9 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 - 9115b978ce10 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -176,8 +176,8 @@ tools: - name: fastq_filter owner: devteam revisions: - - '144275714590' - 10b75444feae + - '144275714590' - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -190,9 +190,9 @@ tools: - name: fastq_groomer owner: devteam revisions: - - e9f8633db0a2 - - 8611b80a14d6 - 47e5dbc3e790 + - 8611b80a14d6 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -204,8 +204,8 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -233,8 +233,8 @@ tools: owner: devteam revisions: - 523c2aff0376 - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -246,8 +246,8 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - b41c2c1bcfbf - 2ccb8dcabddc + - b41c2c1bcfbf - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -260,9 +260,9 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: + - 8d958759cf2a - c885369b207b - 09a2199cd356 - - 8d958759cf2a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -274,10 +274,10 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - 397dc333436b - e39cc71d3ed6 - 249c8393f2d4 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -303,9 +303,9 @@ tools: - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - f0e7deab6518 - f86c27295151 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -317,9 +317,9 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 - f0b18efb97f1 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -331,17 +331,17 @@ tools: - name: fastqtofasta owner: devteam revisions: - - ac3fed111eb6 - 297962e79f39 + - ac3fed111eb6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - - 09070cacefd8 - - d5e9e83cd3d8 - 529bccd5e4a1 + - d5e9e83cd3d8 - 567d5b3c52b1 + - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -353,9 +353,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 0b7ec11b3c7c - 4bedca26c133 + - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -367,10 +367,10 @@ tools: - name: fastx_clipper owner: devteam revisions: + - cb1e251cac37 - 736b8f6ee456 - - 90858c306551 - bdf1ce174e39 - - cb1e251cac37 + - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -382,9 +382,9 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 - - 421f0af4ee95 - 07497255281e + - 421f0af4ee95 + - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -396,9 +396,9 @@ tools: - name: fastx_renamer owner: devteam revisions: - - f984bb114520 - 3599f5451ee2 - b29d37ca9e41 + - f984bb114520 - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -411,10 +411,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 0c2907307ba4 - - e246088b6e34 - 177f0621c266 - 6027ef51ef91 + - 0c2907307ba4 + - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -426,10 +426,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 73194cdd4f57 - 61b4cedc8934 - - 547e8d00f11c - 377ac2829eac + - 73194cdd4f57 + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -444,6 +444,12 @@ tools: - 03acc0e3772e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_fcs_gx + owner: iuc + revisions: + - 32d058f3462a + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu - name: ngsutils_bam_filter owner: iuc revisions: @@ -453,10 +459,10 @@ tools: - name: pear owner: iuc revisions: - - b4c6f054210a - - 2f804526f5fd - - f69501361cec - 037f0acc7830 + - f69501361cec + - 2f804526f5fd + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -468,32 +474,32 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: - - fdc21382376d - 29ef2c5ec205 + - fdc21382376d - 61eb4cfc7313 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - - 795cd16de38f - - 812705bcf39c - fe1ae2ebf63d + - 812705bcf39c + - 795cd16de38f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - 4b494533146a - - a019807f4e67 - 3da72230c066 + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -519,9 +525,9 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - d3f58a0dc09d - - 71f649c23021 - bf04bd405d5b + - 71f649c23021 + - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -533,12 +539,12 @@ tools: - name: umi_tools_count owner: iuc revisions: - - e654095ab143 + - 24013bf85a6f - 71ad4a56c40c - - 8250ea3a1501 + - e654095ab143 - b557acca0b56 + - 8250ea3a1501 - a535cf1e5da4 - - 24013bf85a6f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -550,21 +556,21 @@ tools: - name: umi_tools_dedup owner: iuc revisions: - - f1d33e4c7bd8 - c5a2ee07c4e1 + - f1d33e4c7bd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: - - 6a675c3aa610 - - 7accf7407811 - - 9fa7803d1c51 - - 7a7e33d28f62 - 015cf18f4a15 + - 7a7e33d28f62 + - 9fa7803d1c51 + - f3759eec3018 - 27ac32a22ad2 + - 7accf7407811 + - 6a675c3aa610 - 828dba98cdb4 - - f3759eec3018 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -576,15 +582,15 @@ tools: - name: umi_tools_group owner: iuc revisions: - - d6255614afd7 - 428735be9764 + - d6255614afd7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist owner: iuc revisions: - - 953b4821b183 - 4c8a1c7d3608 - e4e12f0b3af1 + - 953b4821b183 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 9a42333a8..530a0f8c1 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: + - 64e9a6afdd0c + - ce9cd02d5b88 - e41385662e5e - 7b4468117008 - - ce9cd02d5b88 - - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,36 +18,36 @@ tools: - name: fastqc owner: devteam revisions: - - ff9530579d1f - - 2c64fded1286 - - 2b0c9d9fc6ca - e7b2202befea + - 2c64fded1286 - 3d0c7bdf12f5 - - f2e8552cf1d0 - - 5ec9f6bceaee + - 2b0c9d9fc6ca - 9da02be9c6cc + - 5ec9f6bceaee + - ff9530579d1f + - f2e8552cf1d0 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: - - b6b54ba71bd8 - 18a51655db17 + - b6b54ba71bd8 - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - cc0fd298cc17 + - 7306ec78632a - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -62,23 +62,23 @@ tools: - name: multiqc owner: iuc revisions: - - f7e2f1eb3a16 + - 9a913cdee30e + - f7985e0479b9 + - 1c2db0054039 - abfd8a6544d7 + - 3d93dd18d9f8 - b2f1f75d49c4 - 5e33b465d8d5 - - f7985e0479b9 - - 75c93c70d094 - bf675f34b056 - - 3d93dd18d9f8 - - 1c2db0054039 - - 9a913cdee30e + - 75c93c70d094 + - f7e2f1eb3a16 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - - 084bbd8ba7b8 - 949f01671246 + - 084bbd8ba7b8 + - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fetch_alignmentssequences.yml b/staging.gvl.org.au/fetch_alignmentssequences.yml index c01999d90..0dfc5355c 100644 --- a/staging.gvl.org.au/fetch_alignmentssequences.yml +++ b/staging.gvl.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index b248d7a64..0060ed139 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 83a19df00eab - 141612f8c3e3 + - 83a19df00eab - 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 015c87e6d..2fa9d9531 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 @@ -24,8 +24,8 @@ tools: - name: gemini_burden owner: iuc revisions: - - df57188562f0 - 1a4c5adcd587 + - df57188562f0 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -52,15 +52,15 @@ tools: - name: gemini_dump owner: iuc revisions: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -86,30 +86,30 @@ tools: - name: gemini_load owner: iuc revisions: - - b2c25142267e - - 45296e47d565 - cf61daf064fe + - 45296e47d565 + - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors 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 @@ -137,15 +137,15 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -158,14 +158,14 @@ 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 owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 34c4db133..6e2bcd639 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 7c55208a2..45be047b2 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: + - b39347891609 + - e9df53a75f3c - 983bf725dfc2 - c1b437242fee - - e9df53a75f3c - - b39347891609 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -25,45 +25,45 @@ tools: - name: sra_tools owner: iuc revisions: + - 1790dcf3c32d + - 69ebb7f46e45 + - 7068f48d0ef9 + - 653e89d73fc4 - 8848455c0270 - - 4df8de2d0e48 - f8054ea1c365 - - 9a776b080193 - - 69ebb7f46e45 - - e08a7ad4378b - - f5ea3ce9b9b0 + - 1ec814014652 + - 734abc7ac21d - c441583adae5 - - aad3885b3216 + - 83c7d564b128 + - 9a776b080193 - 6591f049cf7e - - 516a54ddf218 - e407b9da183a + - f5ea3ce9b9b0 - 6ea73833cf67 - - 5e6237d58b0c + - e08a7ad4378b - ba931a59dd59 - - 653e89d73fc4 - - 83c7d564b128 - - 734abc7ac21d - - 1790dcf3c32d + - 516a54ddf218 + - aad3885b3216 + - 4df8de2d0e48 - 4317d3cb6cba - - 7068f48d0ef9 - - 1ec814014652 + - 5e6237d58b0c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 21a560af5913 - - 75b3b3d0adbf - 9aaa46d45472 - 34758ab8aaa4 + - 75b3b3d0adbf + - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 054483e27a35 - bfdc6a7ffd3a - - 468c71dac78a + - 054483e27a35 - af5eccf83605 + - 468c71dac78a 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 fbe435194..c1a892875 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -3,14 +3,14 @@ tools: owner: iuc revisions: - 290a11559985 - - df7356989ac1 - - ae9994cf526f - - 4b519282a05b - - 740057a5126d + - c4bde687c846 - 7f13dc906cb9 + - 4b519282a05b - fd59d783248a - - c4bde687c846 + - ae9994cf526f + - df7356989ac1 - a64dc31ab7f2 + - 740057a5126d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,9 +34,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - 867ab348287d - f95284aa2946 + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,56 +48,56 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 374e9062d874 + - 53460afd5115 + - 3b37b1b1c3a7 - ca7cb0eaad62 - - 48b42ee61bc5 + - 374e9062d874 - 51c6ccaace7e - '566197475670' - - 53460afd5115 - - 3b37b1b1c3a7 + - 48b42ee61bc5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b - - 3d059e9c2fba - - 1a72f938213e - 391a4cc45fea - - d3a9e32672ec - 10515715c940 + - 1a72f938213e + - d3a9e32672ec + - 3d059e9c2fba + - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - b0d96516e6a5 - 6fc8bab811da + - b0d96516e6a5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca owner: iuc revisions: - - b1268b7544d3 - ae344ccf9d62 + - b1268b7544d3 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 5fe1dc76176e - - e3a675da7fd0 - 299307abd804 + - 5fe1dc76176e - 1acf88921176 - - d0fc8b746d57 - 5298e06f14f9 + - d0fc8b746d57 + - e3a675da7fd0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 17b666467c32 - 0e7290688b50 + - 17b666467c32 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -109,22 +109,22 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram owner: devteam revisions: - - cdb9e89e2970 - 6f134426c2b0 + - cdb9e89e2970 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse2 @@ -136,16 +136,16 @@ tools: - name: jbrowse owner: iuc revisions: - - fd5dbf0f732e + - 112eb40ba6cf + - 1cfc579079a6 - ca2def38369c + - 4542035c1075 - a6e57ff585c0 - 17359b808b01 - - 667e17248bfe - - 836d1aa3e89a - - 112eb40ba6cf - - 1cfc579079a6 + - fd5dbf0f732e - 2bb2e07a7a21 - - 4542035c1075 + - 836d1aa3e89a + - 667e17248bfe - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -165,8 +165,8 @@ tools: owner: iuc revisions: - 03c13085aecc - - f1691de443a7 - fe154a7af404 + - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -179,18 +179,18 @@ tools: - name: plot_ragtag_paf owner: galaxy-australia revisions: + - 94e0834ae4ed - 501dcf66c0ce - c1bed78b9ed5 - - 94e0834ae4ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: + - 85da91bbdbfb - 1c5dcef5ce0f - - f234e2e59d76 - 62e3a4e8c54c - - 85da91bbdbfb + - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -209,10 +209,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 6c571966cfb9 - - 7c9417381ad5 - 26f2fe7e53a1 + - 7c9417381ad5 - 44c66e8d21e6 + - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -224,23 +224,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 36b848d5f3ec - 360df4999907 + - 4ac4e7083b7e - 2824d77cd8f8 + - 7dd841a32245 - a1abfa420d9d - - 326a3db8d9d1 + - 36b848d5f3ec - 14e7c35f3d00 - - 7dd841a32245 - - 4ac4e7083b7e + - 326a3db8d9d1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - - 83c573f2e73c - 99ace6c1ff57 + - 83c573f2e73c - 73b8cb5bddcd + - 44608d0193ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 @@ -252,7 +252,7 @@ tools: - name: xy_plot owner: devteam revisions: - - ecb437f1d298 - 319fa5a9fc1b + - ecb437f1d298 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 1975ad826..a274a804e 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -21,62 +21,62 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - - bc9e8de21efb - - 7779b9dcf040 - 6417cccad133 + - 7779b9dcf040 + - bc9e8de21efb + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: - - e9283529cba1 - - 361608369dda - bf1e0bdec1db + - e9283529cba1 - 55ccc0a121bc + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: + - da611a744112 - 474a69c47184 - cc64914b0cf4 - 23d838d1569d - - da611a744112 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: - - fc4b3b46dc9d - - 36735850e461 - ad6995afd2e6 + - 36735850e461 + - fc4b3b46dc9d - 2ccd9f9e2cd0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - 81c34e67f262 - 49653e680ea4 - - 0a8e527d1517 + - 81c34e67f262 - d8f5224005bb + - 0a8e527d1517 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 + - 79da59a0b180 - 4667fe07bd68 + - 64dd8bb151e1 - 2861ca3bfe4d - - 79da59a0b180 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -103,9 +103,9 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - ff6decc0f432 - 94697510d55f - 9a2f72d7dbd2 + - ff6decc0f432 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -118,47 +118,47 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 3027cb62adbd - - 6b97ffba31da - 28b1546857b0 - 8d9c22419c56 + - 3027cb62adbd + - 6b97ffba31da tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 73d43034c860 - d4c9061c8fef + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed owner: ebi-gxa revisions: + - 35f6611fb8c3 + - 1be0fc4d8654 - 7d5c97823f8b - 56d22aa6cb3b - - 1be0fc4d8654 - - 35f6611fb8c3 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 6f5509cf3176 - 4a74b45c1ce4 + - 6f5509cf3176 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - cb1992d1804b - d3df472a21dc + - cb1992d1804b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x owner: ebi-gxa revisions: - - 078aa23c9374 - 287503c35cb4 + - 078aa23c9374 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable @@ -200,27 +200,27 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: - - 0cf90e01d9f8 - - 59028945c857 - 4428dba93375 + - 59028945c857 - 3ee74b58c72d + - 0cf90e01d9f8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - 8b0d6f6f44c8 - - 181d61d2f3cd - abdb61e4afa3 + - 181d61d2f3cd - 3fb53f5e46ea tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - bd4a244faeb8 - fe562424a0a6 - 767a675b5254 + - bd4a244faeb8 - ea91cfd0444e - 0f98603d0116 tool_panel_section_label: HCA Single-cell @@ -230,7 +230,7 @@ tools: revisions: - 5605f8452eb3 - e2d0dc8a50ca - - 4cc9362782b4 - f86b2c3bc459 + - 4cc9362782b4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index d718c0578..b47a1b193 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,35 +2,35 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - a4c13ddcc8ee - 9edf8894a22d - - ed2cca6b5de4 - - 0f611e7d7858 + - 29f66c353bcb - d9967770de96 - 921a2da49a0c - - 29f66c353bcb + - ed2cca6b5de4 + - a4c13ddcc8ee + - 0f611e7d7858 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 755df866ad0c - - ec4b948dc6f0 - - 78fb5e286609 - - 5746d61f0a91 - 11de0d28ab30 - - d404277cc87a + - 78fb5e286609 + - ec4b948dc6f0 + - 755df866ad0c - 478aacfbaa37 + - d404277cc87a + - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 4d511437b1e5 + - 11fa44ee0603 + - 9d93c8fbe0a6 - 9e357a8b2ec3 + - 4d511437b1e5 - 977dc15add20 - - 9d93c8fbe0a6 - - 11fa44ee0603 - 03dd3c16ae4e - f72063d9426b tool_panel_section_label: HiCExplorer @@ -38,23 +38,23 @@ tools: - name: hicexplorer_hicpca owner: bgruening revisions: + - f86ca478c6af - 0ba4f56a3613 - - c3e5e2cf12b7 + - 41dbf4d162a2 - 1da5f169b491 - - f86ca478c6af - 77919cc3618e + - c3e5e2cf12b7 - 3b5b54ed6392 - - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: + - 7babd8a46fe0 + - 9939786dd9c9 + - 025a128652dc - b63363075c2e - f741330d4a71 - - 025a128652dc - - 9939786dd9c9 - - 7babd8a46fe0 - 5308ca68ef3d - 12d51d7be66f tool_panel_section_label: HiCExplorer diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index dd9315c67..0df8eb1be 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,37 +2,37 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 7db4fc31dbee - - 0c777d708acc - 81f0cbca04a7 + - 0c777d708acc + - 699a5e9146b3 + - 7db4fc31dbee - 8bccb36e055a - 3df9f0a4bf34 - - 699a5e9146b3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - 5bc8cdc17fd0 - - 2436a8807ad1 - 0a53256b48c6 + - 2436a8807ad1 + - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: + - e576b73a2e2f - 6ad1d3cfdea1 - 9d47aabda459 - - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - 70316d792fc9 - - 77f7159d775a - b1c2c210813c + - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter @@ -47,33 +47,33 @@ tools: owner: imgteam revisions: - fcadded98e61 + - 85edbb7a436b - 10eed33aa9b2 - f3360fbeda64 - b07f4839ca77 - - 85edbb7a436b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - - b58447a2eed2 - - 664232d2a3f7 - 5bf8eb50b280 + - 664232d2a3f7 + - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - 0e4dccaafef5 - - eb6c08714244 - e917a2424690 + - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -87,47 +87,47 @@ tools: owner: bgruening revisions: - e7273daa5ae2 - - 670975e92458 - 6070780813d9 + - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: + - ef4aed1d34c4 - df3ad3ba5c6f - cdf8e3c57dae - - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - - 2484086dee41 - 5d28ac336861 + - 2484086dee41 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f24c370e5ea4 - d0178bdcd00e - f8fa0f6718a3 + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 3245681b2f6d - 31d195bedf6d + - 3245681b2f6d - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -135,23 +135,23 @@ tools: owner: bgruening revisions: - b6eec6087271 - - 993faa34333b - 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 - - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - 3a05117669cf + - b178453ea8d1 - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -174,32 +174,32 @@ tools: - name: cp_measure_image_intensity owner: bgruening revisions: + - b64af54c5c09 - 8536b1ae0254 - 5499dc6f8ac1 - - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - 6f4715b8540a - - e972e07c7845 - d3890df07463 + - e972e07c7845 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 407925835dd9 - 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 + - acf3aa487283 - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -220,17 +220,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - 8083a87d2fdf + - 3a3033222f61 - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - - 27edbb90ab2b - 4ecf93628f97 + - 27edbb90ab2b + - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -249,16 +249,16 @@ tools: - name: idr_download_by_ids owner: iuc revisions: - - f92941d1a85e - 4b794652dcdc + - f92941d1a85e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - f8b4eada923c - - 7b6d9412c7f8 - 236ec78b2e53 + - 7b6d9412c7f8 + - f8b4eada923c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index beb9e628c..ab1f40c8b 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - f362150bef41 - - 1069f6db0a0e - - e319b5b65879 - 3e4f434a69c6 + - e319b5b65879 - a38934e303b9 - - 40737febe339 - - e4ee04da1c19 - - d6e72da3ec35 - 3a72fede57ce + - f362150bef41 + - d6e72da3ec35 + - 40737febe339 + - 1069f6db0a0e - 78bbd17d0703 + - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - c88553ec696e - - 9537184d421f - 0135f1d487a0 + - c88553ec696e + - 2b95d5c04908 - 72ddd32392cd - - 618297d23022 - - fcbeda41d0ac + - 9537184d421f - 8f8df367470d - - 7fe36019c073 - f91cfb73d369 - - 2b95d5c04908 + - 7fe36019c073 + - 618297d23022 + - fcbeda41d0ac tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: + - ad0dc9f4c9e2 - 2cf4a1cafc16 - - d7e79eb3bcb3 - fafb3d685fa9 - - ad0dc9f4c9e2 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: + - 3d18f8c3c0f6 + - 7f1cfa4c0e32 + - 8c05afb547fa + - 6a1515bb0687 - ee29337f905c + - a1c2aecd7a0d - 43aac8d29685 - - ee2beb764a7b - - 9eaadf03e0df - - 3d18f8c3c0f6 - 94df24c6bc00 + - 8d36959b000d - bd2a7d1316b9 + - 9eaadf03e0df + - ee2beb764a7b - 28a6f1908fcc - - 6a1515bb0687 - - 8d36959b000d - - 7f1cfa4c0e32 - - 8c05afb547fa - - a1c2aecd7a0d - 5dc33613c288 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - 5671e1d3d5ee + - 364f4ffec275 + - bcaa0d571ce2 - a250929be21b - 86a20ae274fc - - 5671e1d3d5ee - - cb903c9dc33d - - 8858fa037a15 + - 5d6ed46cc101 + - e3bb03cf207a + - d37ede8589b2 - 9f978da6528a + - cb903c9dc33d - db536ad45f28 + - 8858fa037a15 - c092052ed673 - - d37ede8589b2 - - 5d6ed46cc101 - - 364f4ffec275 - - bcaa0d571ce2 - - e3bb03cf207a tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 230b05597996 - - f95f403841ad + - abbc8041e8ec - e1a015876aa9 - - 584beffa972b + - f95f403841ad + - 230b05597996 + - 12d66d0d05ac - 38b91a3190cd - c5c9f02b6167 - - 12d66d0d05ac - - abbc8041e8ec - 3b6a16d82c1b - - 49236b03e4fd - - ed28dd32141c - 194e3ceee923 + - 584beffa972b + - ed28dd32141c + - 49236b03e4fd 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 179237f07..e3e2207e4 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: + - b8a457820315 - f198773344e4 - 17e3b698dd52 - 0f1724dd59d2 - - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 22c2a1ac7ae3 + - 374cb875d38a + - ba0c40780ecf - a513e3fbb4c5 - ac092723240d - - ba0c40780ecf - - 374cb875d38a + - 22c2a1ac7ae3 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 b5665f481..e23469ca7 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -10,69 +10,69 @@ tools: - 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: + - 2af1346e68c9 - 818f9b69d8a0 - f1b9a42d6809 - - b6ef6d0cb6b7 - - 2af1346e68c9 - e1317b5502fa + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 947c2eacccb8 - - 05143043ca13 - 1588f9076e32 + - 947c2eacccb8 - c80db5d6fd8c + - 05143043ca13 - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 25b46af53232 - - 29e4122c90de + - 1552b8cb4a94 - 9991c4ddde14 - 83228baae3c5 - - 1552b8cb4a94 + - 25b46af53232 + - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 53616c8b0865 - - 1a53edc4b438 - 841a6cc5fc58 - f3dfa4bdf87e - - a07ab242b0b5 + - 1a53edc4b438 - 060ca94ac049 + - 53616c8b0865 + - a07ab242b0b5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 927586a18553 - - 40f4447733b2 - - 91c4e3331208 - - dc4b5fd604a6 - - 2fc89dcd41c8 - d4808d5b83da + - 2fc89dcd41c8 + - dc4b5fd604a6 + - 91c4e3331208 + - 40f4447733b2 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: + - 301e07345c93 - e5a5ad882f1f - 25ab6b4e376e - - 301e07345c93 - c6ae57f774c6 - 7626ea9c2e1b - 36e8d6d5d01b @@ -81,12 +81,12 @@ tools: - name: sklearn_svm_classifier owner: bgruening revisions: + - b7c3e9a3b954 + - 80852884053f - 4ed102b922cb + - 02d2be90dedb - f9639b488779 - 0630258dcf35 - - 80852884053f - - b7c3e9a3b954 - - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical @@ -94,7 +94,7 @@ tools: revisions: - 61634a87efc7 - 14180f9c831e - - ec69cbe34b73 - caeb57858702 + - ec69cbe34b73 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 06d276db7..d32f833ab 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - a6d65b0c67af - - 0d4acadabb04 - - 3ba8d4563129 - - cd659e8cc5fa - 749c918495f7 - - d5ceb9f3c25b - 17062a0decb7 - - 017aba02828d + - 3ba8d4563129 + - d5ceb9f3c25b + - 0d4acadabb04 - 03e9b2fbc005 - - 937aa69e715f - f6877ad76b00 + - 017aba02828d + - 937aa69e715f + - a6d65b0c67af + - cd659e8cc5fa tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - 3fe632431b68 - - 2477830927ec - - 64f11cf59c6e + - dfd8b7f78c37 - 53646aaaafef - e188dc7a68e6 - - dfd8b7f78c37 + - 2477830927ec + - 64f11cf59c6e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - 37b497aa133f - - 60afcc2c1d05 - e7f19d6a9af8 - - 3e1ea2facca6 - 2ff111fac1d7 + - 60afcc2c1d05 + - 3e1ea2facca6 + - 37b497aa133f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 6b1e195506a3 + - 77b2770508f6 + - b3eab4b67562 - 11a0d50a54e6 - - 3f4d6399997b + - c0c2d0941de8 - 53c0b7a1a0c3 + - 09b53c1d4ab1 - 037c6e54df11 + - 6b1e195506a3 - be1d967337e4 - f54f5baedfdd - - 8c6cd2650d1f - - b3eab4b67562 - 5cc34c3f440d - - 77b2770508f6 - - 09b53c1d4ab1 - - c0c2d0941de8 + - 8c6cd2650d1f + - 3f4d6399997b tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 00fbfac99d39 - - 13022c3d3076 - - 178bdbdb6d24 - - ec9cbd6b9a49 - - e403d27e8f24 - - 9ee34ba73ebf - - 79b885ce78d7 - b8f5f6e87f5c - 1cd2511a396e - - 381a32c51141 + - e403d27e8f24 - 42ce70172b72 + - 9ee34ba73ebf + - 79b885ce78d7 - 5ef7ec16b04f + - 00fbfac99d39 + - 381a32c51141 + - ec9cbd6b9a49 + - 13022c3d3076 + - 178bdbdb6d24 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index 932622299..4c72ed3cc 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -63,8 +63,8 @@ tools: - name: isolib owner: recetox revisions: - - 2b1118bce0b1 - 6b0fef8a77c0 + - 2b1118bce0b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -94,22 +94,22 @@ tools: - name: matchms_convert owner: recetox revisions: - - 9e83636da9d3 - b9cc12600553 + - 9e83636da9d3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - 83c4b4359ac4 - a177ac3c752c + - 83c4b4359ac4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - - fd890f162ce6 - 84af792d3a78 + - fd890f162ce6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter @@ -142,8 +142,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - f04b378325e5 - 8147d93d372d + - f04b378325e5 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -167,8 +167,8 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 9ff95a1a2705 - 7ba589b01dbc + - 9ff95a1a2705 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -249,63 +249,63 @@ tools: - name: ramclustr owner: recetox revisions: - - 9b716db0a786 - da7722f665f4 + - 9b716db0a786 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - 7b42ee54d757 - c53a97599181 - - ec196e27a61a + - 7b42ee54d757 - 79ad928a0dae + - ec196e27a61a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - 59c393d35e0e - - 18ec7635bac6 - f3a18e020cdd - 149b9cc7499b + - 18ec7635bac6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - dfebc82ba1f0 - - 481d769e2f7a - 134be5abb208 + - 481d769e2f7a - 50b9918aeff2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 51332c2520c7 - - 9064aecc78a7 + - a82db010c53e - 501a232f3cd5 - - 30bf4e35da3e + - 51332c2520c7 - 02c772a49998 - - a82db010c53e + - 30bf4e35da3e + - 9064aecc78a7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b341cfd4baf8 - - 89178a72388a - b3413f335327 + - 89178a72388a + - b341cfd4baf8 - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - dd7bbc2b99d1 - 17a48d0a80f4 - b7c8a44b9cc1 - - dd7bbc2b99d1 - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -314,17 +314,17 @@ tools: revisions: - d7f5878a98c3 - 99d118321d5f - - f92b1b64da93 - 24278c6b6d1c + - f92b1b64da93 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - d90187b0f247 - - 7acd11ddc061 - ea0758b41473 + - 7acd11ddc061 - ffbabefbd2e2 + - d90187b0f247 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -336,8 +336,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 2c6fa447f6a0 - 6b5dec818827 + - 2c6fa447f6a0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 7a00572c8..a4800bf32 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -9,8 +9,8 @@ tools: owner: iuc revisions: - 0094893f5001 - - 0e63d03c8790 - 18676df0cb3a + - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -22,8 +22,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -95,31 +95,31 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 63f86089423e - 5b5a7af9fbb4 - - 3a89c3f99f3d - 7c2100246a2f - 76d3d2b10738 + - 3a89c3f99f3d + - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 96336c6a2bb7 - 00f5005840fa - - 18a502a9d287 - 1c35dadbe76f + - 96336c6a2bb7 - 84fd33a60b35 + - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - a9f4a217dcd6 + - f732237754fc - 34e55239e68b - addaf9d22850 - - a9f4a217dcd6 - e8fba04706d3 - - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors @@ -127,9 +127,9 @@ tools: revisions: - 04c15826a0b8 - 75403243703a + - 0776d824d896 - 5fe3edf19b9c - 8c202e741d68 - - 0776d824d896 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable @@ -145,86 +145,86 @@ tools: - name: dada2_mergepairs owner: iuc revisions: + - 5c865a382933 + - 1d75bd0595e2 - 35176674168c - 84743da21318 - - 1d75bd0595e2 - - 5c865a382933 - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 78faebd0879c - - 8daf4564ccda + - 32c9ea835770 - 555ccac8a4c5 - ac72310b038a - - 32c9ea835770 + - 8daf4564ccda + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 - - 7b8cb2b02978 - - a58e4a43f49c - cae017b76acb + - a58e4a43f49c - f947b4bb5107 + - 7b8cb2b02978 + - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 04144473e59e - 7f3b59dee073 + - 1bc3657cd694 - 1770d188f72d - - 04144473e59e - 7136e9ab70db - - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 0a1224c4b781 - - 9058d8943303 - - 19299bb1c6af - d943081510da + - 9058d8943303 + - 0a1224c4b781 - a7817705348e + - 19299bb1c6af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - bc939965ce41 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - a68b985913ab - - dbf1798c0dcc - - 5c7ba3d85a01 - - 4d9445dff47b - b907a3c0434f + - c4db8c4de66f + - 4d9445dff47b - 65d52c693b8e + - a68b985913ab - f8f56dd6449f - - c4db8c4de66f + - 5c7ba3d85a01 + - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - 6d364c65c946 - - 6c84982ee6f7 - 654548ae1357 + - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -236,24 +236,24 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - e66ab198ec15 - bd7a9c6efb10 + - e66ab198ec15 - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - d77397f09da1 - b084117133af - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 7f208f1eb64f - 9704f1a3b32d + - 7f208f1eb64f - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -286,40 +286,40 @@ tools: - name: humann_reduce_table owner: iuc revisions: - - 60749924ad62 - 6552df6efe6b + - 60749924ad62 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - - e88b731dad59 - - 31c6d107e7a5 - - 8237a0f225db - 79706f10d680 - c409a495841f + - 31c6d107e7a5 + - 8237a0f225db + - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: + - d24841f5c3d2 - aabf8cfb8fef - - 71ea608ddfa3 + - 172920f67a84 - 094ad9c068af + - 71ea608ddfa3 - 714d5a28cc5c - - 172920f67a84 - - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - 12fb63b5f63f + - 2bdd84912a2b + - d7e9a3c41657 - 4137b492233e - a4d7148ccee4 - a293a742194f - - 2bdd84912a2b - - 12fb63b5f63f - - d7e9a3c41657 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -331,13 +331,13 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 64bc7acc22a9 - 97f7bb0851e7 - - e2c71b852aba - - 6fcb8ac37a3e - 75bedfb2078b - - cf87759761eb + - 6fcb8ac37a3e - a92c06a3afa7 + - 64bc7acc22a9 + - e2c71b852aba + - cf87759761eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -356,22 +356,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c - - 2d35528d2141 - - 4033827c76b8 - - 5e5a999ffaa9 - c82508e76ad1 + - 2d35528d2141 - 4e5e73d03f0d + - 5e5a999ffaa9 + - 4033827c76b8 + - 080ea153677c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 6b7622dda516 - - 95bf7479d53c + - 2cd76b089570 - c2803012bbb3 + - 6b7622dda516 - fc6c328c292f - - 2cd76b089570 + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -389,15 +389,15 @@ tools: - name: jellyfish owner: iuc revisions: - - 11658afb8c87 - dcd30574a456 + - 11658afb8c87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single owner: iuc revisions: - - 385a965c6f87 - 65b382bf9b7c + - 385a965c6f87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution @@ -410,8 +410,8 @@ tools: - name: khmer_count_median owner: iuc revisions: - - b3d513c7093e - 570505540a7b + - b3d513c7093e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions @@ -431,8 +431,8 @@ tools: - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 19607c740d19 - 00f7064c564b + - 19607c740d19 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median @@ -487,8 +487,8 @@ tools: - name: kraken_report owner: devteam revisions: - - 1c677354ab18 - 6c09bed3444f + - 1c677354ab18 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report @@ -520,37 +520,37 @@ tools: - name: krakentools_beta_diversity owner: iuc revisions: - - c254d75b8b67 - 4505d7643673 + - c254d75b8b67 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_combine_kreports owner: iuc revisions: - - 3d2cffa2c4ab - 073c867c5244 + - 3d2cffa2c4ab tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads owner: iuc revisions: - - 4bf1e2701504 - f329328da134 + - 4bf1e2701504 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 - 02bbace216f2 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: - - d33cf727ed94 - bb96a1e6583d + - d33cf727ed94 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -580,22 +580,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 4fd3b5d8706b - - 7f5d7b0e9884 - - 2cff76cf35c6 - - 0270541aaf46 - e073891b2afc - 3cc4a60615c0 + - 4fd3b5d8706b - 27250f92a01a + - 2cff76cf35c6 - 327d9f4cc95f + - 7f5d7b0e9884 + - 0270541aaf46 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 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 @@ -661,33 +661,33 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: + - ec368db926f4 - 1a037928504c + - ef65b083bd0c - 740fd2d16a28 - a92a632c4d9b - - ef65b083bd0c - 289b3807e80c - - 1a6cdf55390f - - fd69c607b43f - - 6dee4abadccb - - 2131d7dca455 - ff8f55893e7d + - 2131d7dca455 - b89b0765695d + - 1a6cdf55390f - a16313517e55 - - ec368db926f4 + - 6dee4abadccb + - fd69c607b43f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - 2a8bc1d26d06 - e3a64a1d2a6e + - 2a8bc1d26d06 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -711,8 +711,8 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 6034c3f3ecf0 - 2f47a294ef49 + - 6034c3f3ecf0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp @@ -804,8 +804,8 @@ tools: - name: polypolish owner: iuc revisions: - - 915637bd1d1a - f355085dd2aa + - 915637bd1d1a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: pynast @@ -823,20 +823,20 @@ tools: - name: recentrifuge owner: iuc revisions: - - d4fbfd31696c - 591175c0f051 + - d4fbfd31696c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - 141afacabcfa + - 3b22de20bd4b - 4d83eccf5f81 - - aeaa20b96ef2 - 4b9a8031ab74 - - 2fd4d4c9c5c2 - - 3b22de20bd4b + - aeaa20b96ef2 - be818ae858e4 + - 141afacabcfa + - 2fd4d4c9c5c2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -866,8 +866,8 @@ tools: - name: vsearch owner: iuc revisions: - - b3c7199d8786 - 9495df9dd6ef + - b3c7199d8786 - 576963db5f1b 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 8c018af31..a43ddad63 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - 12e856482d26 - bdb4a58a2025 + - 12e856482d26 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - ab12df91b47f - 7238968f58f7 + - ab12df91b47f tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 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 d6ae9c075..559fcd7c1 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - a74dbfee5a86 - - 9422c5a87ee2 - 94b8c6013083 - - 2263989660f5 + - 6ae5a7b5a0a2 - bdfbaf0c10aa - - 8b67dd48fec1 - - 9baa871cb1d1 - - 80f03df2e2ce - - cd07731e4434 - 9eeb13a92d79 - - 6ae5a7b5a0a2 - 098506c54016 + - 8b67dd48fec1 + - 2263989660f5 - 48c13389050d + - cd07731e4434 + - 80f03df2e2ce + - 9baa871cb1d1 + - a74dbfee5a86 + - 9422c5a87ee2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - be78f13134e2 - - f0af8936ed41 + - 2e093badc689 + - d7ce0ec78e51 - bc3831dd65c1 - - 5abf2c2249aa - - 3ff17bad4006 + - fc2e49f91e52 + - aaa0d6a8b808 + - d390fe1567dc + - be78f13134e2 - c44f824c051a - - d7ce0ec78e51 + - 5abf2c2249aa - '764845535798' - - aaa0d6a8b808 - - 2e093badc689 + - 3ff17bad4006 + - f0af8936ed41 - f14193ec1f50 - 4a60927aaca5 - c18157c68134 - - fc2e49f91e52 - - d390fe1567dc tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -53,75 +53,75 @@ tools: - name: clustalw owner: devteam revisions: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: - - 5efbd15675ca - 1de657a3198d + - 5efbd15675ca tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: + - a65296ffb4a0 + - 15974dd17515 - f1a5908ea2cb - 6f28e90db932 + - f0d493f8f84f - c5908940967d - bf28a8cff401 - - a65296ffb4a0 - - f0d493f8f84f - 8e649f27aa0d - - 15974dd17515 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - - b3acbb3a6af0 - e8fdceffea4c + - b3acbb3a6af0 + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 5561a1193611 - c9685bc0407c + - 5561a1193611 - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - - 57f042937ba7 - bcd65de9725b + - 57f042937ba7 + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - fb43e8887350 - ebe3b0f84de9 - 4fc0cb2ac8ae + - fb43e8887350 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: + - e18267f90096 - 636b049e6141 - 7cd7a55a678d - - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - cf3c9489c088 - b4124df98b26 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index aedc656c5..d1a9f63d1 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,10 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: + - 9aa9d92c3c51 - 7c47b3c9e493 - 18a8d140ec6f - 28928576e1ea - - 9aa9d92c3c51 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -23,8 +23,8 @@ tools: - name: dorado owner: galaxy-australia revisions: - - fc5b6491cf78 - 63d8ecfcfab1 + - fc5b6491cf78 - 6942f170cc43 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,19 +39,19 @@ tools: revisions: - fc8804320156 - 72b5e9dda577 - - 79e9a869f40e - a7228a7ea146 - - 0e9e7fcdd543 + - 79e9a869f40e - cb34f00cc10f + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - 18505fe2bdb1 - - d6cddc06aeae - fa11aa8103b2 + - 18505fe2bdb1 - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -63,22 +63,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - ec699520444c - - 19f3b583a9b3 - 0f5f4a208660 - edf6d4003fad - - 43815fa60f3a - - cc36773a3681 - - 222669c4afb6 - 2bf63b38ee9b + - 43815fa60f3a + - 19f3b583a9b3 - eb746fa6f514 + - 222669c4afb6 + - ec699520444c + - cc36773a3681 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - b833eff63b10 - c0fb573c1e8d + - b833eff63b10 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -91,59 +91,59 @@ tools: owner: iuc revisions: - 7b379e98b9a9 + - a38bdcec9e4c + - a02b8b3f5a0c - 0f1c34698076 - - 645159bcee2d - a3c4fe6f49ab + - 645159bcee2d - edbb6c5028f5 - - a02b8b3f5a0c - - a38bdcec9e4c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - 3b6f94fc7e1d - - 85a394edc247 - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: + - a8d4be409446 - be95355fef8d - 90a922f32523 - - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: + - 449e9aeded2d - d376944466bf - 4857d5bcce52 - - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - a3afc5f0a96c - bec636361cfd + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - 5f76b20953e5 + - 543cbeef3949 - 93d623d9979c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - daf8518d243a - 1d835c691480 + - daf8518d243a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -155,8 +155,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - d1805f9c4c82 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -181,8 +181,8 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 626b6c2be5c2 - 2e22ebec211a + - 626b6c2be5c2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle @@ -219,8 +219,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - c5c5a3e84989 - 64a83664b814 + - c5c5a3e84989 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 1ea244375..5a37a7982 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -65,11 +65,11 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - adfd6bf710bd + - 97b1b5ad1cda - 3e73c97f025d + - adfd6bf710bd - d74850cf4e42 - baceff842902 - - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder @@ -90,19 +90,19 @@ tools: owner: iuc revisions: - e4b4837f06f5 - - 8c533e19b697 - 1e34d2e3d285 - - edacc4bcd3cb - - ed1518ce2237 - e9ee4d074d5d + - 8c533e19b697 - 2f27f3b86827 + - ed1518ce2237 + - edacc4bcd3cb 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 @@ -114,16 +114,16 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 74af283d8ebd - 472dabcb03bf + - 74af283d8ebd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: - - 5711fc06a63e - - 48a42ca61006 - 38ccd4589990 + - 48a42ca61006 + - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -136,8 +136,8 @@ 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 @@ -163,8 +163,8 @@ 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 @@ -172,15 +172,15 @@ tools: revisions: - 5bcf0e24f42c - 27a6a256cd23 - - b4b2b284230a - 172815da3d41 + - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - df84aaed4769 - 10232d2b5062 + - df84aaed4769 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_hisat2_index_builder @@ -214,8 +214,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 15c2fc266540 - 4c7ebbad42cf + - 15c2fc266540 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -233,36 +233,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 4ba60cb14cb0 - 5fe20c915fa6 - 0cb27ea69dc1 - - d8dc037e3c13 - 9c43baa60906 - 2c61c30a57e7 - - 4ba60cb14cb0 + - d8dc037e3c13 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 0db22932bc39 - - aec831b54a5b - 9d09724f2bf1 + - aec831b54a5b + - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - ed7a967cb11b - 29c738066906 - - 6e24e79d3d69 - df30a2f1db55 + - ed7a967cb11b + - 6e24e79d3d69 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -280,17 +280,17 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - defd3e9ddd2d - ad90c2da4f38 - - 3e4d45aca422 - 1865e693d8b2 + - 3e4d45aca422 + - defd3e9ddd2d 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 @@ -302,10 +302,10 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - 64deddb6a8ec - - d63c1442407f - 71c994a11f71 + - c520a52b5174 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder @@ -1070,16 +1070,16 @@ 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: - c362398df83b - - e4b7d1507a75 - a22969b08177 + - e4b7d1507a75 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -1091,9 +1091,9 @@ tools: - name: salsa owner: iuc revisions: - - ba7b0f11e470 - ab5b7f6b7198 - 9a22227bb6d0 + - ba7b0f11e470 - f77f7a7f3b83 - 58a870ef434c tool_panel_section_label: None diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 94b5e3ab0..98db1f432 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -26,8 +26,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -39,44 +39,44 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - b89cac5156ec - - f73435dc282b - - cce7b18495e4 - - 26de3a7b1cb9 - d033ffc1c161 - - 8834daeb9892 - - 6a457678efcb + - 3b8b5bde0bd9 - 3f59ebfbfe3d - 107d3ba7024a - - 81e66674859e - - d7c7ef3353fe - - a6619171428e + - b89cac5156ec + - 26de3a7b1cb9 + - 8834daeb9892 + - f73435dc282b - 5a7c56a5cc08 + - 6a457678efcb - f04a1264e2a2 - - 3b8b5bde0bd9 + - 81e66674859e - c78f3d7dd1db + - cce7b18495e4 + - a6619171428e + - d7c7ef3353fe - '841557158611' tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 02b8758214b0 - - aa8cc71438cf - - df47d4845b62 - - e75442c7f4da - - 7a2092844346 - - 659517798cc4 + - 6223845127ea + - 5b777002c2de + - b0af57c1a968 - 88c4aa435ded - - 4755f52427c4 + - 7a2092844346 + - 02b8758214b0 - a185b079b095 - 6a726db04d4b - - 5b777002c2de + - df47d4845b62 + - e75442c7f4da + - aa8cc71438cf - 6283babe736e - - b0af57c1a968 - - 6223845127ea - - 3b96e92e8ec3 + - 659517798cc4 - 5fcd1ece3a6e + - 3b96e92e8ec3 + - 4755f52427c4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree @@ -84,11 +84,11 @@ tools: revisions: - 70acec670c30 - f97743d52b87 + - 524d31add34a - b8476e82ac20 - - f87ac61981f0 - - 24d024316465 - d1c340a5664b - - 524d31add34a + - 24d024316465 + - f87ac61981f0 - 111bd54f6bc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -110,26 +110,26 @@ tools: - name: pangolin owner: iuc revisions: + - 2f1019071464 + - 7bb8726be37c - 81804a978fc0 - - abf6dbe8c9d7 - - 03ed9524dcd1 - - 8ad84c5753ea - - b7e297c2ede6 + - ca0d8cf80567 + - 9d61d3fa046c - a2099fb98cdb - - 5f8727ff21e7 - b6abccb1f25b + - abf6dbe8c9d7 + - 14ae456b8cc5 + - 2fa9d4f1b48f - ca337cce3888 - - 2f1019071464 + - 83a69484cb87 - 437e28791761 - - ca0d8cf80567 - - 3a43c3982401 - - 14ae456b8cc5 - - 7bb8726be37c - 36912871ccdc + - b7e297c2ede6 - 42a174224817 - - 83a69484cb87 - - 9d61d3fa046c - - 2fa9d4f1b48f + - 5f8727ff21e7 + - 3a43c3982401 + - 8ad84c5753ea + - 03ed9524dcd1 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: + - 29ff6a849eac - b1e68bbe4cef + - 73a469f7dc96 - a4b71be30c3c - - ea30d3089354 - - 29ff6a849eac - ba29b5e2a4be - - 73a469f7dc96 + - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 809e42326fc2 - - f1ccc8a6eb05 - - 91887494eb97 - e88a7de55d6e - dbe2b2204555 - - 15ac71df11a0 - 9b2b122d0415 + - f1ccc8a6eb05 + - 809e42326fc2 + - 91887494eb97 + - 15ac71df11a0 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 905e50afe..3287e1d83 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - f9242e01365a - - a1f0b3f4b781 + - b502c227b5e6 + - 881d7645d1bf - 3f254c5ced1d - - 7d34178f2812 - - f6ced08779c4 - 1aac2a13842a - - b502c227b5e6 + - a1f0b3f4b781 + - f6ced08779c4 - fc288950c3b7 - - 881d7645d1bf + - f9242e01365a + - 7d34178f2812 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 d88435844..7d6f90ee9 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,18 +2,18 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - 5b85006245f3 - - ca90d17ff51b - - a58f7eb0df2c + - e4a053d67e24 + - c0e71cb2bd1b + - e7f1b552a695 - 3f188450ca4f - - 7fbec959cf2b - - 3bd420ec162d - - 6ab1a261520a + - a58f7eb0df2c - d00e15139065 + - ca90d17ff51b + - 6ab1a261520a + - 7fbec959cf2b - eb085b3dbaf8 - - c0e71cb2bd1b - - e4a053d67e24 + - 3bd420ec162d - 2f7702fd0a4c - - e7f1b552a695 + - 5b85006245f3 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 9f4e0a401..e17af9407 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,94 +2,94 @@ tools: - name: cardinal_classification owner: galaxyp revisions: + - b18329a8ac14 + - b574b84afc4d + - 4c177985028a - f28ad96b76dc - 277dc652246e - 0a18ac48ac53 - - 4c177985028a - - b574b84afc4d - ece627528a78 - - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - bf06d196e23d - - e988563cc6e5 - - 525f201b86c1 - - e215f71d7983 - a9a28e46d54a - b41107d8fe89 + - e988563cc6e5 + - bf06d196e23d + - e215f71d7983 + - 525f201b86c1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - - bb6397b94018 - 8da3511c9467 - 56da27be956a + - bb6397b94018 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - 890845926d4b - - f23d67e28cc8 - b8c79e70516d - - 528fb09022be + - f23d67e28cc8 - a8157342d9a3 + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: + - ae304a72db7b - 80600735685d - - a95a82eb4d50 - - 25b83cbd596a - a69865da6f80 - - ae304a72db7b + - 25b83cbd596a - 59e85306eae5 + - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - f1897eb07081 + - e0669b1854b1 - 611d80c0e29d - 83aac7741200 - ed9ed1e6cca2 - 798da6bdff3d - - e0669b1854b1 + - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - 74b61bf5bc4b + - d426a9107a6c - a7fb9b395ddf - 5a35e3a8d013 - - d426a9107a6c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - cc430977c8ff - - df2187f9013b - 91f0f5922011 - 82f6c2f4332d + - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 1693b2126f30 - - ba92b59cd529 - - c5aa9fca18c6 - - d2483487e077 - 043f9c91f686 - 10566783d718 + - d2483487e077 + - 1693b2126f30 + - c5aa9fca18c6 + - ba92b59cd529 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: + - 9fa3dbf06f17 - ff8c9e0e8a7b - - bf0728e000cd - ae4dc0c041f9 - - 9fa3dbf06f17 + - bf0728e000cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,15 +122,15 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - d0ea7589e95f + - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 0fa397f4f40b - 4081e4faa4ab + - 0fa397f4f40b - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -144,9 +144,9 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - 0d2e93e01e68 - d6a4dfdad269 - ce1a157a41bd + - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -158,38 +158,38 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - d286ff4600dd + - e66f552a3c47 - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar owner: galaxyp revisions: - - 3fc2116ac6d9 - 9cb7dcc07dae + - 3fc2116ac6d9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 2133b0be850a - - 37d669de2828 + - f522c08e900c + - 837224ad1694 - 1f39c833f65f - - 9c52362ae7bb - - 7f432d87c82c - 4d17fcdeb8ff - e42225f8a659 - - f522c08e900c + - 37d669de2828 + - 2133b0be850a - 97a7f34fcb6a - - 837224ad1694 + - 7f432d87c82c + - 9c52362ae7bb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,55 +201,55 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 - a72ac2c7cc5b - 85b8866f06d7 - e63db1aa82ee + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 1974224d63c2 - - 990b4560ead7 - 352b37c66d97 + - 1974224d63c2 - 767c1d761aaf + - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - 35cc7ca0bdc7 - 4f359549383c - 99450519d727 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - 06f6826d380c - - c7745841de24 - e79958768a2c - c1343e3389ca + - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 - d46d64e7964d - d2eac53666f0 - da986f83631b + - b9d453dca8d3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: + - 9bf325045235 - 944b43462104 - - 8bd7734309f6 - 1199751329b0 - - 9bf325045235 + - 8bd7734309f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -262,17 +262,17 @@ tools: - name: msconvert owner: galaxyp revisions: - - ab6c14374bc0 - 6153e8ada1ee + - ab6c14374bc0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats owner: galaxyp revisions: + - 8212e342e482 - 28434abe6c5c - 593839e1f2c3 - de7593c29499 - - 8212e342e482 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -285,46 +285,46 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - f4be248c3d47 - - 01dbaf6a57e0 - 4e77b8f12cd3 - 8960fb791701 + - 01dbaf6a57e0 + - f4be248c3d47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - 370141bc0da3 - - 06cca574e337 - 25529df60a81 + - 06cca574e337 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: + - 518b1730cf2a + - 6ccbf9a2072c - f7fef900f5b2 - - c9eff69a7c62 - 9cdf15d3cfc8 - - 6ccbf9a2072c - - 518b1730cf2a + - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 9876bda3ec53 - 5e948629bc73 - - ca88bd28f116 - dff6c756eee5 + - 9876bda3ec53 + - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 1595601708ec - - 41859bbdc16e - 890025d6e426 - 658494a2cb00 + - 1595601708ec + - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter @@ -332,26 +332,26 @@ tools: revisions: - 2a93a25f0599 - 5ad0b5bf1deb - - 6634cad7d797 - 9b7977080f6d + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - 0bb5056cb775 - - fe4e4587d265 - - d6878d27f051 - 05d5e1ddc985 + - d6878d27f051 + - fe4e4587d265 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 4af67edd5aef - 5ad830edc021 - - 52ba9695e752 - febd569ad26f + - 52ba9695e752 + - 4af67edd5aef tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger @@ -366,64 +366,64 @@ tools: - name: openms_highresprecursormasscorrector owner: galaxyp revisions: + - d3546bb9fd8e - 0efbc235f314 - 9e26f5c770f8 - - d3546bb9fd8e - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - 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c69f69d7867a + - 5d9f175dff81 + - 986e03d3201e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 476b5e296979 - 0e52c85f3b15 + - 476b5e296979 - 4204882495f2 - be74a8cd7d66 tool_panel_section_label: Proteomics @@ -440,41 +440,41 @@ tools: revisions: - 2b2a7551a857 - f5ec766d80cf - - c18d8efa4474 - a407b6790342 + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 4e66c4e73909 - - 021fdb80f204 - d0304fb829c0 + - 021fdb80f204 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - bf32e0bcf554 + - 2735db4dd8d9 - 8098330f6d91 - ee860980edc6 - - 2735db4dd8d9 - - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - 08488066d588 - - a2a6e9551046 - 0ced5bc9f4dd + - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - de7a553552a6 - 2a9ff56cb279 - 8c01da82292c + - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -488,9 +488,9 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: + - 9f505cd4428f - f861ec9fbe59 - 496cf619e311 - - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -504,67 +504,67 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 8b814eafce2c - 4bb198c0bd3e - 89254095cbf6 - - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: + - f82b320ceb90 - f9ed7e074900 - 05ec9fb05ed1 - - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - d31426ef20f6 - 6e8cc5ed2a9b + - d31426ef20f6 - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - bc63b4d12779 - 4a7b96835140 - 2aebe58de46e + - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 6b01678ec2fc - 3d8d4ada5405 - decc397c3b7e - 5ae104d0da6e + - 6b01678ec2fc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - e039cc5c7aed + - dd173849c3d8 - 5182338d5e7c - d6aca689dd48 - 539a3a4dcc9e - - dd173849c3d8 - - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: + - 8a45fd5a608a - d426affe977c - 16026cdb1330 - - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 43b9ed22e8ce - 9c70a651a53e + - 43b9ed22e8ce - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -579,25 +579,25 @@ tools: - name: openms_xmlvalidator owner: galaxyp revisions: - - f036e8cf1a55 - 78c080d36945 - ad2ba3a95a02 + - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - c8b225c69a7f - - 7f6a1f27553e - 5c2a97a234d6 + - 7f6a1f27553e - fb52e95a370c + - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -616,14 +616,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 7fdd9119cc4f - - 07ff622ec007 - - a72c48001f7c - 3634c90301af + - 1beff3ddce58 + - a72c48001f7c + - 3ec27b4cee7c + - 7fdd9119cc4f - 943a34df6047 + - 07ff622ec007 - da885ca16cb2 - - 3ec27b4cee7c - - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -683,8 +683,8 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - a371252a2cf6 - 265c35540faa + - a371252a2cf6 - 4ddc8da62671 - 1a5690a5eedc - 12692567c7f9 diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index a59232894..a140a5a55 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,11 +2,11 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 289b7d6b69a4 - 2f1d464ebfd2 + - cd5f98911089 - 110a346daf36 - - 289b7d6b69a4 - 42201b90e3f4 - - cd5f98911089 - e345aadf914f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b - - fcce77c09289 - - c207119ba5f6 - 42d9087b4789 - 0cd2df8af811 + - fcce77c09289 - 8501601a118d + - 0345dbaaa79b + - c207119ba5f6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: + - 405a212b32ab - 33486216eec0 - 421c33b8bf17 - - ad5ab22ffe24 - - 405a212b32ab - 89eb29319bf4 - 04db7fd6b238 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - f6e91108b7b1 - - eb784fa07f80 - 7b72fde3d27e - - 7370bb65bad4 - 1d839ead7ad3 + - eb784fa07f80 + - f6e91108b7b1 - fa51dc5e8386 + - 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 - - 1544278c272e - - c9b77ced9a78 - - 8a55d29c8fcf - 3d70c2996730 - d30e36c48c93 + - 8a55d29c8fcf + - c9b77ced9a78 + - a3e86cd9cac7 + - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -88,11 +88,11 @@ tools: owner: iuc revisions: - 887cf585cafc - - e2db212d64ad - 7b881f5f5ad5 + - e2db212d64ad + - b242deb58952 - 564c33e5c3e3 - a5969aa9347e - - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -105,10 +105,10 @@ tools: owner: iuc revisions: - 8cff84759bf6 - - 9a171f9a450b + - e897c74a48bb - b4bab607eb05 + - 9a171f9a450b - bd5ff77e2036 - - e897c74a48bb 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: - - 4f65e343ecdf - - 6dafad990086 - - 33f0793edf93 - - adc7a7610d4f - 887e0991eb24 - 5e10f396979e + - 6dafad990086 + - adc7a7610d4f + - 33f0793edf93 + - 4f65e343ecdf 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: - - 97575d01f06b - 4e280b27a831 - - c5d7050e4ad7 + - 43e3eeb2e0ec - c287418eb288 + - 97575d01f06b - 17d39bf0a63a - - 43e3eeb2e0ec + - c5d7050e4ad7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -155,10 +155,10 @@ tools: owner: iuc revisions: - 0b8c84a7fdb5 + - a819ec3b362d - 09b8edb56d80 - - 9586f08634c0 - d9bf483266a1 - - a819ec3b362d + - 9586f08634c0 - cd034465d4a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: + - 69842dd5aa48 - 2645575d1bf2 - 95351dd0fd3f - - bf0e43ab0416 - a4b4bd84f69e - a9c34a289493 - - 69842dd5aa48 + - bf0e43ab0416 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - - 8a35a3bc6752 - - 912f904a6e1e - - d033e1ccb386 - d1fda11e602f - bb0475c884ff + - 8a35a3bc6752 + - d033e1ccb386 + - cfb504394ae1 + - 912f904a6e1e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,8 +235,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - 95286af4139b - d504d945a655 + - 95286af4139b - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 3d70d4ef3..997be0706 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,27 +2,27 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 7acb00fc980a - - 31f8063eedea - 2d4e3aff9dc7 - cf01dd6c6b1f + - 31f8063eedea + - 7acb00fc980a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - 7a5a2d28c539 + - 32e542c2a773 - 703a2cb3fb38 - 125d20cb23d7 - - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - 3d61a698e5e1 - - 01ccd366690d - 45c2ec061cf9 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -34,8 +34,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockclust @@ -78,8 +78,8 @@ tools: owner: devteam revisions: - f648e5180e40 - - e66b9b5b8580 - ad5d061fbdf2 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffcompare @@ -105,11 +105,11 @@ tools: - name: cuffmerge owner: devteam revisions: - - 6a6717a5f421 - 86285ddd4512 - - 04adc9db1581 - cf747d1bd79a + - 6a6717a5f421 - 22cf48ad7b16 + - 04adc9db1581 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -160,10 +160,10 @@ tools: - name: describe_samples owner: iuc revisions: - - e3b16fd7dd08 - 8f0181aacb7a - - 0693ccd171c4 + - e3b16fd7dd08 - 3b36efd62b3e + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -175,13 +175,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 8fe98f7094de - - 24a09ca67621 - 6a3a025714d3 - 0696db066a5b - - d027d1f4984e - cd9874cb9019 - 9a882d108833 + - d027d1f4984e + - 8fe98f7094de + - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -193,11 +193,11 @@ tools: - name: dexseq owner: iuc revisions: - - df929f257179 + - b47c006d90c5 - 62adf13b86ea - 2872c633f07e - - b47c006d90c5 - 9a7c5b6d8f1e + - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -209,17 +209,17 @@ tools: - name: edger owner: iuc revisions: - - a8305cf0c951 - - f2843df56434 + - 334ce9b1bac5 - 9bdff28ae1b1 + - a8305cf0c951 + - 555659de7321 - 0cb907a2a810 - - 334ce9b1bac5 - 070900306913 - - 5bf899c13979 - df0c8d0a5992 - 3d89af8a44f0 - 6e53e565fc6a - - 555659de7321 + - f2843df56434 + - 5bf899c13979 - ae2aad0a6d50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -251,18 +251,18 @@ tools: - name: featurecounts owner: iuc revisions: - - 90d16db017d7 - 1b851f87fbe0 + - a56fbe2d6ba7 + - 7db9d3ea71c9 - 6f66ae7c5f7a - af814359d244 - f3a5f075498f - - a56fbe2d6ba7 - e6a2a912677a - f9d49f5cb597 - a37612abf7f9 - 38b6d12edc68 - ea04b737afa0 - - 7db9d3ea71c9 + - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -292,8 +292,8 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - 3c97c841a443 + - 0f710191a66d - 3c5e024a18cf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -314,11 +314,11 @@ tools: revisions: - 26371a1df031 - 6ab42baa56e9 - - a86e80d3c09c - 3fb01a8c902d - - f4af63aaf57a - 6c19daec423d - d4b55e2beb12 + - a86e80d3c09c + - f4af63aaf57a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -336,8 +336,8 @@ tools: - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - 4418229c501e + - 67b0b160903a - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -356,11 +356,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 - 5ae5c312d718 - - 1c75aa5de15e - ce5d418183c5 + - 87c11c05d238 - 01247aaf0a10 + - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -372,10 +372,10 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 - - c971db6f0fe5 - 4f9c4e6566e5 - 10c98fab6c5a + - c971db6f0fe5 + - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -388,13 +388,13 @@ tools: owner: iuc revisions: - 708348a17fa1 - - d6f5fa4ee473 - - e827f9aae031 - 32511f586472 - 58c35179ebf0 - - 0921444c832d - - 97e06a4c7c75 - 119b069fc845 + - e827f9aae031 + - d6f5fa4ee473 + - 97e06a4c7c75 + - 0921444c832d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -412,8 +412,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -462,21 +462,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 79de45b5069b - - c772497b2c32 + - 3ea5a2a63fa2 + - b0f2be869d6d + - e132e7d02a3e - c7c55b694974 - - 4074fc1940e2 - - 5ec75f5dae3c - 4df95e2d7f61 - 980d2a2e1180 + - 5ec75f5dae3c + - c772497b2c32 + - 79de45b5069b - 0a563fd2f22e - - 3ea5a2a63fa2 - - b9e04854e2bb - - e132e7d02a3e - 99b17b74a8cd - - b0f2be869d6d - - 7ed2edc1337f - 53255f6eecfc + - 7ed2edc1337f + - 4074fc1940e2 + - b9e04854e2bb tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -500,13 +500,13 @@ tools: - name: salmon owner: bgruening revisions: - - 15cd64d7c58b - f4d5237a84f6 - 2c0ca397d302 - ebab418107f5 + - 15cd64d7c58b - e3d32471da11 - - 49121db48873 - 53e9709776a0 + - 49121db48873 - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -519,23 +519,23 @@ tools: - name: seurat owner: iuc revisions: - - fab6ff46e019 - - 8c28affc7c48 - 56242ff81c84 + - 8c28affc7c48 - c0fd285eb553 + - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cbf488da3b2c + - 258d696dbd7e + - cef79931dda5 - 914cfcba0ec8 + - cbf488da3b2c + - dd4df992d93d - ae618321f34a - - 1ebd14235b92 - - cef79931dda5 - 76d290331481 - - dd4df992d93d - - 258d696dbd7e + - 1ebd14235b92 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -571,9 +571,9 @@ tools: - name: transdecoder owner: iuc revisions: + - d0d4cef4f967 - c6334cb383ff - ffd1300599a1 - - d0d4cef4f967 - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -586,9 +586,9 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - 74217fbfba4d - - ba3720d7e68b - d6a479fd4281 + - ba3720d7e68b + - 74217fbfba4d - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -602,8 +602,8 @@ tools: owner: iuc revisions: - 2fb4ee002432 - - 56162e446004 - c2b82a94493e + - 56162e446004 - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -617,8 +617,8 @@ tools: owner: iuc revisions: - fab23c3b5258 - - 3f4094b6a565 - 9ff3765e7172 + - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -630,10 +630,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: + - 870ac06dff8e + - 34a018cbee9c - 4687ecf0eb2d - be3f26533209 - - 34a018cbee9c - - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -645,10 +645,10 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - c5fbddcac63a + - 65e7dea767ea - 5192f657f305 - 33406f5a445c - - 65e7dea767ea - - c5fbddcac63a - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -661,10 +661,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - a35cba31d904 - - 6f0fb35b799c - 1fdb25a8384d + - a35cba31d904 - e406ac71165d + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -677,9 +677,9 @@ tools: owner: iuc revisions: - c2c039e421af + - 964b7efe2639 - 37a1129c89d2 - 7c7fbf13aadd - - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -691,10 +691,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 047c22569787 + - 1d689e4e1caf - eafea3083352 + - 047c22569787 - 24e94d84adc9 - - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -706,10 +706,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 - 9871104ea630 - - 3a4ac03d1266 - 1812dbc5bb7b + - 04bb8bb7c198 + - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -733,15 +733,15 @@ tools: - name: trinity owner: iuc revisions: - - 32b86cd8eb50 - - 48636f857c4b - - 9fa24d5aac68 - 8f1c3df4dd49 - - d2bc35f3d1c5 - - c9cfec002f71 - - db1f362cca3e + - 48636f857c4b - d84caa5a98ad + - 32b86cd8eb50 + - c9cfec002f71 - cee61b3fcf78 + - d2bc35f3d1c5 + - 9fa24d5aac68 + - db1f362cca3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -754,9 +754,9 @@ tools: owner: iuc revisions: - 2b093007fab9 - - 9e61bc67866f - - 4383070d29ed - 6fd16fad465d + - 4383070d29ed + - 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 f931924b3..a0868c72e 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: + - 1a052c827e88 - 080fd5739bb4 - 473382134e56 - - 1a052c827e88 - 27e16a30667a 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 a4cf08ec3..a5c4bcebc 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - 3c661e57a88f - - 10184eaa85fc - 88eedb4abea0 + - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,10 +16,10 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - - 108db6635177 - - 1dfd95ee241e - 993b19f20c76 + - 1dfd95ee241e + - 108db6635177 + - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 19ece8afbaab - - 5f8e69cc4c6e - 30a201c9c310 - e7fd6754d093 + - 5f8e69cc4c6e + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -123,8 +123,8 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -149,8 +149,8 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 56c31114ad4a - dc6ff68ea5e8 + - 56c31114ad4a - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 06dc50b7b711 - - 92ec40abcdcf - - 26b4f9f98aca - 33208952b99d + - 26b4f9f98aca + - 92ec40abcdcf + - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -206,10 +206,10 @@ tools: owner: iuc revisions: - a8d69aee190e - - 66e23b11feae - 720217c23995 - - b906586a6596 - b3d99709fe1a + - 66e23b11feae + - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -228,11 +228,11 @@ tools: - name: samtools_flagstat owner: devteam revisions: + - db17d5321bad - cc61ade70eb8 - 22970df7a40e - - fefd89ab563c - - db17d5321bad - fe34990e5ce7 + - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,10 +244,10 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 7def34e6cf4d - fa5d3e61e429 - - 88b8c2916784 - 7a6034296ae9 + - 88b8c2916784 + - 7def34e6cf4d - 811fc2d75ad4 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,10 +267,10 @@ tools: - name: samtools_merge owner: iuc revisions: - - 36677f429310 - - 65a38e8c8e2a - b40e2d865d52 + - 36677f429310 - 740ce0a18f0d + - 65a38e8c8e2a - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -278,10 +278,10 @@ tools: owner: devteam revisions: - 583abf29fc8e + - fa7ad9b89f4a + - b61f5d6a7f25 - 9da0311ab1dd - 329deb17a9f7 - - b61f5d6a7f25 - - fa7ad9b89f4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - 85e38b31e8b3 - - 30388d878f81 - db000c6007a0 - bb8cfc6f6e0c + - 30388d878f81 + - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -327,9 +327,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - - b8beef827165 - a4a10c7924d1 + - b8beef827165 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c + - 6c2c1836728b - cab3f8d35989 - d54a4df48867 - - 6c2c1836728b + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,12 +356,12 @@ tools: - name: samtools_split owner: devteam revisions: + - 5d9ae78f34d3 + - 135c85f4cfaf + - bd850490c7f1 - b7f7826ef1cd - 818030fa6bbf - - 5d9ae78f34d3 - bcedabb53ddf - - bd850490c7f1 - - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,11 +373,11 @@ tools: - name: samtools_stats owner: devteam revisions: - - 541082d03bef - 3a0efe14891f - - 1cc79f49b8d5 - - 24c5d43cb545 - 5a08c09b9311 + - 541082d03bef + - 24c5d43cb545 + - 1cc79f49b8d5 - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: + - 6be888be75f9 - 350bbc5c2ffd - - 5826298f6a73 - - bf328cec6a42 - - 0dbf49c414ae + - b01db2684fa5 - 2dce91e11ca7 - 32dc5f781059 - - 6be888be75f9 - - c370440f901e - - b01db2684fa5 + - bf328cec6a42 - b72793637686 + - 5826298f6a73 + - 0dbf49c414ae + - c370440f901e 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 42dbb53bc..b070fb4fc 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: - - 4aab5ae907b6 - - 6f6537780379 - - ea5e944f447d - - 59bb6d34fca6 - a62c4a11a67d + - ea5e944f447d + - 5cb6146337d8 - 480d9e9d156b - d147d6455873 - - 5cb6146337d8 + - 4aab5ae907b6 + - 59bb6d34fca6 + - 6f6537780379 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 0f6d5ad9c..080221143 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,32 +8,32 @@ tools: - name: alevin owner: bgruening revisions: - - e4c01dcece8b - - f2000bc73102 - ecb9ea6269ee - - e32b215b7c04 - b0fe3e482cb7 + - f2000bc73102 + - e4c01dcece8b + - e32b215b7c04 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - e1c3c2f2a834 - - 707023fa62fe - 7a6655aa6eb2 + - 707023fa62fe - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - fb9e030ffae4 - - cfc3f5a57dc6 + - 00712416fdaa - 55e35e9203cf - - 6f143dfe902a + - fb9e030ffae4 - 93dd15e13e6a + - 6f143dfe902a - 32e547223c9e - - 00712416fdaa + - cfc3f5a57dc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -45,13 +45,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 688357ad5e61 + - 39e945f0b2c1 - 038e32885fec - b9fac48532eb + - 6f0d0c784f09 - 14c576ea6148 - ee98d611afc6 - - 6f0d0c784f09 - - 39e945f0b2c1 + - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -63,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - b85871dd69f9 - d4af736e7b83 - - 43cb7b5a6fe7 - - c4209ea387d4 + - b85871dd69f9 - 3d748954434b + - 43cb7b5a6fe7 - ed4996a16f7f - 9bd945a03d7b + - c4209ea387d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -81,46 +81,46 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: - - 890fb06a2893 - a4774b7b2e85 - 7ebc22f77d86 - 2e8022f1923c + - 890fb06a2893 - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 769d815e4b0d - - 4fff5a293013 - 02b1fe7aed76 + - 4fff5a293013 - 0e70b2dfe4be + - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: + - 344c2af50552 - c29e7bb492bf - - aa4a6f0916b4 - a90f8efe08b4 - - 344c2af50552 + - aa4a6f0916b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - b13d3e4c48e1 - - 5b7c81b35b89 - - c32347702e12 - 050cf43887d3 + - c32347702e12 + - 5b7c81b35b89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - 02fc39c8610d - - 1d77986f9ddc - ae969fdb8442 + - 1d77986f9ddc - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -158,10 +158,10 @@ tools: owner: iuc revisions: - a9caad671439 - - cdf4443d5625 - - 2c1200fba922 - 8855361fcfc5 - cfe1e6c28d95 + - 2c1200fba922 + - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -197,8 +197,8 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 952abbc4b1de - fb7068d30ec9 + - 952abbc4b1de - c3ffb2c1e314 - 01c37e54e86e tool_panel_section_label: Single-cell @@ -206,126 +206,126 @@ tools: - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - f1c35f3f310d - 9d42a6133690 - 45828071edc3 + - f1c35f3f310d - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: + - 23b8d6b8960c + - cab616fe7e64 - 163fd744e235 - 1a31e75e979e - - cab616fe7e64 - - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - f47ac4a0b337 - '920526260066' - - b9ab56aecd18 - 013e53ccc7ac + - f47ac4a0b337 + - b9ab56aecd18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - f6a169b5e43b - 9ea228a9afc8 - - a63e9713c39d + - f6a169b5e43b - b892fa1fcaec + - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 45a386d18509 - ff1af7bac1cb - f8320df1866b + - 45a386d18509 - 640e0e45518a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - f963c251ac77 - c354255ff705 - 9d02f1819e81 - 6f8debcf2ac9 + - f963c251ac77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - f881c94fb3b3 - 37125838e360 - - 40fee49bc6c3 + - f881c94fb3b3 - c4ed35f4f77f + - 40fee49bc6c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - e06265d204f6 - - 2dccb6bb0add - 782bdcb775fb - e8760fc0e29b + - 2dccb6bb0add tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - f0216498a666 - - 63c8377c58b3 - - 30677e95bc89 - b05f662f9f35 + - 30677e95bc89 + - 63c8377c58b3 + - f0216498a666 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: + - fe3aa71590d5 - c72fa6cb8817 - 3240e8a7c54f - 8a11d70b6cd8 - - fe3aa71590d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 5dd1aae12f03 - 3ee5332bf57c - - e03780179ee5 - 4f9305d3bb34 + - e03780179ee5 + - 5dd1aae12f03 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - a315574104c6 + - 3a6a5381db36 - 87eb9c58cd19 - 4401ed529d2c - - 3a6a5381db36 + - a315574104c6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: + - 2ba6cee8e4db + - a83732c79949 - c0737631eea1 - 574f295b5ba4 - - a83732c79949 - - 2ba6cee8e4db tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: + - ea19190ce5e0 - 30d7390bc918 - 62b720dceb56 - - ea19190ce5e0 - 937b7b9832d0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -341,136 +341,136 @@ tools: - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - ffc33339cd3e - - 0410b6aada45 - - 4375e25de06a - bf9379529c3e + - 4375e25de06a + - 0410b6aada45 + - ffc33339cd3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - 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- 32173084d53f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - febfddb0b3e8 - b6b8c8672756 - b376ef118807 - 4b194e675916 + - febfddb0b3e8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1d9799f4b854 - - 1511a8ebe906 - - 910c6a1c3a27 - ed900cd4a0a9 + - 910c6a1c3a27 + - 1511a8ebe906 + - 1d9799f4b854 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: + - f34ab9882252 + - 2aa5b6b65197 - 6d042c96aceb - 5e83c077e31d - - 2aa5b6b65197 - - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - ea5d67ec94ab - 3f1b286a5c34 - dd9988943f53 - 9b383d429659 + - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 11f39d7f6c64 + - 6326cd29c1c3 - 06ced663d24f - 89cfe7de541b - - 6326cd29c1c3 + - 11f39d7f6c64 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - 337705015ee8 - - 1602cc5b673c - b4e780e93c91 - beb5b5917d2f + - 337705015ee8 + - 1602cc5b673c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - a10fce08c2dc - - 8d203e74869b - - 58de3c7c8e89 - e285920f8585 + - 58de3c7c8e89 + - 8d203e74869b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: - b13e7a200525 - - 21d859ad4502 - ea8fb5e899e8 + - 21d859ad4502 - 5cbd7a902a8d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 1d6af10874d5 - - 36dfa2825a59 - d74cf4a61d65 - f81750434d70 + - 1d6af10874d5 + - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -488,30 +488,30 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 1de2276f633f - - 27fe5cd1729c - f36828ebdc54 - df64cc4dfb4d + - 27fe5cd1729c + - 1de2276f633f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 1d201e8378b3 - d890828ab02a - - cef9fb4ece1c - 11a3385e03b5 + - cef9fb4ece1c + - 1d201e8378b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - db575b4c8b22 + - e98619de2776 - 59be31ac9dc3 - eeab712b0b99 - - 7784821452ac - 4b0adaa31c95 - - e98619de2776 + - 7784821452ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -523,23 +523,23 @@ tools: - name: music_construct_eset owner: bgruening revisions: + - 7ffaa0968da3 - 2cfd0db49bbc - 48f0fb3061b1 - - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 8cd2ecfa2e61 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - fde4c972e7c5 - 8c64a2da3869 + - fde4c972e7c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -557,11 +557,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - c4f39bf4a068 - - a4b734cd253b - f911a64454fb + - a4b734cd253b - 49776718ae90 - 7e014059a88d + - c4f39bf4a068 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -573,10 +573,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - d45f092caf24 - - 7608d5faee41 - 8b917923f7d4 + - 7608d5faee41 - 43c146e25a43 + - d45f092caf24 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -588,9 +588,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - c7ddb719554d - 37a47c4fd84d - 2b0d3e2f402a + - c7ddb719554d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -602,9 +602,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: + - 69018f285aa3 - df8e4e54d367 - 6e90c8adf84f - - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -616,10 +616,10 @@ tools: - name: raceid_trajectory owner: iuc revisions: + - c92d0f9338c5 - 2bfd55b87af3 - - 44b935f2271b - e93b008c637a - - c92d0f9338c5 + - 44b935f2271b - 72979cac22b2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -644,17 +644,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - b2df381a6004 - - 6acb08931836 - - 6f83f8fd381f - - 4d8f983cd751 - - 38db3fef7aad - - aaa5da8e73a9 + - f9353ee6a0d4 - cb43c5d3acd3 - - 8983e7a04ba7 + - 38db3fef7aad - edec35114f72 - 77b91b9bdf52 - - f9353ee6a0d4 + - 4d8f983cd751 + - b2df381a6004 + - 8983e7a04ba7 + - aaa5da8e73a9 + - 6acb08931836 + - 6f83f8fd381f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -666,16 +666,16 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 64388be6d510 - 72a6bebab2a5 - - d636ce5cde16 - 277313130da5 + - 64388be6d510 - a03ff8633507 + - b409c2486353 + - d636ce5cde16 + - fc0321c000a3 - 8cb783c81905 - 3c86f71498bc - - b409c2486353 - a97abb8cd15b - - fc0321c000a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -687,17 +687,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - 6c145a6868cc + - 6bd82ed14acd + - 18262103fa61 + - 5e9171dc8244 + - c5d3684f7c4c - c0a80a16560f + - f54f0f0598ad + - 6c145a6868cc - cc0deb593fc8 - 5c3ebe2adc77 - - f54f0f0598ad - - 5e9171dc8244 - - c5d3684f7c4c - - 3081ff5c84a3 - d86cb2ce311b - - 18262103fa61 - - 6bd82ed14acd + - 3081ff5c84a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -709,17 +709,17 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 3bcd5445cd7a - - 94c19fb1281c - c9cb76cf8d6c - - 4bda4412b8c2 - - ab55fe8030b6 - 56c0d4acef02 - - a407e7f8bdc1 + - 3bcd5445cd7a - 9f354c7c8c92 + - 4bda4412b8c2 - 7b9fafe32c86 - - 146ae5d70b47 - d844935c906c + - a407e7f8bdc1 + - 94c19fb1281c + - ab55fe8030b6 + - 146ae5d70b47 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -731,18 +731,18 @@ tools: - name: scanpy_plot owner: iuc revisions: - - 6adf98e782f3 - 7647e5cd1b8b - - 6f5349dd5c49 + - 6adf98e782f3 + - 40812a65a78b - dbbe1ea8ecb1 - - f7446fd8d5e7 + - 6f5349dd5c49 - aa0c474463c2 + - 0185bd174ea0 + - 9b0cdb8cf6be + - f7446fd8d5e7 + - 95777145cb92 - 62acdd96d4a0 - 1072ce66b426 - - 95777145cb92 - - 40812a65a78b - - 9b0cdb8cf6be - - 0185bd174ea0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -754,17 +754,17 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - a39040ae0a38 - - 215733a383f2 - 9fb627495ec2 - - 73ab2ac53d06 - - c5541bfb8feb - - fe8f16c594ec - - f2f6c703da06 - - bf2017df9837 - - d18e7a6e5cd4 - 458e8f43a775 + - 215733a383f2 + - bf2017df9837 + - f2f6c703da06 - c65fce500915 + - d18e7a6e5cd4 + - fe8f16c594ec + - a39040ae0a38 + - c5541bfb8feb + - 73ab2ac53d06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -790,9 +790,9 @@ tools: - name: scater_filter owner: iuc revisions: - - 7a365ec81b52 - b7ea9f09c02f - 652923ce664f + - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -811,8 +811,8 @@ tools: owner: iuc revisions: - 81e5bdff4853 - - 2e41b35b5bdd - ef4c80837bc5 + - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -1081,15 +1081,15 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 64fa083411f1 - 588c811fdd48 + - 64fa083411f1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - 05bd4db20227 - fecf9664c885 + - 05bd4db20227 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index fddb0bd9a..48c974bce 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -33,17 +33,17 @@ tools: owner: iuc revisions: - 2f3c6f2dcf39 - - 4c07ddedc198 - - 419027d822d6 - 746e8e4bf929 + - 419027d822d6 + - 4c07ddedc198 - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -56,23 +56,23 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - cb1c59d69557 - - 7a15159140d1 - 6c29c7e347e8 + - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - 9c3e1d3235c8 + - aef56d0e7a61 - 7442b94d6a1e + - 840f29aad145 - b1eda492f063 - - aef56d0e7a61 - 4c4ec859c31a - - 840f29aad145 - - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 9fda0b82f419 - - 30d21a6041f6 - - d0352e8b4c10 - 07843f917990 + - 30d21a6041f6 + - 9fda0b82f419 - 375bbd555f4a + - d0352e8b4c10 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 8b1b2b91f8d0 - 2c58b83c9bad - - cd02bf168d23 + - 8b1b2b91f8d0 - 4cc980df6265 + - cd02bf168d23 - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - bb9fc9d46ea4 - - 4bbaf77573ef - - ad7e0b4291ee - e10e776f2109 + - ad7e0b4291ee + - 4bbaf77573ef - 7dd3fb35904f - 1dd433d2c92c + - 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 0e7164428..06da6b52b 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -34,15 +34,15 @@ tools: - name: column_maker owner: devteam revisions: - - 02026300aa45 - 626658afe4cb - - be25c075ed54 - 9cd341095afd - 464b9305180e - aff5135563c6 - - 6595517c2dd8 + - 02026300aa45 - 6e8d94597139 - 13b6f0007d9e + - 6595517c2dd8 + - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -54,8 +54,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 6f54dc6b37da - 3a4694d4354f + - 6f54dc6b37da tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 9cc411a62277 - - 37cde8134c6a + - 34d29339abab - 90f657745fea + - 9cc411a62277 - 557ec8d7087d - - 34d29339abab + - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,30 +107,30 @@ tools: - name: merge_cols owner: devteam revisions: - - f2aac0c5c60d - dd40b1e9eebe - ae7843d06f8f + - f2aac0c5c60d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 2e8f945f7285 - - 623f3eb7aa48 - - cf4397560712 - 3a6b78c39dca - cf34c344508d - - 33d61c89fb8d - - 1ea4e668bf73 - 83069b38aa85 + - 623f3eb7aa48 + - 1ea4e668bf73 + - 2e8f945f7285 + - 33d61c89fb8d + - cf4397560712 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - 503bcd6ebe4b - - 399da6b5ec21 - ae8c4b2488e7 + - 399da6b5ec21 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -142,8 +142,8 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - b722161a845a - bce29ec10b78 + - b722161a845a - c4d18aa4ec4a - f768f6183386 tool_panel_section_label: Text Manipulation @@ -151,22 +151,22 @@ tools: - name: table_compute owner: iuc revisions: - - 60ff16842fcd - 3bf5661c0280 + - 60ff16842fcd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: + - 9ff72e942410 - 0a8c6b61f0f4 - - ddf54b12c295 - - 86755160afbf - 74a8bef53a00 - - f46f0e4f75c4 - - a6f147a050a2 - - 9ff72e942410 - - d698c222f354 + - 86755160afbf - fbf99087e067 + - d698c222f354 - 12615d397df7 + - ddf54b12c295 + - a6f147a050a2 + - 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 e76986af4..d25b676de 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -15,8 +15,8 @@ tools: owner: iuc revisions: - 0d18a3ba2d1c - - 82fb5e3bb93e - 85c57cc9b558 + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -29,18 +29,18 @@ tools: owner: iuc revisions: - c0f8fe52948e - - 23d7e75d850e - cb441f258c37 + - 23d7e75d850e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: + - 57def2d7c093 + - 156b60c1530f - a5937157062f - - 3e954e7125bf - ef2c525bd8cd - - 156b60c1530f - - 57def2d7c093 + - 3e954e7125bf - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,22 +48,22 @@ tools: owner: iuc revisions: - 09d6e4693887 - - e61c9ac190ad - 435b157bed6d - 791f73caa0c8 + - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - dfadc322b065 - - 4805fe3d8fda - - b11e8e9c23bf - e1461b5c52a0 - - 3b4b2121842f - 03627f24605f + - b11e8e9c23bf + - 3b4b2121842f + - dfadc322b065 - 074d44697036 - 65432c3abf6c + - 4805fe3d8fda tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter @@ -77,10 +77,10 @@ tools: - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 - f4473557ffc7 - c27549b9aa1f - 971e07ca4456 + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi @@ -100,18 +100,18 @@ tools: - name: sniffles owner: iuc revisions: - - 43fffeed243f - - 93c4b04a0769 - ceff2f6a5368 + - 93c4b04a0769 + - 43fffeed243f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: + - 9bccc8404a3c - d220115f882b - c9a8ef2aa380 - 5bbf9eada9c2 - - 9bccc8404a3c - fa016f1eea1a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -154,21 +154,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 3b1e7c170b10 - - ee4a90760848 + - e7aff4a85df5 - 40f0591deda0 - 32f14a2723ec - - e7aff4a85df5 + - 3b1e7c170b10 + - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - 42818629ec4c + - 4934c0ac6197 - 02d81b994ef5 - 9793bc5d741b - adc0645b945c - - 4934c0ac6197 - - 42818629ec4c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index f3c594fbd..9b0f4251b 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,14 +2,14 @@ tools: - name: bcftools_annotate owner: iuc revisions: + - e075b1be5abb - b7ea370b8f5d - - ebe5fc018e72 - - 6a88248893c4 - - 95815a0bb307 + - 8a2e296c07ef - 265fe0f9ea64 - 2c372041ed8c - - e075b1be5abb - - 8a2e296c07ef + - ebe5fc018e72 + - 95815a0bb307 + - 6a88248893c4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -21,13 +21,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 1001172b5089 - 0fba2c15b40d + - b03984136ce4 + - 21687e35f066 - 22637b1a55bf - 544cb432072b - - 21687e35f066 - - b03984136ce4 - c37b684e7f4e + - 1001172b5089 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,14 +39,14 @@ tools: - name: bcftools_cnv owner: iuc revisions: + - 8627b2b383b4 + - 3a7084316a6e + - 8408bffd5616 - ccb83bf54de0 - 01d6b7d6365e - - bf1f4994f104 - 143796b504eb - - 3a7084316a6e - - 8627b2b383b4 - 8ca3647c90fd - - 8408bffd5616 + - bf1f4994f104 - 0238f68ad641 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -59,13 +59,13 @@ tools: - name: bcftools_concat owner: iuc revisions: - - 03e0645395d2 - - 81426b3cf18b + - f430a1ec7ee4 - abd489215f73 - 6b6c992d3a14 - - 62ca6da715bf + - 81426b3cf18b + - 03e0645395d2 - 9b5abbf50d23 - - f430a1ec7ee4 + - 62ca6da715bf - d144af39073a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - 1171446da5db - - d3081540d175 - - d37e313a41be - - 95c6f3f4c77f - - 2363ef414c9b - e522022137f6 - - 8aa352093d73 + - 2363ef414c9b + - d37e313a41be - 1829900b5dcd + - 8aa352093d73 + - 95c6f3f4c77f + - 1171446da5db + - d3081540d175 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: + - d58d2e8c7a57 - b14ff40958cb - - 1137ce8efc1e - 012656fd329f - - 9b29129fb491 - - 348cd212dbad - - d58d2e8c7a57 - 09f37afb3621 + - 348cd212dbad - 92c0aff8b53e + - 1137ce8efc1e + - 9b29129fb491 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - ecc9192912b8 - 7291189e98b4 - - 55c0e906c14c + - ecc9192912b8 - 367ba501b6eb - - de68c11034f6 - - cfd81f17580b - 1f2183a23823 + - cfd81f17580b + - 55c0e906c14c + - de68c11034f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,12 +134,12 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 039ea3f1dea9 - - d237eaef451f + - ae68ceb4cca3 - 7cbf3c66d4ad - 64a8f7dae3ad - - ae68ceb4cca3 + - 039ea3f1dea9 - 6c790a091c7c + - d237eaef451f - e6f4badbe6f3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -152,14 +152,14 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 6ea7170a016d - - 33bd9301568c - 5d6653c989cb - - e7452697afd9 + - 277719af4dd7 + - 963a3635b2e1 - cdb7b4927742 - 46fcafba49ec - - 963a3635b2e1 - - 277719af4dd7 + - 6ea7170a016d + - e7452697afd9 + - 33bd9301568c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 26d97cdd5410 - - 501bfb078342 - - a1213a0b7b66 - b7f0f59baa7e + - a1213a0b7b66 - 91c1e57d5c7f + - 5a321fab1fe4 + - 26d97cdd5410 - a29a2f40b665 + - 501bfb078342 - 7b4454382d39 - - 5a321fab1fe4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: + - d7d1663559e9 - 39bca000353d + - c803c34361e0 + - 97d19c008d15 - 5f27e814a119 - 709dd8291b83 - - c803c34361e0 + - 81e4014fa809 - 768d04526638 - 15da1ddcfeff - - 81e4014fa809 - - d7d1663559e9 - - 97d19c008d15 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -210,13 +210,13 @@ tools: - name: bcftools_merge owner: iuc revisions: + - 2215287d5cc9 - 7ba36babba2d - - 86296490704e - b84fda8ebef0 - b1eba148b35b + - 86296490704e - b931e65638b8 - 5b006286a458 - - 2215287d5cc9 - 85ee7e6c4204 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -229,15 +229,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 56556e1267de - - 0a5dcc9a8ec2 - f506df85c652 - - 37757ffb4c5f - - 5660b21a0dbd - - 31ea13dfe5e6 + - ce9396ddcb2b - 9c711df3258d - cf06b44624c7 - - ce9396ddcb2b + - 5660b21a0dbd + - 31ea13dfe5e6 + - 56556e1267de + - 0a5dcc9a8ec2 + - 37757ffb4c5f - 4e1d23e5c691 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -250,13 +250,13 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 6deb4d549bc9 - - 19905c025d2a + - 1ca7418e46ee - 271965b55437 + - 021693fdadaa + - 6deb4d549bc9 - a404f786a94c - - 1ca7418e46ee - 48291658fdf6 - - 021693fdadaa + - 19905c025d2a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 97e8145d7e30 - - f7879f1e77f9 - 3f6fadf8b8ff + - 97e8145d7e30 - dadbd61dc4cf - 71c78e0eea52 + - 69d8b7567281 - c450406f722b + - f7879f1e77f9 - 5ad5d4243987 - - 69d8b7567281 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -288,13 +288,13 @@ tools: owner: iuc revisions: - 79f7a1acc2cd + - 52f9e4a660e3 - 6cf13a657cf6 - 283911fe7e1a - - 52f9e4a660e3 - - d31a2e310a52 - 0fe007201caf - - cc7f9a4e186b - 2514e684f8a3 + - d31a2e310a52 + - cc7f9a4e186b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 0a62420cb9cd - - 75ddd081f608 - 6963a6841d22 - - 80e6e399ccd0 - - a12844ca467a + - 75ddd081f608 - 1411bef27a75 - 230e424bde67 + - 0a62420cb9cd - 026a989b7cee + - a12844ca467a + - 80e6e399ccd0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - e493702b19eb - - b10d1510fa84 - 5808f77b2bb6 - - 450a265f92e8 - - bca7ce81688f - ba20340426fe + - 450a265f92e8 - 444e6a756c35 + - bca7ce81688f + - b10d1510fa84 - 5acfca5a76af + - e493702b19eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -345,13 +345,13 @@ tools: owner: iuc revisions: - 4d236c696844 - - 68fec03a63b7 - 12152af85697 + - dd72ff87cfd0 - d52b8947b269 - - c43399f161f4 - - f2482aa4862e - 157ffcdd3fa7 - - dd72ff87cfd0 + - 68fec03a63b7 + - f2482aa4862e + - c43399f161f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -363,13 +363,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 29ba253e2e05 - - 8dbce095986c - - 6f8e223f78f3 - 75becf493cd3 - - 0e5d11004815 - 8f2fc0ab30fb + - 6f8e223f78f3 + - 8dbce095986c - cbe39e530cbf + - 0e5d11004815 + - 29ba253e2e05 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -381,14 +381,14 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 9708e3086f32 - f544f71adb73 - - 8f5962c43868 - - 3ff5654b4e7d - - 88bb477f45f7 - a8630d4fbaf8 - a367a15c6de5 - e0a856def0b0 + - 8f5962c43868 + - 88bb477f45f7 + - 9708e3086f32 + - 3ff5654b4e7d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -400,13 +400,13 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 96d0145c041a - - 6ce175385dd9 + - 4ed46189d6c6 + - 34dc0bbc7e93 - 31c096c6b156 + - 96d0145c041a - 5c9729d54721 - 8b260d252ff4 - - 4ed46189d6c6 - - 34dc0bbc7e93 + - 6ce175385dd9 - 03e30f06f15f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -419,14 +419,14 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: + - 09f5e45a8212 + - 46eb13bc2c73 - a1aad8b559c6 - a730269af659 - - 11af7fce71cf + - 681bdf1e22ff - 40daf124be88 - - 09f5e45a8212 - - 46eb13bc2c73 - 2c4941386820 - - 681bdf1e22ff + - 11af7fce71cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 12038f59c0f4 - - 6cbb9c47795c - 8cb121b6a1d2 - - 743cd1472aeb - - f272b8ba0983 - b74b8cbfc1f1 + - 743cd1472aeb + - 0594ea1417c8 - 3897eaadfbff + - f272b8ba0983 + - 12038f59c0f4 + - 6cbb9c47795c - 882b2e649602 - - 0594ea1417c8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -458,13 +458,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - a9826db86d9a - dba06328556a - eccb508bb678 - - adee7e8b746f + - a9826db86d9a - 238f78e38a8b - - 18cf9de1cf73 - cced6715f926 + - adee7e8b746f + - 18cf9de1cf73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: - - f64e7ca2efd2 - - fdec14f69010 - - 9f36041495a3 + - 3ce32adc55b2 + - c9935c9e8a24 - e53501abf992 - 31a1b89eab9b + - fdec14f69010 + - f64e7ca2efd2 - e0ad88dec40d - - 3ce32adc55b2 - - c9935c9e8a24 + - 9f36041495a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - 4db0695a6fc7 + - 2331ddcbd5aa + - d68c43202172 - 79489d5685dd + - b7be725976b6 + - d43eb39b989e - fd3539749127 - 3b7b1fe7b937 - - d43eb39b989e - - b7be725976b6 - - d68c43202172 - - 2331ddcbd5aa + - 4db0695a6fc7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,11 +514,11 @@ tools: - name: bcftools_roh owner: iuc revisions: - - b0d39ef600a7 - - 1a989b4110da - - 78cd8b69da4c - 5296d26b0373 + - b0d39ef600a7 - 58091e1be01b + - 78cd8b69da4c + - 1a989b4110da - 1ccf0e7fb4f6 - 6a636d58dfc2 tool_panel_section_label: VCF/BCF @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: - - '388983871932' - - 591cc8518033 - - baa8823f8073 + - b641062a2587 - 4d3ce9dc1525 - - bf8325a07ce7 + - baa8823f8073 + - '388983871932' - b17394940c7a - e8af591435d1 - - b641062a2587 + - 591cc8518033 + - bf8325a07ce7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: - - c2ab91a0d506 - - e6b5cbbf449b - - 3a233c8eb814 - - 3ca3de4e5291 - 59fa8742285e - - 38d75661c235 + - 3ca3de4e5291 + - e6b5cbbf449b - 1a2ef636f48e + - c2ab91a0d506 - d1f8f55f564d + - 38d75661c235 + - 3a233c8eb814 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -584,15 +584,15 @@ tools: - name: vcfallelicprimitives owner: devteam revisions: - - a8a4f94aa321 - 57a16b310fe8 + - a8a4f94aa321 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 01e0321aca98 - 6faa2c4c71d2 + - 01e0321aca98 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -626,15 +626,15 @@ tools: - name: vcfcombine owner: devteam revisions: - - 53edb91ed051 - 1f0ba67cc85a + - 53edb91ed051 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples owner: devteam revisions: - - f1852ecef841 - 254f285dbaaa + - f1852ecef841 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance @@ -648,8 +648,8 @@ tools: owner: devteam revisions: - eae7c08ebb6f - - 4bdc111b2470 - 6b935ab36d7b + - 4bdc111b2470 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -662,8 +662,8 @@ tools: - name: vcfflatten owner: devteam revisions: - - f285aa6bdcfb - b24e368ae7b1 + - f285aa6bdcfb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo @@ -697,8 +697,8 @@ 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 @@ -711,15 +711,15 @@ 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 - ee60203e68d9 + - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/staging.gvl.org.au/viral_tools.yml b/staging.gvl.org.au/viral_tools.yml index 15250eab7..06370d956 100644 --- a/staging.gvl.org.au/viral_tools.yml +++ b/staging.gvl.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 9def47f3c1e4 - 18aad692772a + - 9def47f3c1e4 tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 1bed75e74..ba014588a 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,54 +2,54 @@ tools: - name: abricate owner: iuc revisions: - - 6e9aea89e388 - - 78c75f134c16 - 3f3e247c053d - c2ef298da409 + - 6e9aea89e388 + - 78c75f134c16 - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - 3f438bf5475d - c45c9dd066e2 + - 3f438bf5475d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval owner: iuc revisions: - - 8dc7512c9dc9 - 1dd7adc21b6d + - 8dc7512c9dc9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - cd2480f35935 - fe3ca740a485 - - 4f2967b27e67 + - f29602ae449e + - 44018dd6b447 - b5d8e5475247 - - a79ee60b6926 + - 3e1f6f6d557e + - cd2480f35935 + - 4f2967b27e67 - 133f36c29579 - - 44018dd6b447 + - a79ee60b6926 - 1aae04680c4b - - 3e1f6f6d557e - - f29602ae449e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,21 +62,21 @@ tools: - name: augustus_training owner: bgruening revisions: - - aada0deea587 + - f1e653756174 - 7be22100e5e1 - 6519ebe25019 - - f1e653756174 - dc027fa56d55 + - aada0deea587 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: + - 28433faa6e42 + - 0fc0f9cf035a - 09855551d713 - bd0e53f3a891 - ca6d970d931c - - 0fc0f9cf035a - - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -84,16 +84,16 @@ tools: revisions: - 728dacaf08a9 - d77802fe76f7 - - 92eee5f31117 - da5f1924bb2e + - 92eee5f31117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: + - fe48aa4ccd5e - 8fd427007e93 - 7355bbf5e05f - - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -105,8 +105,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -118,9 +118,9 @@ tools: - name: cpat owner: bgruening revisions: + - 7ccc6234b54e - 1ac12c0cc7a0 - 8e9e228c54c4 - - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper @@ -158,61 +158,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 9f2455341fac + - 14f588312c56 + - 9c15ca7e764e - 582fd74dc2a1 - 756376aeb1ae - - 14f588312c56 - b6b5cd37f2a2 - 3bbe70fef6df - - 9c15ca7e764e - - 9f2455341fac tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 30fb23d4c31c - - 73428a792541 - - a230ea445788 - - 1691af4a0d17 + - 989f7c061f35 - 8e1ace8f77c6 - 0ffe5be70caf - - 989f7c061f35 + - a230ea445788 + - 73428a792541 + - 1691af4a0d17 + - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 30f08d74024f + - 494f0bb4a993 - 563a19373357 - - e94187d661df - 0418d28136de - - 57c6718cbfcc - - 494f0bb4a993 + - 30f08d74024f + - e94187d661df - 5a5ae61da69c + - 57c6718cbfcc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 2bba2ff070d9 - 7abc5f6dd595 - - f77d7b685bb3 + - 1bc5a03faf2e - 4b96ced19f75 - - f31125bb85ea - d6c7106b7b2e - - 1bc5a03faf2e + - f31125bb85ea + - 2bba2ff070d9 + - f77d7b685bb3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 54961e026fe4 - - b3cf4684e9c7 - - fed64e676186 - d77fdcca400e + - 520e30695ec3 - 52af33194019 - d3af38b9c7e1 - - 520e30695ec3 + - fed64e676186 + - b3cf4684e9c7 + - 54961e026fe4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -224,8 +224,8 @@ 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 @@ -240,8 +240,8 @@ tools: revisions: - 602de62d995b - 43798b4caee0 - - 8b3e3657034e - ef2ad746b589 + - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -272,9 +272,9 @@ tools: - name: interproscan owner: bgruening revisions: + - 74810db257cc - c55643c3d813 - 98cafcbd2578 - - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -299,19 +299,19 @@ tools: - name: maker owner: iuc revisions: - - 3c1a01127868 - - 370c210d9541 - d46d803ca6cc + - 370c210d9541 + - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - c8ac28e8ac44 - - 624606f7c996 + - 033755194fe9 - e95d52d295d7 + - 624606f7c996 - b815ec682418 - - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -359,10 +359,10 @@ tools: - name: prokka owner: crs4 revisions: - - bf68eb663bc3 + - d643e3b03500 - 8a22554cdde2 + - bf68eb663bc3 - a17498c603ec - - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -406,30 +406,30 @@ tools: - name: snpeff owner: iuc revisions: - - 268d162b9c49 - - 8f92c2b26e6d - - 5b80f544c67f - - c7275bd8b4d6 - 6322be79bd8e - cfcf33df7fc0 - - 68693743661e - 5c7b70713fb5 + - 5b80f544c67f + - 68693743661e + - 268d162b9c49 + - c7275bd8b4d6 - 5a29ab10dba6 + - 8f92c2b26e6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - 09d6806c609e - 2b3e65a4252f + - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -442,16 +442,16 @@ tools: owner: iuc revisions: - ac8250086ac3 - - 037a11682176 + - 37213cf56392 + - 809dfc93d593 + - 4839e590cb26 + - 8cb134b8c1a5 + - d03af1c7002c - e1a9d6fd258d - 200c378d85f3 - 45083d070fb8 - - d03af1c7002c - - 4839e590cb26 - - 8cb134b8c1a5 - ba6f87115e13 - - 37213cf56392 - - 809dfc93d593 + - 037a11682176 - 51dd22484644 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 19340ed67..88f1a6f1c 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,28 +2,28 @@ tools: - name: abyss owner: iuc revisions: + - 7547fcab5d19 + - 553bfe8bd0b5 + - a929ce596a34 - d6d5ccc2c581 - - 0124fce4654a + - fa5259cc561b - 841084c5fc46 - 890b794c997d - - 7547fcab5d19 + - 8f1b150a2487 + - 0124fce4654a - db9b10824c61 - - a929ce596a34 - - fa5259cc561b - 0e93176640ac - - 553bfe8bd0b5 - - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - 94fe43e75ddc - b9e31c5c01c7 - - b2860df42e16 - 067592b6b312 - 21e491ad532a + - b2860df42e16 - ddddce450736 - - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -36,48 +36,48 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - a7f16f24e9a1 - - faee8629b460 - 3371c5bdc17a + - faee8629b460 + - 22286dab5aa1 - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - '392811378515' + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - e4bd1e99bacf - - 2babe6d5c561 - - 1440ae06552f - - e824f5d958d0 - - bb935709506a - - 2dd755c1c6ff - - 94170eee0ad8 + - 46ae58b1d792 + - 41030a6c03b7 + - 1e62c28ba91d - cf13a1e03e5b + - bb935709506a - 602fb8e63aa7 - - ea8146ee148f + - 94170eee0ad8 + - 2dd755c1c6ff - e5c372c91e46 - - 46ae58b1d792 + - 2babe6d5c561 - 4048d82f0c88 - - 1e62c28ba91d - - 0d243f458b53 - 5ecdeca79a0d - - 41030a6c03b7 + - 0d243f458b53 + - 1440ae06552f + - ea8146ee148f + - e824f5d958d0 + - e4bd1e99bacf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 86f150c8019d - c5b7390290b1 - 5732f959936a - - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -89,24 +89,24 @@ tools: - name: flye owner: bgruening revisions: - - 276f5d8712d5 - - 1ce9b1d72ec3 - 1f0769f0b56b + - 276f5d8712d5 - 8d4f03b5fe9d - - 3ee0ef312022 - - cb8dfd28c16f - 3e4f8642c77e - - 291923e6f276 + - 1ce9b1d72ec3 + - 3ee0ef312022 - e27815e82dd4 + - cb8dfd28c16f - cd11366d92cf + - 291923e6f276 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - 3169a38c2656 - 01210c4e9144 - b2f674562a18 - - 3169a38c2656 - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -114,21 +114,21 @@ tools: owner: iuc revisions: - ba88bc5a6446 - - 06bcf65179fb - 8b330a577046 - 7348b69e5109 + - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 5127a713de83 - 6ec1b853c8fd - - 3fba9c77550a - 690c2caa367e - - 764f2516d837 - - 3ef480892a9f + - 3fba9c77550a + - 5127a713de83 - f4a3eff8ab85 + - 3ef480892a9f + - 764f2516d837 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -140,24 +140,24 @@ tools: - name: hifiasm owner: bgruening revisions: + - 60024a528cbd + - 366a11d316a7 - 5161f204ba63 + - 5f625c63b8bc + - 5bec28269d95 + - 0ee0c3089254 + - df25d4fb79b7 - 9ef6920c3089 - - ec9e21e9c71b - - 60024a528cbd + - 6505bd37670d + - 2061fb3b81b4 - f3c89da3af16 - 3f7be05a1597 - - 2061fb3b81b4 - - 41cea2aa2dce - - 366a11d316a7 + - 045c7c3d8e59 + - ec9e21e9c71b - 71740308d412 - da9d8bf98802 - - 5f625c63b8bc - - 6505bd37670d - - df25d4fb79b7 + - 41cea2aa2dce - 284a1cb82b61 - - 5bec28269d95 - - 0ee0c3089254 - - 045c7c3d8e59 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -182,42 +182,42 @@ tools: owner: iuc revisions: - 14ddfc8ffb93 - - 7518ee87b53d - de387b2b2803 - a96f3ad4e0d8 + - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 09c589057ee8 - - 9d79beb19ac3 + - f8113c25bc6b - d7edbc9c3a07 - - 39edec572bae - eb7b00ec347d - - f8113c25bc6b + - 9d79beb19ac3 + - 39edec572bae + - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - fd128c111ab0 - - 99ecfdafc64f - - eb7a370f6588 - - e731ea24e48d - - f338e9942b27 + - 2ecf5a570907 - 3ca2d2a9068c - f369ef5f210b - - 2ecf5a570907 + - 99ecfdafc64f + - f338e9942b27 - 606b09cc9860 + - e731ea24e48d + - fd128c111ab0 + - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -229,11 +229,11 @@ tools: - name: miniasm owner: iuc revisions: - - 73a3846701e1 - a7b889b90140 - - 8dee0218ac7d + - 73a3846701e1 - b799a615995d - 8b6d0d85252b + - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -251,9 +251,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 15200570e926 - - 64a1c751d99b - 7c2f5268d01c + - 64a1c751d99b + - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -265,46 +265,46 @@ tools: - name: pretext_map owner: iuc revisions: + - 8fef980d48b5 + - c6cec5ab35c1 + - 2b16ba799da9 - bbe19ef04a74 - - 02831bf9e95f - dfb8a4497339 - - 8fef980d48b5 - d256a51a656b - - 2b16ba799da9 - - c6cec5ab35c1 + - 02831bf9e95f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - 76d4cbefff85 - - a315c25dc813 - e9bd16ba5ebd + - a315c25dc813 + - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 6fcbee531de6 - - 7594365c546b - - 675488238c96 - - 72472698a2df - 59db8ea8c845 - - 342a1d1fed7b + - 3061c8b029e5 - ebb0dcdb621a + - 342a1d1fed7b + - 7594365c546b + - 72472698a2df + - 675488238c96 - 875d0f36d66f - - 3061c8b029e5 + - 6fcbee531de6 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - a199cd7ac344 + - aa39b19ca11e + - cd06929b224b - 39bed8de8017 - d865b62f501c + - a199cd7ac344 - 78c533842eeb - - aa39b19ca11e - - cd06929b224b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -316,31 +316,31 @@ tools: - name: raven owner: iuc revisions: - - f8564b2d7f63 + - f11b994b7eb2 - 3edba9afc9bc - 5c55448d0f33 - - 2b2a352488fa - 33b7d8481a76 - - f11b994b7eb2 + - f8564b2d7f63 + - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - f73ab5187eed - 8e66f695d859 + - f73ab5187eed tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - e122f9101584 + - 28189050e437 - 378e55aeeb25 - - ef69617ecb42 + - 1d06c8b38e77 - 5fc94b3a4704 + - ef69617ecb42 - 53c2bc8c2ae3 - - 1d06c8b38e77 - - 28189050e437 + - e122f9101584 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -352,170 +352,170 @@ tools: - name: shovill owner: iuc revisions: - - 865119fcb694 - 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name: spades_metaplasmidspades owner: iuc revisions: - - 6b5a5842531e + - 8d4b90bf9caf - e5a3b75a271f - - 21da31ed41a1 - - b8002c3f7141 + - 6b5a5842531e - 7e27faaad80e + - 21da31ed41a1 - 037f9927c4ff - - 8d4b90bf9caf + - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 86f66ab58e14 - 9de69775f512 - 328aa71f0f3c + - 2a10645aeadd - 7922870efcca - - 5b26685e5d3b + - 86f66ab58e14 - f1532cb33c75 - - 2a10645aeadd + - 5b26685e5d3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 8cc856b935ee - - 85fb02c43042 - 340bc17f49cf - - 6aad515a5270 - - e41dcb0e913b - 1708851f8804 + - 8cc856b935ee + - e41dcb0e913b + - 6aad515a5270 + - 85fb02c43042 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - d159735a6a9f - 249f6a28c751 - - d5fb354f745d + - 6357b127161e - 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name: trycycler_partition owner: iuc revisions: + - 80a17897564d + - 7673a6c920b2 - 4688ae3b49b5 - b23249f81bc4 - - 6dd935e4984b - ebd801e712bc - - 7673a6c920b2 - - 80a17897564d + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - 937ea677d437 - - b5e35a2ca4f3 - - 59bd28f6265d + - ed312479d9eb - b64696992ee9 + - 59bd28f6265d + - b5e35a2ca4f3 - cb1e3db43020 - - ed312479d9eb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6015aa0303f2 - - 383bb5ad32e2 - - b9b0246a2be3 - - cb4768eeca3b - 05bd7504fdb2 + - cb4768eeca3b + - 6015aa0303f2 - 2628f6790eda + - b9b0246a2be3 + - 383bb5ad32e2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 6e26c9afd301 - 0a3a602cd1e3 - - e022dff952df + - 6e26c9afd301 - 8f9f06995f98 - 3e44ef016b45 + - e022dff952df - 9e3e80cc4ad4 - e92675014ac9 tool_panel_section_label: Assembly @@ -524,16 +524,16 @@ tools: owner: devteam revisions: - 8d09f8be269e - - 08256557922f - 5da9a0e2fb2d - 920677cd220f + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 82398ba86ba7 - 37d88f41c810 + - 82398ba86ba7 - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -546,8 +546,8 @@ tools: - name: yahs owner: iuc revisions: - - 425e63adcc5d - 39495e107274 - ff4031bfaa22 + - 425e63adcc5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index b8e74aa6f..9e5375443 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,26 +2,26 @@ tools: - name: integron_finder owner: iuc revisions: + - 392f100eebcd - bfd290fe1588 - 1ae00120dd24 - 4768f7f8e93f - - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: + - 8e8dc9a1e3e5 + - 31812e7a1315 - ded48b36f3b7 - 1f5641a52664 - - 31812e7a1315 - - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - 5c8ff92e38a9 - - 24a7a95867b0 - 17fcac7ddf54 + - 24a7a95867b0 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 a6ea10902..0a595555c 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,27 +2,27 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 159b04e36791 - - a9c9d768b751 + - 204a131e47db + - d1f62024a08b - d58c27d2c5a7 - - 0840ba83860c - 1c427e24fb79 + - 0840ba83860c - 7beb76ffbc0f - - 204a131e47db - - d1f62024a08b + - 159b04e36791 + - a9c9d768b751 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge owner: iuc revisions: - - cab19c0452c4 - 1bb2b5b52030 + - cab19c0452c4 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_tadpole owner: iuc revisions: - - ce13b4678f18 - 0ddf147d1897 + - ce13b4678f18 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index aad7eab53..52cc9eb18 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 589e7e57fd6d + - 07e8b80f278c + - 87ee588b3d45 - 0a5c785ac6db - - a68aa6c1204a - 64e2edfe7a2c - - b28e0cfa7ba1 - dde39ba9c031 - - 87ee588b3d45 - - 07e8b80f278c - - e19bebe96cd2 + - a68aa6c1204a + - 589e7e57fd6d + - b28e0cfa7ba1 - ce3c7f062223 - a8eabd2838f6 - a1a923cd89e8 + - e19bebe96cd2 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 c73f29817..cb4c72229 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,30 +8,30 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 - - 54f751e413f4 - f921014aba5a - 62c9df8382c2 + - 54f751e413f4 + - e8ac2b53f262 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: + - d999e774072a + - acf4e47b734c - 0e3cf9594bb7 - - cbf3f518b668 + - 5edc472ec434 + - a52d2d93e595 - e25d3acf6e68 - 6f386c5dc4fb - - acf4e47b734c - 2889433c7ae1 - - 5edc472ec434 - - d999e774072a - - a52d2d93e595 + - cbf3f518b668 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 73163f6eb..97b2c0741 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 710301bc46fa - - f4230f116196 - - 6ca543ec1bf8 + - 095ad4d096d1 - da6bd1975a71 - - 27ee142314a9 + - 6ca543ec1bf8 - c8cdde00b105 - - 095ad4d096d1 + - 710301bc46fa + - 27ee142314a9 + - f4230f116196 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -111,8 +111,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -130,62 +130,62 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 88076940fa94 + - 0fac8e2afc13 + - 79cfd9ead848 - bfb65cb551d8 + - 88076940fa94 - 3b8a9d5ced85 - - 79cfd9ead848 - - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - d532b7e5f64b - - eb6564a60136 - - 715cd0e87781 + - 55918daa5651 - f5d979cb4b54 + - d532b7e5f64b - b46d4b4d995c - - 55918daa5651 + - 715cd0e87781 + - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - dae135dfd519 - - f26afd1b7104 - d2f955aea23a - - fdf2cc80adb5 - 5579659312e6 + - fdf2cc80adb5 + - dae135dfd519 + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - 319a28774da9 - d1d0efda35c0 - bc31d02be922 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - cac1886249a2 - - 4da9ee404eab - 2c349b027a01 - - 070e3ecc3fda - ed736e6eee39 + - cac1886249a2 + - 070e3ecc3fda + - 4da9ee404eab tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 2e219a2d9327 + - da8753545526 + - 525ca7c8065f + - d1f803b5943c - f197e34c33a9 + - 2e219a2d9327 - 73008ef1f487 - 807aa4c9293d - - 525ca7c8065f - - da8753545526 - - d1f803b5943c - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -193,11 +193,11 @@ tools: owner: chemteam revisions: - 27ea4e1a3f95 - - 7568ae18908a - 2c8ed1b52bf7 - - 1809414a9454 - 61094e01eff9 + - 7568ae18908a - c4fbab8e03c5 + - 1809414a9454 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,18 +209,18 @@ tools: - name: md_converter owner: chemteam revisions: - - ccfbd956a2d3 + - 79e8ab8f1e81 - 730ef07b90ae - - ba83f0923369 - d7ec25187599 - - 79e8ab8f1e81 + - ccfbd956a2d3 + - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -269,9 +269,9 @@ tools: owner: bgruening revisions: - e2c36f62e22f - - e6011617c748 - 4242b4d68e9c - b59c91adeac1 + - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -353,8 +353,8 @@ tools: revisions: - 85fad59f8168 - d4c67ced6abc - - 9b48456a96fe - bf99565cec1f + - 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 c1639187e..50212377b 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,11 +2,11 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - - c97a786e8fb5 - 2605cbdaa7d8 - - fa56d93f7980 - f907216064f6 + - c97a786e8fb5 + - fa56d93f7980 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -18,17 +18,17 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 11cf21ee4242 - 4124781932db + - 11cf21ee4242 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 495a4173006f - - 86e2413cf3f8 - 424aefbd7777 + - 86e2413cf3f8 - 640d3af5d833 + - 495a4173006f - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,7 +42,7 @@ tools: - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 161c19e92..2307509d2 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,10 +9,10 @@ tools: - name: collapse_collections owner: nml revisions: - - 830961c48e42 + - 33151a38533a - 25136a2b0cfe + - 830961c48e42 - 90981f86000f - - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,10 +31,10 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 + - 2dae863c8f42 - baabc30154cd + - 0046692724f9 - 6cbe2f30c2d7 - - 2dae863c8f42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 8db015a5b..1177ac0bf 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - d6ede73082da - - abba05ead5d7 - e7449b2c14bf + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 3b6f97e7094c - 4a6ee918c13a - - f3a19509108a + - a3b86937ead6 + - e3cbd2287f63 + - 3b6f97e7094c + - 0b3c3ad92827 - 6ef0b5664c69 - 5e1240a87bcb - ab9350a8ab4d + - f3a19509108a - 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a40dd4fd3096 + - 3c19c84fbce2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_twobittofa owner: iuc revisions: - - 8067dfa00ed2 - 3c6f9e8a4c17 + - 8067dfa00ed2 - e9bbe2f71784 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - 98704d357ede - fa49730d1d4b + - 98704d357ede - a2f83a375bf2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 9d30d193a..620b159c8 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,48 +2,48 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - de72ba3ed6f2 - c929a006727f + - a1ca9bccc7f2 - e821645ef8fc + - 29451af70c52 - 5f6d123679f4 - 268e91e540ee - - 29451af70c52 - - a1ca9bccc7f2 + - de72ba3ed6f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 5d11599b8a7d - - 2d2cf5c1ea8a - 12af64f93288 - - 0e143b4c3987 - - bb1e4f63e0e6 + - 2d2cf5c1ea8a - 7a7fd0f5f15d - 0e49b109abc2 + - bb1e4f63e0e6 + - 0e143b4c3987 + - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - c06951d10364 - - 1d848bc4585f - - 195e98217334 - - dc059492a995 - 7c1beb6d6eca - 81b1e3e1fc6c + - 1d848bc4585f + - dc059492a995 + - c06951d10364 + - 195e98217334 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 93eb012d9eed - - 71aa86af6762 - a67ac707496a - - bfff7454b59a - - 26e7304d6737 - 07418a30ed01 + - 26e7304d6737 + - 71aa86af6762 - 3d211717a775 + - bfff7454b59a + - 93eb012d9eed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias @@ -51,156 +51,156 @@ tools: revisions: - 56d5b797ce84 - b8858746dc1f + - dd0b7398bb96 + - 5be24eba848d - 29fcfd36e90a - 26983857c91a - - 5be24eba848d - 2bc10a9ca58b - - dd0b7398bb96 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 9384cd033f30 + - c3e012dfe21f + - 7e6bcd2e5128 - 72bfafe3330b + - ee3a1b0f45f1 - 7ef978dc1b8a + - 9384cd033f30 - e6d0bff01239 - - 7e6bcd2e5128 - - ee3a1b0f45f1 - - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - 514fa53b5efb - - 9470f29702f8 + - fd1275e01605 - a60c359ec43c - - d9a637e83828 + - 514fa53b5efb - fb9cf9c97ec4 + - d9a637e83828 - b73e213add0c + - 9470f29702f8 - 167788df3b46 - - fd1275e01605 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 86febdcc4283 - a02cfa31e9cb - - 5bffaa8354a1 - e479c7ca5570 - c34d11ea4ba6 - - ca0616bb2cdf + - 5bffaa8354a1 + - 86febdcc4283 - 2c37ce318bc3 + - ca0616bb2cdf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 69a8621ca2f0 + - 1fcb7adc39b8 - 78f405266706 + - 004aea905d4d - 192ef85c0b0b - - 2d466b530754 - 01fb6a7654e6 - - 1fcb7adc39b8 - - 004aea905d4d + - 69a8621ca2f0 + - 2d466b530754 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 137c4beed34b - - 2f9e4843f480 - - d9ce4897dbb2 + - 3c9f0c486cca - 459cfa861f0b - db940c262830 - - 9ecba5e225a6 + - 137c4beed34b - d580d6acd1df - - 3c9f0c486cca + - 9ecba5e225a6 + - 2f9e4843f480 + - d9ce4897dbb2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 32e451def88c + - bd7db9e2f2cb - 2c66e43f1c86 - f264afa9fa6f - - bd7db9e2f2cb - fd408d755394 - - bad3ca889618 - fbe773640707 + - 32e451def88c + - bad3ca889618 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 7e361d147872 - - 231994413f89 - - 56bce3c82278 - - 3b9d990a0a0e - 9368fbc49c8b - - 4e12ea27f788 - 7fda5607e777 + - 56bce3c82278 + - 4e12ea27f788 + - 231994413f89 + - 7e361d147872 + - 3b9d990a0a0e tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - ce4ce3316f74 - - 4431f39ede55 - - e65d16fb2724 + - c03c3384cd81 - d9114ef1c8a5 - - 94ca68515826 + - e65d16fb2724 + - 4431f39ede55 + - ce4ce3316f74 - b1779366c8e9 - - c03c3384cd81 + - 94ca68515826 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - 23f7c5f1fdaf - - b88ebb3672a1 + - 4ed32329e0ed + - d57251071381 + - 793665fff0f8 - 2da482e408b8 - f8fc4e5aff9d - - 793665fff0f8 - - d57251071381 - - 4ed32329e0ed + - b88ebb3672a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - 010e58e9d822 + - a7849312d328 + - a4dfb122e52b + - 512155688d98 - e4c7985d4585 - - 25d830337d31 - ba6efa77fb79 + - 25d830337d31 - c60570fa602f - - 512155688d98 - - a4dfb122e52b - - a7849312d328 - - 010e58e9d822 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 69264da0ce77 - - aa200e4f3939 - - 443d9a9d6d11 - 38e3f226248b + - 69264da0ce77 - 4d678170d29b - - 00d869ea03a1 - c899e0ccff8c + - 00d869ea03a1 + - aa200e4f3939 + - 443d9a9d6d11 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 10301d137111 - - d806504e96d9 - - a2d70c4fd406 - - aac8444d6681 - c361b12d207a + - d806504e96d9 - 6662b1a8d326 + - aac8444d6681 + - a2d70c4fd406 + - 10301d137111 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index e21626217..d6bf8ce14 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 7d16de45c021 - 08d873cdd5f6 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -23,8 +23,8 @@ tools: - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - 02bab5ff7c37 + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -44,28 +44,28 @@ tools: - name: obi_sort owner: iuc revisions: - - b6d9ea2fb41b - 12b9e285ca1c + - b6d9ea2fb41b tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat owner: iuc revisions: - - 5f4544915893 - 39320fee9d70 + - 5f4544915893 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 4cf47c504672 - 3299c7d5268f + - 4cf47c504672 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 08bf8c016..9e65a9209 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - ce385837c160 + - 832c20329690 - dba489bfcd62 - 63dd26468588 - - 832c20329690 - - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 208286509..1a3ca1996 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - cf1322aeb137 - - 6da3972210ee - - 29bdbc353f20 - 62f5fab76dfb + - 6da3972210ee - d82648ad25a3 + - 29bdbc353f20 + - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 5c36150ee..9bf967aed 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 5915ea1ec9b1 + - 8c0175e03cee + - fe74900d6dc7 + - 4e5056fefd88 + - 093678460093 - c4b82dce8335 - de6cebe3c043 - - 49370cb85f0f - - 48f587c13075 - 8665bcc8b847 + - 5915ea1ec9b1 - c053d4cad713 - - 44e2cc14f75b - - 660cffd8d92a - - 4e5056fefd88 - - b1c926deaa2d - - c5e2e5902201 - 288f97432497 + - e4691e1589d3 + - 49370cb85f0f + - b1c926deaa2d - 5eb7e84243f2 - 64172f1c1202 - - fe74900d6dc7 - - e4691e1589d3 - - 093678460093 - - 8c0175e03cee + - 48f587c13075 + - c5e2e5902201 - 135b80fb1ac2 + - 660cffd8d92a + - 44e2cc14f75b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: falco @@ -39,16 +39,16 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: + - f666895cbebd - 8889eb864cef - 9db07fd39f85 - - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length owner: devteam revisions: - - 5cbde03c1103 - de2db1bdfbf8 + - 5cbde03c1103 - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -75,77 +75,77 @@ tools: - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - f546e7278f04 - 2904d46167da + - f546e7278f04 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - ec0b5076173a - f81d4362b6c1 + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd - 9c620a950d3a - - 0dbb995c7d35 - cd0874854f51 + - 0dbb995c7d35 + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - dbfc505896e9 - - 1d8fe9bc4cb0 - - a626e8c0e1ba - - d60c3f704da0 - dbf9c561ef29 + - 1d8fe9bc4cb0 - c59d48774d03 - - 65b93b623c77 - ecb9f4854617 + - d60c3f704da0 + - 65b93b623c77 + - a626e8c0e1ba tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: + - f1dc2a761c30 - 9115b978ce10 - b05e39b9c170 - - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: + - 10b75444feae - 81a9090d6df3 - '144275714590' - - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - 8611b80a14d6 - - e9f8633db0a2 - 47e5dbc3e790 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - - 5b87038565bb - e30352e889fe + - 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 - 4e1d64e6385f + - 9282652e7234 - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -160,8 +160,8 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 3e396e702cea - b41c2c1bcfbf + - 3e396e702cea - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -169,8 +169,8 @@ tools: owner: devteam revisions: - 8d958759cf2a - - 09a2199cd356 - c885369b207b + - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -186,57 +186,57 @@ tools: owner: devteam revisions: - 74db4cffab1f - - 54053ea6c77e - 045f0e1043f7 + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - f86c27295151 - f0e7deab6518 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - f0b18efb97f1 - 33794bdb7fe0 + - f0b18efb97f1 - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: - - 297962e79f39 - ac3fed111eb6 + - 297962e79f39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - - 09070cacefd8 - - 529bccd5e4a1 - 567d5b3c52b1 - d5e9e83cd3d8 + - 09070cacefd8 + - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 0b7ec11b3c7c - 4bedca26c133 + - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - cb1e251cac37 - - 90858c306551 - 736b8f6ee456 - bdf1ce174e39 + - 90858c306551 + - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -250,27 +250,27 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 02f8a17a4ebd + - f984bb114520 - b29d37ca9e41 + - 02f8a17a4ebd - 3599f5451ee2 - - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - e246088b6e34 - - 177f0621c266 - 0c2907307ba4 - 6027ef51ef91 + - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - 73194cdd4f57 - - 61b4cedc8934 - 377ac2829eac + - 61b4cedc8934 - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -283,41 +283,41 @@ tools: - name: pear owner: iuc revisions: - - 037f0acc7830 - f69501361cec - - b4c6f054210a - 2f804526f5fd + - 037f0acc7830 + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: + - 61eb4cfc7313 - 29ef2c5ec205 - fdc21382376d - - 61eb4cfc7313 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: + - fe1ae2ebf63d - 795cd16de38f - 812705bcf39c - - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 3da72230c066 - - a019807f4e67 - 4b494533146a + - a019807f4e67 + - 3da72230c066 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic @@ -330,40 +330,40 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - bf04bd405d5b - - d3f58a0dc09d - 71f649c23021 + - d3f58a0dc09d + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - b557acca0b56 - - 8250ea3a1501 - - 71ad4a56c40c - a535cf1e5da4 - - e654095ab143 + - 8250ea3a1501 - 24013bf85a6f + - e654095ab143 + - 71ad4a56c40c + - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup owner: iuc revisions: - - f1d33e4c7bd8 - c5a2ee07c4e1 + - f1d33e4c7bd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: - - 6a675c3aa610 + - 7a7e33d28f62 + - 7accf7407811 + - 015cf18f4a15 + - 828dba98cdb4 - 9fa7803d1c51 + - 6a675c3aa610 - f3759eec3018 - 27ac32a22ad2 - - 7accf7407811 - - 828dba98cdb4 - - 015cf18f4a15 - - 7a7e33d28f62 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index 35dd35987..24702c60e 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,84 +2,84 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c - 7b4468117008 - - ce9cd02d5b88 - e41385662e5e + - ce9cd02d5b88 + - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: + - 9da02be9c6cc - ff9530579d1f - - e7b2202befea + - f2e8552cf1d0 - 5ec9f6bceaee - - 3d0c7bdf12f5 - - 9da02be9c6cc - 2b0c9d9fc6ca - - f2e8552cf1d0 - 2c64fded1286 + - e7b2202befea + - 3d0c7bdf12f5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 - c1a33f603da2 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: + - 18a51655db17 - 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: - - cc0fd298cc17 - 7306ec78632a + - cc0fd298cc17 - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - a72af9de6bf5 - 1f296803dfa3 - 8880fb74ef56 - - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 75c93c70d094 - - f7e2f1eb3a16 - - 9a913cdee30e - - 5e33b465d8d5 - - 3d93dd18d9f8 - - c1a4b5f3b432 - - b2f1f75d49c4 - abfd8a6544d7 + - c1a4b5f3b432 - 1c2db0054039 + - 9a913cdee30e + - f7e2f1eb3a16 - bf675f34b056 + - 3d93dd18d9f8 + - 5e33b465d8d5 + - b2f1f75d49c4 + - 75c93c70d094 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 949f01671246 - - cd7e644cae1d - 084bbd8ba7b8 + - cd7e644cae1d + - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index b329fac45..b5ac011a6 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index e121c021a..104443280 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -16,23 +16,23 @@ tools: - name: gemini_annotate owner: iuc revisions: - - 0c8f7322f8fc - - 8f53b238a360 - f2f3bc622a16 + - 8f53b238a360 + - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets owner: iuc revisions: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -108,8 +108,8 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -123,8 +123,8 @@ tools: owner: iuc revisions: - da74170c55c7 - - 666f60a9331a - 840fb4850be3 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -144,8 +144,8 @@ tools: - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -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/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index ba4164156..2e186f768 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -9,28 +9,28 @@ tools: - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 65bae993e..c6211d3ad 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -3,9 +3,9 @@ tools: owner: galaxyp revisions: - 983bf725dfc2 - - e9df53a75f3c - - c1b437242fee - b39347891609 + - c1b437242fee + - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,54 +17,54 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 1c58de56d587 - 28587613264f - e063168e0a81 + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 653e89d73fc4 - - 6591f049cf7e - - aad3885b3216 - - 9a776b080193 - - e08a7ad4378b - - 1ec814014652 - - 4317d3cb6cba - - e407b9da183a - - 83c7d564b128 + - 734abc7ac21d + - 516a54ddf218 + - 4df8de2d0e48 - ba931a59dd59 - - 5e6237d58b0c - - 69ebb7f46e45 - - 6ea73833cf67 - f8054ea1c365 + - 69ebb7f46e45 + - e407b9da183a - 7068f48d0ef9 - - 4df8de2d0e48 - - f5ea3ce9b9b0 + - e08a7ad4378b + - 9a776b080193 + - 83c7d564b128 - 1790dcf3c32d - - 8848455c0270 - c441583adae5 - - 734abc7ac21d - - 516a54ddf218 + - f5ea3ce9b9b0 + - aad3885b3216 + - 5e6237d58b0c + - 8848455c0270 + - 6ea73833cf67 + - 653e89d73fc4 + - 1ec814014652 + - 4317d3cb6cba + - 6591f049cf7e tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 21a560af5913 + - 9aaa46d45472 - 75b3b3d0adbf - 34758ab8aaa4 - - 9aaa46d45472 + - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - af5eccf83605 + - 054483e27a35 - 468c71dac78a - bfdc6a7ffd3a - - 054483e27a35 + - af5eccf83605 - 95fb5712344f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 849cc3962..cc2610713 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: + - fd59d783248a - c4bde687c846 - 7f13dc906cb9 - - 290a11559985 - - fd59d783248a - - 4b519282a05b - - ae9994cf526f - - 740057a5126d - a64dc31ab7f2 + - 290a11559985 - df7356989ac1 + - 740057a5126d + - ae9994cf526f + - 4b519282a05b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,9 +28,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 867ab348287d - 7cf5b1d072b5 - f95284aa2946 + - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,31 +42,31 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 48b42ee61bc5 - 3b37b1b1c3a7 - - ca7cb0eaad62 - - '566197475670' + - 48b42ee61bc5 - 53460afd5115 - 374e9062d874 - 51c6ccaace7e + - ca7cb0eaad62 + - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 1a72f938213e - 391a4cc45fea + - da4c086cff5b + - d3a9e32672ec - 10515715c940 - 3d059e9c2fba - - d3a9e32672ec - - da4c086cff5b + - 1a72f938213e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - b0d96516e6a5 - 6fc8bab811da + - b0d96516e6a5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca @@ -79,12 +79,12 @@ tools: - name: ggplot2_point owner: iuc revisions: - - e3a675da7fd0 - 1acf88921176 + - d0fc8b746d57 - 5fe1dc76176e - - 5298e06f14f9 - 299307abd804 - - d0fc8b746d57 + - e3a675da7fd0 + - 5298e06f14f9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -103,8 +103,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -129,17 +129,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 112eb40ba6cf - - 17359b808b01 - - 836d1aa3e89a + - 6cd09d7b5f37 - fd5dbf0f732e + - 667e17248bfe - 4542035c1075 - - 2bb2e07a7a21 - - 1cfc579079a6 - a6e57ff585c0 + - 112eb40ba6cf + - 2bb2e07a7a21 + - 17359b808b01 - ca2def38369c - - 667e17248bfe - - 6cd09d7b5f37 + - 1cfc579079a6 + - 836d1aa3e89a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -157,9 +157,9 @@ tools: - name: pathview owner: iuc revisions: - - 03c13085aecc - f1691de443a7 - fe154a7af404 + - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -172,8 +172,8 @@ tools: - name: plot_ragtag_paf owner: galaxy-australia revisions: - - 501dcf66c0ce - c1bed78b9ed5 + - 501dcf66c0ce tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots @@ -188,8 +188,8 @@ tools: - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 9958188c6195 - 7b21a9b5922f + - 9958188c6195 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -201,10 +201,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 26f2fe7e53a1 - 6c571966cfb9 - 44c66e8d21e6 - 7c9417381ad5 + - 26f2fe7e53a1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -216,23 +216,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 2824d77cd8f8 - - 326a3db8d9d1 - - a1abfa420d9d - 14e7c35f3d00 - - 360df4999907 - - 7dd841a32245 + - 326a3db8d9d1 - 36b848d5f3ec + - a1abfa420d9d - 4ac4e7083b7e + - 7dd841a32245 + - 360df4999907 + - 2824d77cd8f8 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 73b8cb5bddcd - 83c573f2e73c - 44608d0193ed - 99ace6c1ff57 + - 73b8cb5bddcd 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 e5b212b1c..6298709e3 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -21,62 +21,62 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: + - 6417cccad133 - 7779b9dcf040 - - 22bd5861706d - bc9e8de21efb - - 6417cccad133 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: + - 361608369dda - 55ccc0a121bc - - bf1e0bdec1db - e9283529cba1 - - 361608369dda + - bf1e0bdec1db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: + - da611a744112 + - 23d838d1569d - cc64914b0cf4 - 474a69c47184 - - 23d838d1569d - - da611a744112 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: + - 36735850e461 + - ad6995afd2e6 - 2ccd9f9e2cd0 - fc4b3b46dc9d - - ad6995afd2e6 - - 36735850e461 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - 81c34e67f262 - - 49653e680ea4 - 0a8e527d1517 + - 49653e680ea4 + - 81c34e67f262 - d8f5224005bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 79da59a0b180 - - 2861ca3bfe4d - 64dd8bb151e1 + - 79da59a0b180 - 4667fe07bd68 + - 2861ca3bfe4d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -89,8 +89,8 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony @@ -103,9 +103,9 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - - 9a2f72d7dbd2 - ff6decc0f432 + - 9a2f72d7dbd2 + - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -118,10 +118,10 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 28b1546857b0 + - 3027cb62adbd - 8d9c22419c56 + - 28b1546857b0 - 6b97ffba31da - - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -134,10 +134,10 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 1be0fc4d8654 - - 56d22aa6cb3b - 35f6611fb8c3 - 7d5c97823f8b + - 1be0fc4d8654 + - 56d22aa6cb3b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet @@ -157,23 +157,23 @@ tools: - name: scanpy_read_10x owner: ebi-gxa revisions: - - 287503c35cb4 - 078aa23c9374 + - 287503c35cb4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable owner: ebi-gxa revisions: - - 0bab2ae44e7a - - 36daab33aecf - d18ed15697bb + - 36daab33aecf + - 0bab2ae44e7a tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 79cc06a557b0 - 6a6364b488db + - 79cc06a557b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -186,8 +186,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - 65c3ec07502b - be019b069e31 + - 65c3ec07502b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -200,37 +200,37 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: + - 4428dba93375 - 3ee74b58c72d - - 0cf90e01d9f8 - 59028945c857 - - 4428dba93375 + - 0cf90e01d9f8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - 3fb53f5e46ea - - abdb61e4afa3 - - 8b0d6f6f44c8 - 181d61d2f3cd + - 8b0d6f6f44c8 + - abdb61e4afa3 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: + - ea91cfd0444e + - 767a675b5254 - fe562424a0a6 - 0f98603d0116 - bd4a244faeb8 - - ea91cfd0444e - - 767a675b5254 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: + - e2d0dc8a50ca + - 4cc9362782b4 - 5605f8452eb3 - f86b2c3bc459 - - 4cc9362782b4 - - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 66c65ee5a..10fd5b8c1 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,25 +2,25 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - d9967770de96 - - ed2cca6b5de4 - - a4c13ddcc8ee - - 0f611e7d7858 - 29f66c353bcb - 9edf8894a22d - 921a2da49a0c + - ed2cca6b5de4 + - 0f611e7d7858 + - a4c13ddcc8ee + - d9967770de96 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - d404277cc87a + - 11de0d28ab30 + - 478aacfbaa37 - 78fb5e286609 - - 755df866ad0c - ec4b948dc6f0 - - 11de0d28ab30 - - d404277cc87a - 5746d61f0a91 - - 478aacfbaa37 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins @@ -28,23 +28,23 @@ tools: revisions: - 9d93c8fbe0a6 - 11fa44ee0603 + - 977dc15add20 - 03dd3c16ae4e - - f72063d9426b - 9e357a8b2ec3 + - f72063d9426b - 4d511437b1e5 - - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 77919cc3618e - - 3b5b54ed6392 - - 41dbf4d162a2 - c3e5e2cf12b7 - - 0ba4f56a3613 - 1da5f169b491 - f86ca478c6af + - 77919cc3618e + - 0ba4f56a3613 + - 3b5b54ed6392 + - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix @@ -52,11 +52,11 @@ tools: revisions: - 025a128652dc - 7babd8a46fe0 - - f741330d4a71 - - 5308ca68ef3d + - 12d51d7be66f - 9939786dd9c9 - b63363075c2e - - 12d51d7be66f + - f741330d4a71 + - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index 8a9b13728..e6469fdb1 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,44 +2,44 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 8bccb36e055a - 0c777d708acc - 699a5e9146b3 + - 81f0cbca04a7 - 7db4fc31dbee - 3df9f0a4bf34 - - 8bccb36e055a - - 81f0cbca04a7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 0a53256b48c6 - - 5791a7f65275 - 5bc8cdc17fd0 + - 5791a7f65275 - 2436a8807ad1 + - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 6ad1d3cfdea1 - - 9d47aabda459 - e576b73a2e2f + - 9d47aabda459 + - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - 77f7159d775a - b1c2c210813c + - 77f7159d775a - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - d51310ab328a - f70b215d155c + - d51310ab328a - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -52,34 +52,34 @@ tools: - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 - fcadded98e61 - - b07f4839ca77 + - f3360fbeda64 - 85edbb7a436b + - b07f4839ca77 - 10eed33aa9b2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 984358e43242 - 6e65fd971e13 + - 984358e43242 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - 5bf8eb50b280 - - b58447a2eed2 - 664232d2a3f7 + - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - eb6c08714244 - 0e4dccaafef5 - e917a2424690 + - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -92,9 +92,9 @@ 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 @@ -108,17 +108,17 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - 2484086dee41 + - 5d28ac336861 - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - f2ed92b011a9 - - 11f177b1a59e - bace5a93a97c + - 11f177b1a59e + - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet @@ -132,8 +132,8 @@ tools: - name: cp_gray_to_color owner: bgruening revisions: - - 3245681b2f6d - ad271f78a87a + - 3245681b2f6d - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -149,8 +149,8 @@ tools: owner: bgruening revisions: - ff1a86a87364 - - c09dcda1143f - 6100a22bf4f2 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -164,24 +164,24 @@ tools: - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - ac5bea85a391 - 2564f461de62 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - a32c3f810ade - 91e03287f285 + - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - 8536b1ae0254 + - b64af54c5c09 - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -189,32 +189,32 @@ tools: owner: bgruening revisions: - e972e07c7845 - - d3890df07463 - 6f4715b8540a + - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - 407925835dd9 - - 980aed9e8fd5 - e52c75a28c4b + - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - d85f11570109 - - acf3aa487283 - 79e10d12d90a + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - 035a58c7f54a - - 80b200ae516b - b76841ee5560 + - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -227,9 +227,9 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - - 8083a87d2fdf - 48102a685037 + - 8083a87d2fdf + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images @@ -249,23 +249,23 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids owner: iuc revisions: - - f92941d1a85e - 4b794652dcdc + - f92941d1a85e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - 7b6d9412c7f8 - - f8b4eada923c - 236ec78b2e53 + - f8b4eada923c + - 7b6d9412c7f8 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index d8357bdfc..cc12b95e8 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 40737febe339 - - 3e4f434a69c6 + - a38934e303b9 + - 78bbd17d0703 - 1069f6db0a0e - 3a72fede57ce - - 78bbd17d0703 + - 40737febe339 - e319b5b65879 + - 3e4f434a69c6 - d6e72da3ec35 - f362150bef41 - - a38934e303b9 - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 0135f1d487a0 - - fcbeda41d0ac - c88553ec696e - - 8f8df367470d - - 9537184d421f - - 2b95d5c04908 - - 72ddd32392cd + - fcbeda41d0ac - 618297d23022 - 7fe36019c073 + - 9537184d421f + - 8f8df367470d - f91cfb73d369 + - 72ddd32392cd + - 0135f1d487a0 + - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: + - fafb3d685fa9 - d7e79eb3bcb3 - 2cf4a1cafc16 - - fafb3d685fa9 - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 6a1515bb0687 - - 3d18f8c3c0f6 + - 5dc33613c288 - a1c2aecd7a0d - - ee29337f905c - 8d36959b000d - - ee2beb764a7b - - bd2a7d1316b9 + - 7f1cfa4c0e32 + - 6a1515bb0687 - 9eaadf03e0df - - 5dc33613c288 + - 43aac8d29685 - 8c05afb547fa - - 7f1cfa4c0e32 + - ee29337f905c + - bd2a7d1316b9 + - 3d18f8c3c0f6 - 28a6f1908fcc - 94df24c6bc00 - - 43aac8d29685 + - ee2beb764a7b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - bcaa0d571ce2 + - 5d6ed46cc101 + - 5671e1d3d5ee + - c092052ed673 - 86a20ae274fc + - e3bb03cf207a + - bcaa0d571ce2 - a250929be21b - 364f4ffec275 - - 5d6ed46cc101 - - 9f978da6528a - - db536ad45f28 - - c092052ed673 + - d37ede8589b2 - cb903c9dc33d + - 9f978da6528a - 8858fa037a15 - - d37ede8589b2 - - 5671e1d3d5ee - - e3bb03cf207a + - db536ad45f28 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 38b91a3190cd - - 194e3ceee923 - - f95f403841ad - c5c9f02b6167 - - abbc8041e8ec + - 230b05597996 - ed28dd32141c - 49236b03e4fd - - 12d66d0d05ac + - abbc8041e8ec - 3b6a16d82c1b - - 230b05597996 + - f95f403841ad - e1a015876aa9 + - 194e3ceee923 + - 38b91a3190cd + - 12d66d0d05ac - 584beffa972b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/join_subtract_and_group.yml b/usegalaxy.org.au/join_subtract_and_group.yml index 8169d9cf6..6a544bee0 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: + - f198773344e4 - b8a457820315 - - 0f1724dd59d2 - 17e3b698dd52 - - f198773344e4 + - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ac092723240d - - ba0c40780ecf - a513e3fbb4c5 - - 374cb875d38a + - ba0c40780ecf - 22c2a1ac7ae3 + - ac092723240d + - 374cb875d38a tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 0f500eede..620d6b2b9 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -3,65 +3,65 @@ tools: owner: bgruening revisions: - 772e0e89fc68 - - 522137aaa9c4 - 66d7efc06000 + - 522137aaa9c4 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - f22a9297440f - - 4d81e3e2fb63 - 8a794e6d3388 + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 818f9b69d8a0 - - f1b9a42d6809 - 2af1346e68c9 - - e1317b5502fa - b6ef6d0cb6b7 + - e1317b5502fa + - f1b9a42d6809 + - 818f9b69d8a0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - 947c2eacccb8 + - 05143043ca13 - 1588f9076e32 - 8334dc98c48e - - 05143043ca13 + - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 29e4122c90de - - 83228baae3c5 - - 25b46af53232 - 1552b8cb4a94 + - 83228baae3c5 + - 29e4122c90de - 9991c4ddde14 + - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: + - 841a6cc5fc58 - 53616c8b0865 - a07ab242b0b5 - - 841a6cc5fc58 - - f3dfa4bdf87e - 060ca94ac049 + - f3dfa4bdf87e - 1a53edc4b438 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - dc4b5fd604a6 - - 40f4447733b2 - 2fc89dcd41c8 + - 40f4447733b2 + - dc4b5fd604a6 - d4808d5b83da - 91c4e3331208 - 927586a18553 @@ -70,31 +70,31 @@ tools: - name: sklearn_searchcv owner: bgruening revisions: + - c6ae57f774c6 - 36e8d6d5d01b + - 25ab6b4e376e + - e5a5ad882f1f - 301e07345c93 - 7626ea9c2e1b - - e5a5ad882f1f - - 25ab6b4e376e - - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 - - 02d2be90dedb - 4ed102b922cb - f9639b488779 + - 0630258dcf35 - 80852884053f + - 02d2be90dedb - b7c3e9a3b954 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - caeb57858702 - - ec69cbe34b73 - 14180f9c831e - 61634a87efc7 + - ec69cbe34b73 + - caeb57858702 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 cb98520c0..bed3714d4 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - d5ceb9f3c25b - 749c918495f7 - - f6877ad76b00 + - 17062a0decb7 - 0d4acadabb04 - a6d65b0c67af + - 017aba02828d + - cd659e8cc5fa + - d5ceb9f3c25b - 03e9b2fbc005 - - 17062a0decb7 + - f6877ad76b00 - 3ba8d4563129 - 937aa69e715f - - 017aba02828d - - cd659e8cc5fa tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: + - 53646aaaafef + - 64f11cf59c6e - 2477830927ec - - e188dc7a68e6 - dfd8b7f78c37 - - 64f11cf59c6e + - e188dc7a68e6 - 3fe632431b68 - - 53646aaaafef tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: + - 60afcc2c1d05 - 3e1ea2facca6 - 2ff111fac1d7 - - 37b497aa133f - e7f19d6a9af8 - - 60afcc2c1d05 + - 37b497aa133f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - f54f5baedfdd + - 5cc34c3f440d + - c0c2d0941de8 - 77b2770508f6 + - 8c6cd2650d1f - 3f4d6399997b + - 037c6e54df11 - 11a0d50a54e6 - - 5cc34c3f440d + - f54f5baedfdd + - 53c0b7a1a0c3 - b3eab4b67562 - - 6b1e195506a3 - 09b53c1d4ab1 - - c0c2d0941de8 + - 6b1e195506a3 - be1d967337e4 - - 53c0b7a1a0c3 - - 8c6cd2650d1f - - 037c6e54df11 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 5ef7ec16b04f - - ec9cbd6b9a49 - 79b885ce78d7 + - b8f5f6e87f5c - 00fbfac99d39 - 13022c3d3076 - - 381a32c51141 - - e403d27e8f24 + - 9ee34ba73ebf + - 5ef7ec16b04f - 1cd2511a396e + - ec9cbd6b9a49 - 178bdbdb6d24 - - b8f5f6e87f5c - - 9ee34ba73ebf - 42ce70172b72 + - e403d27e8f24 + - 381a32c51141 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metabolomics.yml b/usegalaxy.org.au/metabolomics.yml index b68850522..9129c521d 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -90,15 +90,15 @@ tools: - name: matchms_fingerprint_similarity owner: recetox revisions: - - fd890f162ce6 - 84af792d3a78 + - fd890f162ce6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - - 1b09315a3f87 - a5a5b147da70 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -111,8 +111,8 @@ tools: - name: matchms_metadata_match owner: recetox revisions: - - 330b0dfae8da - 03bc9b7f40f6 + - 330b0dfae8da tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -124,8 +124,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - f04b378325e5 - 8147d93d372d + - f04b378325e5 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -218,8 +218,8 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - 5f2b58dadb39 - f2c1d0bbb074 + - 5f2b58dadb39 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr @@ -232,48 +232,48 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - 79ad928a0dae - - ec196e27a61a - - 7b42ee54d757 - c53a97599181 + - 7b42ee54d757 + - ec196e27a61a + - 79ad928a0dae tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - 59c393d35e0e - - f3a18e020cdd - - 149b9cc7499b - 18ec7635bac6 + - 149b9cc7499b + - f3a18e020cdd + - 59c393d35e0e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - 481d769e2f7a - 134be5abb208 - - 50b9918aeff2 + - 481d769e2f7a - dfebc82ba1f0 + - 50b9918aeff2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 9064aecc78a7 - a82db010c53e + - 30bf4e35da3e - 501a232f3cd5 - 51332c2520c7 + - 9064aecc78a7 - 02c772a49998 - - 30bf4e35da3e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - 89178a72388a - - b3413f335327 - b341cfd4baf8 + - 89178a72388a - e7305ba0dd38 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table @@ -288,8 +288,8 @@ tools: - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - 99d118321d5f - 24278c6b6d1c + - 99d118321d5f - f92b1b64da93 - d7f5878a98c3 tool_panel_section_label: Metabolomics @@ -297,10 +297,10 @@ tools: - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ffbabefbd2e2 - - 7acd11ddc061 - ea0758b41473 + - 7acd11ddc061 - d90187b0f247 + - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -331,8 +331,8 @@ tools: - name: rmassbank owner: recetox revisions: - - 5a6bb93ec656 - 0b28816c1c2c + - 5a6bb93ec656 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 2b3e4f37d..f642a888b 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,16 +2,16 @@ tools: - name: bracken owner: iuc revisions: - - 0c7b6eb7e752 - 1d4bd12f01cf + - 0c7b6eb7e752 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_bins owner: iuc revisions: + - 0e63d03c8790 - 0094893f5001 - 18676df0cb3a - - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -91,99 +91,99 @@ tools: owner: iuc revisions: - 3a89c3f99f3d - - 5b5a7af9fbb4 - 63f86089423e - - 7c2100246a2f + - 5b5a7af9fbb4 - 76d3d2b10738 + - 7c2100246a2f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 18a502a9d287 - - 1c35dadbe76f - 00f5005840fa - - 96336c6a2bb7 - 84fd33a60b35 + - 1c35dadbe76f + - 96336c6a2bb7 + - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - f732237754fc - - a9f4a217dcd6 - - e8fba04706d3 - 34e55239e68b - addaf9d22850 + - a9f4a217dcd6 + - e8fba04706d3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - 5fe3edf19b9c + - 04c15826a0b8 - 8c202e741d68 - 75403243703a - 0776d824d896 - - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - 1c9b3bcd4261 - - 8470de786d47 - 75c8945b0da2 - - e96bbb9e24ea - 43c99742158b + - e96bbb9e24ea + - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 35176674168c + - 306a40d4bb8f - 1d75bd0595e2 - - 5c865a382933 - 84743da21318 - - 306a40d4bb8f - - 35176674168c + - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - ac72310b038a - - 555ccac8a4c5 - - 32c9ea835770 - 78faebd0879c + - 32c9ea835770 + - 8daf4564ccda + - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 - f947b4bb5107 - - cae017b76acb + - d60df8727f59 - 7b8cb2b02978 - a58e4a43f49c + - cae017b76acb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e - 7136e9ab70db - - 1bc3657cd694 - - 7f3b59dee073 - 1770d188f72d + - 7f3b59dee073 + - 04144473e59e + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - a7817705348e - - d943081510da - 19299bb1c6af + - a7817705348e - 9058d8943303 + - d943081510da - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -197,14 +197,14 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: + - 65d52c693b8e + - c4db8c4de66f - f8f56dd6449f - - a68b985913ab + - 4d9445dff47b + - b907a3c0434f - 5c7ba3d85a01 - - c4db8c4de66f - dbf1798c0dcc - - 65d52c693b8e - - b907a3c0434f - - 4d9445dff47b + - a68b985913ab tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -217,9 +217,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: + - 6c84982ee6f7 - 6d364c65c946 - 654548ae1357 - - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -232,23 +232,23 @@ tools: owner: iuc revisions: - e66ab198ec15 - - bd7a9c6efb10 - 6aad8ca3918b + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - b084117133af - d77397f09da1 - c6676a890f50 + - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - 7f208f1eb64f + - 9704f1a3b32d - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -274,15 +274,15 @@ tools: - name: humann_join_tables owner: iuc revisions: - - f01ca38fb6c5 - 6bf703133209 + - f01ca38fb6c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table owner: iuc revisions: - - 60749924ad62 - 6552df6efe6b + - 60749924ad62 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table @@ -290,31 +290,31 @@ tools: revisions: - e88b731dad59 - c409a495841f - - 79706f10d680 - 31c6d107e7a5 + - 79706f10d680 - 8237a0f225db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - aabf8cfb8fef - - 71ea608ddfa3 - - 172920f67a84 - 714d5a28cc5c + - 71ea608ddfa3 - 094ad9c068af - d24841f5c3d2 + - 172920f67a84 + - aabf8cfb8fef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - a293a742194f - 4137b492233e + - 2bdd84912a2b - d7e9a3c41657 - - a293a742194f - - 12fb63b5f63f - a4d7148ccee4 - - 2bdd84912a2b + - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -326,20 +326,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - a92c06a3afa7 + - e2c71b852aba - 6fcb8ac37a3e - - cf87759761eb + - 75bedfb2078b - 97f7bb0851e7 - - e2c71b852aba + - a92c06a3afa7 + - cf87759761eb - 64bc7acc22a9 - - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - e9d12c223a80 - 81c5dd1c777f + - e9d12c223a80 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -351,22 +351,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: + - 080ea153677c + - 2d35528d2141 + - c82508e76ad1 - 5e5a999ffaa9 - 4e5e73d03f0d - - 2d35528d2141 - 4033827c76b8 - - 080ea153677c - - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 95bf7479d53c - fc6c328c292f + - 2cd76b089570 - c2803012bbb3 - 6b7622dda516 - - 2cd76b089570 + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: itsx @@ -378,22 +378,22 @@ tools: - name: jellyfish owner: iuc revisions: - - dcd30574a456 - 11658afb8c87 + - dcd30574a456 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single owner: iuc revisions: - - 65b382bf9b7c - 385a965c6f87 + - 65b382bf9b7c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution owner: iuc revisions: - - e699e2747356 - 7624945cacd3 + - e699e2747356 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median @@ -406,15 +406,15 @@ tools: - name: khmer_extract_partitions owner: iuc revisions: - - 1061711538c6 - adb3dd5a899f + - 1061711538c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance owner: iuc revisions: - - b86562b4f3fd - 29a4d6e2ae9c + - b86562b4f3fd tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_below_abundance_cutoff @@ -427,8 +427,8 @@ tools: - name: khmer_normalize_by_median owner: iuc revisions: - - 4d23ab83ea29 - b1fe2ef3d244 + - 4d23ab83ea29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -447,10 +447,10 @@ tools: - name: kraken2 owner: iuc revisions: - - cdee7158adf3 - - 328c607150ff - 4a9da2b6c2e3 - 20e2f64aa1fe + - cdee7158adf3 + - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -469,8 +469,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -483,8 +483,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - 27d65c78863c - bfae8da6082c + - 27d65c78863c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -496,8 +496,8 @@ tools: - name: kraken owner: devteam revisions: - - 8ba2174315aa - 766d5f63b0f4 + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -509,37 +509,37 @@ tools: - name: krakentools_beta_diversity owner: iuc revisions: - - c254d75b8b67 - 4505d7643673 + - c254d75b8b67 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_combine_kreports owner: iuc revisions: - - 3d2cffa2c4ab - 073c867c5244 + - 3d2cffa2c4ab tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads owner: iuc revisions: - - f329328da134 - 4bf1e2701504 + - f329328da134 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona owner: iuc revisions: - - 88d274322340 - 02bbace216f2 - 2deaada69b14 + - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: - - bb96a1e6583d - d33cf727ed94 + - bb96a1e6583d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -569,22 +569,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 27250f92a01a - - 3cc4a60615c0 - - e073891b2afc - - 4fd3b5d8706b - - 327d9f4cc95f - 7f5d7b0e9884 + - 327d9f4cc95f + - 3cc4a60615c0 + - 27250f92a01a - 2cff76cf35c6 + - 4fd3b5d8706b - 0270541aaf46 + - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 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 @@ -650,33 +650,33 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - a16313517e55 - - 740fd2d16a28 - - 6dee4abadccb - - 2131d7dca455 + - fd69c607b43f - a92a632c4d9b - - 289b3807e80c - - b89b0765695d - - 1a037928504c - - ef65b083bd0c - 1a6cdf55390f - - fd69c607b43f + - ef65b083bd0c - ff8f55893e7d + - 1a037928504c + - b89b0765695d + - 740fd2d16a28 + - a16313517e55 + - 289b3807e80c + - 6dee4abadccb + - 2131d7dca455 - ec368db926f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - e3a64a1d2a6e - 2a8bc1d26d06 + - e3a64a1d2a6e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -700,15 +700,15 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 6034c3f3ecf0 - 2f47a294ef49 + - 6034c3f3ecf0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline @@ -721,29 +721,29 @@ tools: - name: picrust2_pathway_pipeline owner: iuc revisions: - - 6077821e8ae7 - f53beb324696 + - 6077821e8ae7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - 540aedfc81c7 - d6bb2e3febda + - 540aedfc81c7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 680fb3eb574c - 73b56418e7f4 + - 680fb3eb574c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions owner: iuc revisions: - - 881f2faa5fe7 - 677f3c8db525 + - 881f2faa5fe7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -755,8 +755,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 8e2ac1b8f70a - 0ba7dfaa941d + - 8e2ac1b8f70a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -774,8 +774,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 2e62e32d4f33 - 65e5f9caefcc + - 2e62e32d4f33 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -793,8 +793,8 @@ tools: - name: polypolish owner: iuc revisions: - - f355085dd2aa - 915637bd1d1a + - f355085dd2aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: recentrifuge @@ -807,12 +807,12 @@ tools: - name: staramr owner: nml revisions: - - 141afacabcfa - - 2fd4d4c9c5c2 - - 4d83eccf5f81 - - be818ae858e4 - 4b9a8031ab74 + - 4d83eccf5f81 - 3b22de20bd4b + - be818ae858e4 + - 141afacabcfa + - 2fd4d4c9c5c2 - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -820,7 +820,7 @@ tools: owner: iuc revisions: - 576963db5f1b - - b3c7199d8786 - 9495df9dd6ef + - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index a43ddad63..2f857a822 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - bdb4a58a2025 - 12e856482d26 + - bdb4a58a2025 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - 7238968f58f7 - ab12df91b47f + - 7238968f58f7 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 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 736db1f62..6345e5bdf 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 6ae5a7b5a0a2 - - 9baa871cb1d1 - - 80f03df2e2ce - - 098506c54016 - - cd07731e4434 - - 2263989660f5 - a74dbfee5a86 + - cd07731e4434 + - 8b67dd48fec1 + - 9eeb13a92d79 + - 6ae5a7b5a0a2 + - 94b8c6013083 - bdfbaf0c10aa + - 098506c54016 + - 80f03df2e2ce + - 9baa871cb1d1 - 9422c5a87ee2 - - 94b8c6013083 - - 8b67dd48fec1 + - 2263989660f5 - 48c13389050d - - 9eeb13a92d79 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 2e093badc689 - - bc3831dd65c1 + - c44f824c051a - '764845535798' - - c18157c68134 - - aaa0d6a8b808 - - d390fe1567dc - - f0af8936ed41 - - 4a60927aaca5 - - d7ce0ec78e51 - - 5abf2c2249aa - f14193ec1f50 - fc2e49f91e52 - - c44f824c051a - be78f13134e2 + - c18157c68134 + - 4a60927aaca5 + - bc3831dd65c1 + - f0af8936ed41 - 3ff17bad4006 + - d7ce0ec78e51 + - d390fe1567dc + - 2e093badc689 + - 5abf2c2249aa + - aaa0d6a8b808 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,8 +46,8 @@ 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 @@ -60,44 +60,44 @@ tools: - name: gecko owner: iuc revisions: - - 5efbd15675ca - 1de657a3198d + - 5efbd15675ca tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - c5908940967d - - 15974dd17515 - - a65296ffb4a0 - - bf28a8cff401 - - 8e649f27aa0d - - f0d493f8f84f - 6f28e90db932 - f1a5908ea2cb + - bf28a8cff401 + - f0d493f8f84f + - 8e649f27aa0d + - 15974dd17515 + - a65296ffb4a0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 - e8fdceffea4c + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - 5561a1193611 + - 60698466facd - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - 57f042937ba7 + - 48823c9635a4 - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -112,9 +112,9 @@ tools: - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - - 7cd7a55a678d - 636b049e6141 + - 7cd7a55a678d + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 50eb7fa22..87a7757ed 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -8,10 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 9aa9d92c3c51 - - 18a8d140ec6f - 7c47b3c9e493 - 28928576e1ea + - 18a8d140ec6f + - 9aa9d92c3c51 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -23,8 +23,8 @@ tools: - name: dorado owner: galaxy-australia revisions: - - 63d8ecfcfab1 - 6942f170cc43 + - 63d8ecfcfab1 - 99c9427219d3 - fc5b6491cf78 tool_panel_section_label: Nanopore @@ -32,21 +32,21 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - - 72b5e9dda577 - - 79e9a869f40e + - 0e9e7fcdd543 - fc8804320156 + - 79e9a869f40e + - 72b5e9dda577 - a7228a7ea146 - - 0e9e7fcdd543 + - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - 18505fe2bdb1 - - db25ec99c3ea - - fa11aa8103b2 - d6cddc06aeae + - fa11aa8103b2 + - db25ec99c3ea + - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -58,15 +58,15 @@ tools: - name: medaka_variant owner: iuc revisions: - - ec699520444c - edf6d4003fad - - 43815fa60f3a - - 19f3b583a9b3 - - eb746fa6f514 - - 222669c4afb6 - - 2bf63b38ee9b - 0f5f4a208660 + - 222669c4afb6 + - 19f3b583a9b3 + - ec699520444c - cc36773a3681 + - 2bf63b38ee9b + - 43815fa60f3a + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -85,13 +85,13 @@ tools: - name: nanoplot owner: iuc revisions: + - a38bdcec9e4c + - a3c4fe6f49ab - 0f1c34698076 - - 645159bcee2d - edbb6c5028f5 - 7b379e98b9a9 - - a38bdcec9e4c - - a3c4fe6f49ab - a02b8b3f5a0c + - 645159bcee2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -105,33 +105,33 @@ tools: - name: nanopolish_methylation owner: bgruening revisions: + - 90a922f32523 - a8d4be409446 - be95355fef8d - - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - 4857d5bcce52 - - 449e9aeded2d - d376944466bf + - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - a3afc5f0a96c - bec636361cfd + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 5f76b20953e5 - - 93d623d9979c - 543cbeef3949 + - 93d623d9979c + - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -163,8 +163,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 0433aad600e9 - 336791b5665f + - 0433aad600e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -176,15 +176,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 626b6c2be5c2 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - 26e6c9362b7b - ce8af9373061 + - 26e6c9362b7b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 01516b776..f9e388178 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - 592ef3959907 - a5921c09b7b7 + - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -27,19 +27,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: + - adfd6bf710bd - 97b1b5ad1cda + - d74850cf4e42 - baceff842902 - - adfd6bf710bd - 3e73c97f025d - - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 83da94c0e4a6 - - 9dd107db92c2 - 1586b111d2a3 + - 9dd107db92c2 + - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -52,20 +52,20 @@ tools: owner: iuc revisions: - 2f27f3b86827 - - 1e34d2e3d285 - - e9ee4d074d5d - 13851aefa67a - - 19b6a2f0dbe2 - - 8c533e19b697 - ed1518ce2237 + - 8c533e19b697 + - e9ee4d074d5d - e4b4837f06f5 + - 19b6a2f0dbe2 + - 1e34d2e3d285 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 @@ -84,9 +84,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 48a42ca61006 - - 38ccd4589990 - 5711fc06a63e + - 38ccd4589990 + - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -99,8 +99,8 @@ 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 @@ -113,8 +113,8 @@ tools: - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -134,9 +134,9 @@ tools: owner: iuc revisions: - 52b6a4d98009 + - b4b2b284230a - 27a6a256cd23 - 172815da3d41 - - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -161,9 +161,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 19bbd19b74b3 - 87febc68b45b - fea85c467896 + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -195,36 +195,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 2c61c30a57e7 - d8dc037e3c13 - - 9c43baa60906 - 0cb27ea69dc1 - - 4ba60cb14cb0 - - 2c61c30a57e7 - 5fe20c915fa6 + - 4ba60cb14cb0 + - 9c43baa60906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - 14785f8a3725 - d9339bb8127e + - 14785f8a3725 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - 9d09724f2bf1 - 0db22932bc39 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - 29c738066906 - - ed7a967cb11b - 6e24e79d3d69 + - ed7a967cb11b + - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -242,10 +242,10 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: + - defd3e9ddd2d - 3e4d45aca422 - - ad90c2da4f38 - 1865e693d8b2 - - defd3e9ddd2d + - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -264,10 +264,10 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - - 64deddb6a8ec - - 71c994a11f71 - d63c1442407f + - 71c994a11f71 + - 64deddb6a8ec + - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder @@ -320,6 +320,12 @@ tools: - 70227007b991 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_fcs_gx + owner: iuc + revisions: + - 32d058f3462a + tool_panel_section_label: None + tool_shed_url: toolshed.g2.bx.psu.edu - name: no_unzip_datatype owner: lecorguille revisions: @@ -329,8 +335,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 @@ -786,8 +792,8 @@ 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 @@ -799,9 +805,9 @@ tools: - name: salsa owner: iuc revisions: - - 58a870ef434c - ab5b7f6b7198 - f77f7a7f3b83 + - 58a870ef434c - ba7b0f11e470 - 9a22227bb6d0 tool_panel_section_label: None diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 7b1ec6d28..97e568efe 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,64 +33,64 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - b89cac5156ec - - 3f59ebfbfe3d - - '841557158611' - - 81e66674859e - - d033ffc1c161 - - c78f3d7dd1db - 107d3ba7024a + - 3f59ebfbfe3d + - d7c7ef3353fe - f04a1264e2a2 + - 6a457678efcb + - cce7b18495e4 - f73435dc282b + - d033ffc1c161 - 5a7c56a5cc08 - - 3b8b5bde0bd9 + - 8834daeb9892 + - c78f3d7dd1db - 26de3a7b1cb9 - - d7c7ef3353fe - - cce7b18495e4 + - b89cac5156ec - a6619171428e - - 8834daeb9892 - - 6a457678efcb + - '841557158611' + - 81e66674859e + - 3b8b5bde0bd9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 659517798cc4 + - aa8cc71438cf + - 3b96e92e8ec3 - 4755f52427c4 + - 6283babe736e - 6a726db04d4b - - 88c4aa435ded + - 02b8758214b0 - a185b079b095 - - 6283babe736e - b0af57c1a968 + - 88c4aa435ded - 5fcd1ece3a6e - df47d4845b62 - - aa8cc71438cf - - 6223845127ea - 7a2092844346 - 5b777002c2de - - 3b96e92e8ec3 + - 659517798cc4 + - 6223845127ea - e75442c7f4da - - 02b8758214b0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 70acec670c30 + - f87ac61981f0 - d1c340a5664b - f97743d52b87 - - b8476e82ac20 - - 24d024316465 - - f87ac61981f0 - c1d53e95327f + - 24d024316465 + - b8476e82ac20 - 111bd54f6bc4 + - 70acec670c30 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - feb40665d7cd - 4f6349228462 + - feb40665d7cd - daddf188c13f - 9e10ba792be2 tool_panel_section_label: Phylogenetics @@ -104,26 +104,26 @@ tools: - name: pangolin owner: iuc revisions: - - 36912871ccdc - - a2099fb98cdb - - ca337cce3888 - - ca0d8cf80567 + - 03ed9524dcd1 - 3a43c3982401 - - 81804a978fc0 - - 9d61d3fa046c - - abf6dbe8c9d7 - - b6abccb1f25b + - 83a69484cb87 + - a2099fb98cdb + - 2fa9d4f1b48f + - b7e297c2ede6 - 8ad84c5753ea + - 81804a978fc0 - 5f8727ff21e7 + - b6abccb1f25b + - abf6dbe8c9d7 + - 36912871ccdc + - 42a174224817 + - ca337cce3888 + - ca0d8cf80567 + - 7bb8726be37c - 14ae456b8cc5 - - 2fa9d4f1b48f - - 03ed9524dcd1 + - 9d61d3fa046c - 2f1019071464 - - b7e297c2ede6 - - 7bb8726be37c - - 83a69484cb87 - 437e28791761 - - 42a174224817 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: + - ea30d3089354 - 29ff6a849eac - - 73a469f7dc96 + - b1e68bbe4cef - ba29b5e2a4be + - 73a469f7dc96 - a4b71be30c3c - - b1e68bbe4cef - - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: + - 91887494eb97 - dbe2b2204555 - e88a7de55d6e - f1ccc8a6eb05 - - 91887494eb97 - - 809e42326fc2 - 9b2b122d0415 + - 809e42326fc2 - 15ac71df11a0 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 b8545ec3e..4255d381c 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - 1aac2a13842a - - b502c227b5e6 - - 881d7645d1bf + - fc288950c3b7 - a1f0b3f4b781 - - f9242e01365a + - b502c227b5e6 - 3f254c5ced1d + - 881d7645d1bf - f6ced08779c4 - - fc288950c3b7 + - f9242e01365a + - 1aac2a13842a - 7d34178f2812 tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index 672b46a1a..d2d66817e 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,18 +2,18 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - e7f1b552a695 - - 3f188450ca4f - - ca90d17ff51b + - 5b85006245f3 - 6ab1a261520a + - a58f7eb0df2c + - 3f188450ca4f - c0e71cb2bd1b - - 7fbec959cf2b + - 2f7702fd0a4c + - e7f1b552a695 - 3bd420ec162d - - 5b85006245f3 + - ca90d17ff51b - eb085b3dbaf8 - - e4a053d67e24 - d00e15139065 - - a58f7eb0df2c - - 2f7702fd0a4c + - 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 e0cf2c6c0..1ceb4d7d9 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,13 +2,13 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - ece627528a78 + - b18329a8ac14 - 277dc652246e - - 4c177985028a - 0a18ac48ac53 - b574b84afc4d + - 4c177985028a - f28ad96b76dc - - b18329a8ac14 + - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine @@ -16,80 +16,80 @@ tools: revisions: - a9a28e46d54a - bf06d196e23d - - 525f201b86c1 - - e988563cc6e5 - e215f71d7983 + - 525f201b86c1 - b41107d8fe89 + - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - bb6397b94018 + - 56da27be956a - 4fbffddde8cd - 8da3511c9467 - - 56da27be956a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - f23d67e28cc8 - - a8157342d9a3 + - 528fb09022be - 890845926d4b + - a8157342d9a3 - b8c79e70516d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a95a82eb4d50 - - 25b83cbd596a - 80600735685d - - a69865da6f80 - - 59e85306eae5 + - 25b83cbd596a - ae304a72db7b + - 59e85306eae5 + - a69865da6f80 + - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - f1897eb07081 - ed9ed1e6cca2 - 83aac7741200 - - e0669b1854b1 - - 611d80c0e29d - 798da6bdff3d + - 611d80c0e29d + - e0669b1854b1 + - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 74b61bf5bc4b - d426a9107a6c - - 5a35e3a8d013 - a7fb9b395ddf + - 5a35e3a8d013 + - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - cc430977c8ff + - df2187f9013b - 91f0f5922011 - 82f6c2f4332d - - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - ba92b59cd529 - - 10566783d718 - - 1693b2126f30 + - 043f9c91f686 - c5aa9fca18c6 + - ba92b59cd529 - d2483487e077 - - 043f9c91f686 + - 1693b2126f30 + - 10566783d718 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - 9fa3dbf06f17 - ae4dc0c041f9 - - bf0728e000cd - ff8c9e0e8a7b + - bf0728e000cd + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,8 +122,8 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - d0ea7589e95f + - d263296cd73e - eac99effe86f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -131,8 +131,8 @@ tools: owner: galaxyp revisions: - 0fa397f4f40b - - 1c5cbf8f79ce - 4081e4faa4ab + - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -145,8 +145,8 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - ce1a157a41bd - d6a4dfdad269 + - ce1a157a41bd - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -159,8 +159,8 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - e66f552a3c47 + - 160538a890a6 - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -174,23 +174,23 @@ tools: - 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 + - 7f432d87c82c + - 97a7f34fcb6a - 837224ad1694 + - 9c52362ae7bb - 1f39c833f65f - 2133b0be850a - - 9c52362ae7bb + - 4d17fcdeb8ff - f522c08e900c - 37d669de2828 - - 7f432d87c82c - - 97a7f34fcb6a + - e42225f8a659 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,26 +202,26 @@ tools: - 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16026cdb1330 + - 8a45fd5a608a + - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter @@ -565,25 +565,25 @@ tools: - name: openms_textexporter owner: galaxyp revisions: - - d063e2fe4ba4 - - 1b03536aa3c9 - 9020199dba0a + - 1b03536aa3c9 + - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - - f036e8cf1a55 - ad2ba3a95a02 + - f036e8cf1a55 + - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 5c2a97a234d6 - - 7f6a1f27553e - c8b225c69a7f + - 7f6a1f27553e + - 5c2a97a234d6 - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -603,21 +603,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 07ff622ec007 - - 1beff3ddce58 - - da885ca16cb2 - - 3ec27b4cee7c - a72c48001f7c + - 3634c90301af + - 1beff3ddce58 - 7fdd9119cc4f + - 3ec27b4cee7c - 943a34df6047 - - 3634c90301af + - da885ca16cb2 + - 07ff622ec007 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -677,11 +677,11 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 12692567c7f9 - 1a5690a5eedc - 265c35540faa - 4ddc8da62671 - a371252a2cf6 + - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index bf015d3f9..52697721b 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 10447a4b0cc3 - 18c6b2b6740f + - 10447a4b0cc3 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 65a7c0234..c962cc92d 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,75 +2,75 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 2f1d464ebfd2 - 42201b90e3f4 + - 2f1d464ebfd2 + - 110a346daf36 - cd5f98911089 - 289b7d6b69a4 - e345aadf914f - - 110a346daf36 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b + - c207119ba5f6 + - 8501601a118d - 42d9087b4789 + - 0345dbaaa79b - 0cd2df8af811 - fcce77c09289 - - c207119ba5f6 - - 8501601a118d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 33486216eec0 - 405a212b32ab - - ad5ab22ffe24 - 89eb29319bf4 + - ad5ab22ffe24 - 04db7fd6b238 - 421c33b8bf17 + - 33486216eec0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - eb784fa07f80 - - 1d839ead7ad3 - - 7b72fde3d27e + - 7370bb65bad4 - fa51dc5e8386 - f6e91108b7b1 - - 7370bb65bad4 + - 1d839ead7ad3 + - eb784fa07f80 + - 7b72fde3d27e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - 3d70c2996730 + - d30e36c48c93 - c9b77ced9a78 - a3e86cd9cac7 - - 8a55d29c8fcf - - d30e36c48c93 - 1544278c272e + - 8a55d29c8fcf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - 887cf585cafc - a5969aa9347e - - b242deb58952 + - 887cf585cafc - e2db212d64ad - - 564c33e5c3e3 - 7b881f5f5ad5 + - 564c33e5c3e3 + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - e897c74a48bb - - 9a171f9a450b - bd5ff77e2036 + - 9a171f9a450b - b4bab607eb05 - 8cff84759bf6 tool_panel_section_label: RAD-seq @@ -78,56 +78,56 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 4f65e343ecdf + - adc7a7610d4f - 5e10f396979e - - 33f0793edf93 + - 4f65e343ecdf - 6dafad990086 - - adc7a7610d4f + - 33f0793edf93 - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 17d39bf0a63a - - 4e280b27a831 - - 97575d01f06b - - 43e3eeb2e0ec - c287418eb288 - c5d7050e4ad7 + - 17d39bf0a63a + - 43e3eeb2e0ec + - 97575d01f06b + - 4e280b27a831 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 0b8c84a7fdb5 - - cd034465d4a4 - - 9586f08634c0 - - a819ec3b362d - d9bf483266a1 - 09b8edb56d80 + - cd034465d4a4 + - a819ec3b362d + - 9586f08634c0 + - 0b8c84a7fdb5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: + - a4b4bd84f69e - 95351dd0fd3f - 2645575d1bf2 - - a9c34a289493 - 69842dd5aa48 + - a9c34a289493 - bf0e43ab0416 - - a4b4bd84f69e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - d033e1ccb386 - cfb504394ae1 + - 912f904a6e1e + - d1fda11e602f - 8a35a3bc6752 - bb0475c884ff - - d1fda11e602f - - 912f904a6e1e + - d033e1ccb386 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d504d945a655 - 95286af4139b - d1fad35bdb4a + - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index a4a1d2452..f2e3e7b49 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,10 +2,10 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - 7acb00fc980a - cf01dd6c6b1f - 2d4e3aff9dc7 - 31f8063eedea - - 7acb00fc980a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters @@ -34,8 +34,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cemitool @@ -105,19 +105,19 @@ tools: - name: cuffmerge owner: devteam revisions: + - cf747d1bd79a - 22cf48ad7b16 - - 04adc9db1581 - 6a6717a5f421 - - cf747d1bd79a + - 04adc9db1581 - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 9a854107dbb2 - - 6cbfede05833 - 28b94cfbfdb9 + - 6cbfede05833 + - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -142,56 +142,56 @@ tools: - name: describe_samples owner: iuc revisions: - - 3b36efd62b3e - - e3b16fd7dd08 - 0693ccd171c4 + - e3b16fd7dd08 + - 3b36efd62b3e - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 0696db066a5b - d027d1f4984e - - 8fe98f7094de - 9a882d108833 - - cd9874cb9019 - 24a09ca67621 - 6a3a025714d3 + - 8fe98f7094de + - 0696db066a5b + - cd9874cb9019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 9a7c5b6d8f1e - - 62adf13b86ea + - df929f257179 - b47c006d90c5 - 2872c633f07e - - df929f257179 + - 62adf13b86ea + - 9a7c5b6d8f1e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 334ce9b1bac5 - - 9bdff28ae1b1 - - f2843df56434 + - ae2aad0a6d50 - 5bf899c13979 - - df0c8d0a5992 - - 555659de7321 + - f2843df56434 - 0cb907a2a810 - - 3d89af8a44f0 - - ae2aad0a6d50 - - a8305cf0c951 + - 334ce9b1bac5 + - 9bdff28ae1b1 - 6e53e565fc6a - 070900306913 + - 3d89af8a44f0 + - a8305cf0c951 + - df0c8d0a5992 + - 555659de7321 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: express @@ -203,18 +203,18 @@ tools: - name: featurecounts owner: iuc revisions: - - 7db9d3ea71c9 + - e6a2a912677a + - a37612abf7f9 + - f9d49f5cb597 + - a56fbe2d6ba7 - 90d16db017d7 + - ea04b737afa0 - f3a5f075498f - - a56fbe2d6ba7 - - e6a2a912677a - - af814359d244 + - 7db9d3ea71c9 - 38b6d12edc68 - - ea04b737afa0 - 1b851f87fbe0 + - af814359d244 - 6f66ae7c5f7a - - f9d49f5cb597 - - a37612abf7f9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -238,8 +238,8 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - 3c5e024a18cf + - 3c97c841a443 - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -252,21 +252,21 @@ tools: - name: hisat2 owner: iuc revisions: - - f4af63aaf57a - - 26371a1df031 - 3fb01a8c902d + - 26371a1df031 - 6ab42baa56e9 - 6c19daec423d - a86e80d3c09c - d4b55e2beb12 + - f4af63aaf57a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - 67b0b160903a - - 916cb26bd9d3 - 4418229c501e + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -278,33 +278,33 @@ tools: - name: kallisto_pseudo owner: iuc revisions: + - 01247aaf0a10 - ce5d418183c5 - 1c75aa5de15e - - 01247aaf0a10 - - 5ae5c312d718 - 87c11c05d238 + - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 4f9c4e6566e5 - - 40985510cd98 - c971db6f0fe5 + - 40985510cd98 - 10c98fab6c5a + - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - e827f9aae031 - 97e06a4c7c75 - - 119b069fc845 + - 58c35179ebf0 - 32511f586472 - - 0921444c832d - - 708348a17fa1 + - 119b069fc845 - d6f5fa4ee473 - - 58c35179ebf0 + - e827f9aae031 + - 708348a17fa1 + - 0921444c832d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -316,8 +316,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -341,8 +341,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - d696cf0a9622 - 72927fc9e9ed + - d696cf0a9622 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -360,21 +360,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - c7c55b694974 - - 980d2a2e1180 - - 7ed2edc1337f - - b0f2be869d6d - - 5ec75f5dae3c - - b9e04854e2bb - - 99b17b74a8cd - - 53255f6eecfc - 0a563fd2f22e - - c772497b2c32 - - 4df95e2d7f61 - - 3ea5a2a63fa2 - e132e7d02a3e + - 53255f6eecfc + - 99b17b74a8cd + - 7ed2edc1337f - 79de45b5069b + - 980d2a2e1180 + - c772497b2c32 - 4074fc1940e2 + - 3ea5a2a63fa2 + - c7c55b694974 + - 4df95e2d7f61 + - 5ec75f5dae3c + - b0f2be869d6d + - b9e04854e2bb tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -386,35 +386,35 @@ tools: - name: salmon owner: bgruening revisions: + - e3d32471da11 - 49121db48873 - - f4d5237a84f6 - - 53e9709776a0 - - cc05793bb896 - ebab418107f5 - - e3d32471da11 - - 2c0ca397d302 + - cc05793bb896 - 15cd64d7c58b + - 2c0ca397d302 + - f4d5237a84f6 + - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - 56242ff81c84 + - 8c28affc7c48 - c0fd285eb553 - fab6ff46e019 - - 8c28affc7c48 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: + - 1ebd14235b92 + - 76d290331481 + - cef79931dda5 - 914cfcba0ec8 + - 258d696dbd7e - cbf488da3b2c - - cef79931dda5 - ae618321f34a - - 258d696dbd7e - - 76d290331481 - - 1ebd14235b92 - dd4df992d93d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -445,27 +445,27 @@ tools: - name: transdecoder owner: iuc revisions: - - ffd1300599a1 - c6334cb383ff - 0db979fead3a + - 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 - d6a479fd4281 - - ba3720d7e68b - 74217fbfba4d + - bcc5f03f1900 + - ba3720d7e68b 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 @@ -473,63 +473,63 @@ tools: owner: iuc revisions: - fab23c3b5258 - - 3f4094b6a565 - 9ff3765e7172 + - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - 870ac06dff8e - - 4687ecf0eb2d - be3f26533209 + - 4687ecf0eb2d - 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: - - 65e7dea767ea - - c5fbddcac63a - - 5192f657f305 - 05ab8d5e04a2 - 33406f5a445c + - 5192f657f305 + - 65e7dea767ea + - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - - a35cba31d904 - e406ac71165d + - 1fdb25a8384d - 6f0fb35b799c + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: + - 37a1129c89d2 - 964b7efe2639 - c2c039e421af - 7c7fbf13aadd - - 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 - 047c22569787 + - eafea3083352 - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 + - 9871104ea630 - 3a4ac03d1266 - 1812dbc5bb7b - - 9871104ea630 + - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -547,15 +547,15 @@ tools: - name: trinity owner: iuc revisions: - - 9fa24d5aac68 + - 48636f857c4b - d2bc35f3d1c5 + - 32b86cd8eb50 - 8f1c3df4dd49 - - db1f362cca3e - c9cfec002f71 - d84caa5a98ad - - 32b86cd8eb50 + - 9fa24d5aac68 - cee61b3fcf78 - - 48636f857c4b + - db1f362cca3e 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 a3d6f6f22..700ffb5e7 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 1a052c827e88 - - 473382134e56 - 27e16a30667a + - 473382134e56 + - 1a052c827e88 - 080fd5739bb4 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 0438886af..4ba8d551c 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -3,16 +3,16 @@ tools: owner: devteam revisions: - 10184eaa85fc - - 88eedb4abea0 - 3c661e57a88f + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - 1dfd95ee241e - - 108db6635177 - 993b19f20c76 + - 108db6635177 - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,15 +25,15 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 5325e44297b9 - 75d5afa09972 + - 5325e44297b9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag owner: iuc revisions: - - e30af4e78cd3 - e9b9c489aacc + - e30af4e78cd3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools @@ -75,10 +75,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 19ece8afbaab - - 5f8e69cc4c6e - - e7fd6754d093 - 30a201c9c310 + - e7fd6754d093 + - 5f8e69cc4c6e + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -103,8 +103,8 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -130,18 +130,18 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 6856f8a01905 - 9149ad20699a - - 12749212f61b - 46c6639921f1 + - 6856f8a01905 + - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 06dc50b7b711 - 92ec40abcdcf - 26b4f9f98aca + - 06dc50b7b711 - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -160,11 +160,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 720217c23995 - - b906586a6596 + - a8d69aee190e - b3d99709fe1a + - 720217c23995 - 66e23b11feae - - a8d69aee190e + - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate @@ -177,28 +177,28 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - fefd89ab563c - - 22970df7a40e - cc61ade70eb8 + - fefd89ab563c - db17d5321bad + - 22970df7a40e - fe34990e5ce7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: + - 7def34e6cf4d + - 7a6034296ae9 - 88b8c2916784 - fa5d3e61e429 - 811fc2d75ad4 - - 7def34e6cf4d - - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup owner: iuc revisions: - - a389f74c3630 - 40fa6c240105 + - a389f74c3630 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge @@ -214,25 +214,25 @@ tools: - name: samtools_mpileup owner: devteam revisions: - - 8da515fbc1bf - - b61f5d6a7f25 - 583abf29fc8e - - 329deb17a9f7 + - b61f5d6a7f25 - 9da0311ab1dd + - 329deb17a9f7 + - 8da515fbc1bf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - - 30388d878f81 - db000c6007a0 + - 30388d878f81 - 85e38b31e8b3 - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM @@ -255,45 +255,45 @@ tools: owner: devteam revisions: - cab3f8d35989 - - 6c2c1836728b - d54a4df48867 - e613c1ad4c4c + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - bd850490c7f1 + - 818030fa6bbf - 5d9ae78f34d3 + - bd850490c7f1 - 135c85f4cfaf - - b7f7826ef1cd - bcedabb53ddf - - 818030fa6bbf + - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 5a08c09b9311 - - 1cc79f49b8d5 - 145f6d74ff5e - - 24c5d43cb545 + - 1cc79f49b8d5 - 3a0efe14891f - 541082d03bef + - 24c5d43cb545 + - 5a08c09b9311 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - b72793637686 - - 350bbc5c2ffd - - 6be888be75f9 - - c370440f901e - - bf328cec6a42 - - b01db2684fa5 - - 5826298f6a73 - 32dc5f781059 + - c370440f901e - 2dce91e11ca7 + - 6be888be75f9 - 0dbf49c414ae + - 350bbc5c2ffd + - b01db2684fa5 + - bf328cec6a42 + - 5826298f6a73 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 415c14a35..073253e2c 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -9,12 +9,12 @@ tools: owner: iuc revisions: - 59bb6d34fca6 - - ea5e944f447d - - 4aab5ae907b6 - - 6f6537780379 - - 5cb6146337d8 - a62c4a11a67d - - 480d9e9d156b - d147d6455873 + - 480d9e9d156b + - 5cb6146337d8 + - 4aab5ae907b6 + - ea5e944f447d + - 6f6537780379 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 e354b0963..17b6a2d09 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,101 +8,101 @@ tools: - name: alevin owner: bgruening revisions: - - ecb9ea6269ee - e4c01dcece8b - - e32b215b7c04 - b0fe3e482cb7 + - e32b215b7c04 - f2000bc73102 + - ecb9ea6269ee tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - c0b037b12765 - - 7a6655aa6eb2 - 707023fa62fe - e1c3c2f2a834 + - c0b037b12765 + - 7a6655aa6eb2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - 6f143dfe902a - - cfc3f5a57dc6 - - 00712416fdaa - - 32e547223c9e - - 55e35e9203cf - 93dd15e13e6a + - 55e35e9203cf - fb9e030ffae4 + - 32e547223c9e + - cfc3f5a57dc6 + - 00712416fdaa tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 038e32885fec - - 688357ad5e61 - - 14c576ea6148 - b9fac48532eb + - 14c576ea6148 + - 688357ad5e61 + - 39e945f0b2c1 + - 038e32885fec - 6f0d0c784f09 - ee98d611afc6 - - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b - - ed4996a16f7f - c4209ea387d4 - - b85871dd69f9 - - 43cb7b5a6fe7 - 3d748954434b - d4af736e7b83 + - 43cb7b5a6fe7 + - b85871dd69f9 + - ed4996a16f7f + - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - 890fb06a2893 - - fe75d2414dc0 - a4774b7b2e85 - 2e8022f1923c + - 890fb06a2893 - 7ebc22f77d86 + - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - 02b1fe7aed76 + - 769d815e4b0d - 4fff5a293013 - 0e70b2dfe4be - - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf - - a90f8efe08b4 - 344c2af50552 - aa4a6f0916b4 + - a90f8efe08b4 + - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - c32347702e12 + - 5b7c81b35b89 - 050cf43887d3 - b13d3e4c48e1 - - 5b7c81b35b89 - - c32347702e12 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - 239193b96d72 - - 02fc39c8610d - 1d77986f9ddc + - 02fc39c8610d - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -140,10 +140,10 @@ tools: owner: iuc revisions: - 2c1200fba922 - - cdf4443d5625 - a9caad671439 - - 8855361fcfc5 - cfe1e6c28d95 + - 8855361fcfc5 + - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -173,163 +173,163 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: + - c3ffb2c1e314 - fb7068d30ec9 - - 952abbc4b1de - 01c37e54e86e - - c3ffb2c1e314 + - 952abbc4b1de tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 45828071edc3 - - 57aeaf6b237d - 9d42a6133690 + - 57aeaf6b237d + - 45828071edc3 - f1c35f3f310d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - - 1a31e75e979e - 163fd744e235 - cab616fe7e64 + - 1a31e75e979e + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - 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name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - a315574104c6 - - 3a6a5381db36 + - 4401ed529d2c - 87eb9c58cd19 + - 3a6a5381db36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - c0737631eea1 - - 574f295b5ba4 - - a83732c79949 - 2ba6cee8e4db + - a83732c79949 + - 574f295b5ba4 + - c0737631eea1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: + - 937b7b9832d0 - ea19190ce5e0 - 30d7390bc918 - - 937b7b9832d0 - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2786a931cad2 - - 0f5786ffa10d - cd40ca76865a + - 2786a931cad2 - 2b4d6a8dab36 + - 0f5786ffa10d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - 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name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 89cfe7de541b - 11f39d7f6c64 - 6326cd29c1c3 - 06ced663d24f + - 89cfe7de541b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - 1602cc5b673c - 337705015ee8 - b4e780e93c91 + - 1602cc5b673c - beb5b5917d2f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - - 58de3c7c8e89 - e285920f8585 - 8d203e74869b + - 58de3c7c8e89 - a10fce08c2dc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -435,18 +435,18 @@ tools: owner: bgruening revisions: - b13e7a200525 - - 5cbd7a902a8d - ea8fb5e899e8 + - 5cbd7a902a8d - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - d74cf4a61d65 - - f81750434d70 - 1d6af10874d5 - 36dfa2825a59 + - d74cf4a61d65 + - f81750434d70 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -464,9 +464,9 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 1de2276f633f - - df64cc4dfb4d - 27fe5cd1729c + - df64cc4dfb4d + - 1de2276f633f - f36828ebdc54 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -482,12 +482,12 @@ tools: - name: modify_loom owner: iuc revisions: - - 4b0adaa31c95 - 7784821452ac - db575b4c8b22 - - 59be31ac9dc3 - - e98619de2776 - eeab712b0b99 + - e98619de2776 + - 59be31ac9dc3 + - 4b0adaa31c95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -499,9 +499,9 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 48f0fb3061b1 - - 7ffaa0968da3 - 2cfd0db49bbc + - 7ffaa0968da3 + - 48f0fb3061b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -533,46 +533,46 @@ tools: - name: raceid_clustering owner: iuc revisions: - - a4b734cd253b - - 49776718ae90 - 7e014059a88d - - f911a64454fb - c4f39bf4a068 + - 49776718ae90 + - f911a64454fb + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - d45f092caf24 - - 43c146e25a43 - - 8b917923f7d4 - 7608d5faee41 + - 8b917923f7d4 + - 43c146e25a43 + - d45f092caf24 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - 2b0d3e2f402a + - 37a47c4fd84d - c7ddb719554d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory owner: iuc revisions: + - df8e4e54d367 - 6e90c8adf84f - 69018f285aa3 - - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - e93b008c637a - 44b935f2271b - - 2bfd55b87af3 - c92d0f9338c5 - 72979cac22b2 + - e93b008c637a + - 2bfd55b87af3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -590,95 +590,95 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - b2df381a6004 + - 6acb08931836 + - 6f83f8fd381f - aaa5da8e73a9 + - b2df381a6004 - 8983e7a04ba7 - 4d8f983cd751 - f9353ee6a0d4 - - cb43c5d3acd3 - - 38db3fef7aad - - 6f83f8fd381f - 77b91b9bdf52 - - 6acb08931836 + - 38db3fef7aad + - cb43c5d3acd3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - a03ff8633507 - - a97abb8cd15b - b409c2486353 - - 3c86f71498bc - - 8cb783c81905 - 72a6bebab2a5 - - d636ce5cde16 + - 8cb783c81905 + - fc0321c000a3 - 277313130da5 - 64388be6d510 - - fc0321c000a3 + - a97abb8cd15b + - a03ff8633507 + - 3c86f71498bc + - d636ce5cde16 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 18262103fa61 - - d86cb2ce311b + - 5c3ebe2adc77 - f54f0f0598ad + - 3081ff5c84a3 - 6c145a6868cc + - 5e9171dc8244 + - d86cb2ce311b - 6bd82ed14acd + - 18262103fa61 - c0a80a16560f - c5d3684f7c4c - - 5e9171dc8244 - - 3081ff5c84a3 - - 5c3ebe2adc77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 7b9fafe32c86 - - 94c19fb1281c - - 4bda4412b8c2 - - ab55fe8030b6 - - 146ae5d70b47 - - d844935c906c - 56c0d4acef02 - - a407e7f8bdc1 - 3bcd5445cd7a - c9cb76cf8d6c - 9f354c7c8c92 + - a407e7f8bdc1 + - 94c19fb1281c + - ab55fe8030b6 + - d844935c906c + - 7b9fafe32c86 + - 146ae5d70b47 + - 4bda4412b8c2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 62acdd96d4a0 - - 1072ce66b426 - aa0c474463c2 - - dbbe1ea8ecb1 + - 7647e5cd1b8b - 6f5349dd5c49 - - 95777145cb92 - - 9b0cdb8cf6be + - 40812a65a78b - 0185bd174ea0 + - 9b0cdb8cf6be + - 95777145cb92 + - dbbe1ea8ecb1 + - 1072ce66b426 + - 62acdd96d4a0 - f7446fd8d5e7 - - 7647e5cd1b8b - - 40812a65a78b - 6adf98e782f3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - c65fce500915 - - fe8f16c594ec + - 73ab2ac53d06 + - d18e7a6e5cd4 + - 9fb627495ec2 - bf2017df9837 + - f2f6c703da06 - 215733a383f2 + - fe8f16c594ec - c5541bfb8feb - - f2f6c703da06 - - 458e8f43a775 - a39040ae0a38 - - 73ab2ac53d06 - - d18e7a6e5cd4 - - 9fb627495ec2 + - 458e8f43a775 + - c65fce500915 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -692,8 +692,8 @@ tools: - name: scater_filter owner: iuc revisions: - - 7a365ec81b52 - b7ea9f09c02f + - 7a365ec81b52 - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -706,8 +706,8 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 81e5bdff4853 - 2e41b35b5bdd + - 81e5bdff4853 - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -720,9 +720,9 @@ tools: - 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 - name: scater_plot_tsne @@ -944,8 +944,8 @@ tools: - name: sinto_barcode owner: iuc revisions: - - d1b34ac42b8f - fb61eb03e313 + - d1b34ac42b8f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: sinto_fragments @@ -971,15 +971,15 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 64fa083411f1 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - 05bd4db20227 - fecf9664c885 + - 05bd4db20227 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing @@ -998,8 +998,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 90e95e9ee190 - 883c33ef3372 + - 90e95e9ee190 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 74d7386c2..83951bb7b 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,10 +32,10 @@ tools: - name: datamash_ops owner: iuc revisions: + - 419027d822d6 + - 4c07ddedc198 - 562f3c677828 - 746e8e4bf929 - - 4c07ddedc198 - - 419027d822d6 - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,15 +49,15 @@ tools: - 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 @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - 7a15159140d1 - 6c29c7e347e8 - cb1c59d69557 + - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - aef56d0e7a61 - b1eda492f063 - - 7442b94d6a1e + - 9c3e1d3235c8 - 4c4ec859c31a - - aef56d0e7a61 - 840f29aad145 - - 9c3e1d3235c8 + - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 07843f917990 - - 9fda0b82f419 - - 375bbd555f4a - d0352e8b4c10 - 30d21a6041f6 + - 07843f917990 + - 375bbd555f4a + - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - cd02bf168d23 - 8b1b2b91f8d0 - 2c58b83c9bad - - 7ae443e6217d - - cd02bf168d23 - 4cc980df6265 + - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 1dd433d2c92c - - e10e776f2109 - - 7dd3fb35904f - bb9fc9d46ea4 + - e10e776f2109 - 4bbaf77573ef - ad7e0b4291ee + - 1dd433d2c92c + - 7dd3fb35904f tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index cee56526f..c18f4ec0d 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -34,14 +34,14 @@ tools: - name: column_maker owner: devteam revisions: - - 6e8d94597139 - 13b6f0007d9e - - 464b9305180e - - aff5135563c6 + - 6e8d94597139 - 6595517c2dd8 + - aff5135563c6 - 02026300aa45 - - 9cd341095afd - be25c075ed54 + - 9cd341095afd + - 464b9305180e tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -53,8 +53,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 557ec8d7087d - 34d29339abab - - 37cde8134c6a - - 90f657745fea - 9cc411a62277 + - 90f657745fea + - 557ec8d7087d + - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -106,29 +106,29 @@ tools: - name: merge_cols owner: devteam revisions: - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 623f3eb7aa48 - cf4397560712 + - 623f3eb7aa48 - 1ea4e668bf73 - - 33d61c89fb8d - 83069b38aa85 - - 2e8f945f7285 - - cf34c344508d - 3a6b78c39dca + - cf34c344508d + - 33d61c89fb8d + - 2e8f945f7285 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 503bcd6ebe4b - - 399da6b5ec21 - ae8c4b2488e7 + - 399da6b5ec21 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -140,30 +140,30 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - bce29ec10b78 + - c4d18aa4ec4a - b722161a845a + - bce29ec10b78 - f768f6183386 - - c4d18aa4ec4a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 3bf5661c0280 - 60ff16842fcd + - 3bf5661c0280 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - ddf54b12c295 - - fbf99087e067 - - 12615d397df7 + - 9ff72e942410 - 86755160afbf - - 74a8bef53a00 - - d698c222f354 + - ddf54b12c295 - a6f147a050a2 + - d698c222f354 + - 74a8bef53a00 + - 12615d397df7 + - fbf99087e067 - f46f0e4f75c4 - - 9ff72e942410 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml index 46e6a3328..b209fc588 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -14,8 +14,8 @@ tools: - name: breseq owner: iuc revisions: - - 0d18a3ba2d1c - 82fb5e3bb93e + - 0d18a3ba2d1c - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -28,42 +28,42 @@ tools: - name: cutesv owner: iuc revisions: + - c0f8fe52948e - 23d7e75d850e - cb441f258c37 - - c0f8fe52948e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: - - 156b60c1530f - - a5937157062f + - 57def2d7c093 - 04fa42777df9 - - ef2c525bd8cd - 3e954e7125bf - - 57def2d7c093 + - 156b60c1530f + - ef2c525bd8cd + - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 09d6e4693887 - - 791f73caa0c8 - e61c9ac190ad + - 791f73caa0c8 + - 09d6e4693887 - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: + - 074d44697036 + - 65432c3abf6c + - e1461b5c52a0 - 3b4b2121842f + - 4805fe3d8fda + - b11e8e9c23bf - 03627f24605f - - e1461b5c52a0 - dfadc322b065 - - 65432c3abf6c - - b11e8e9c23bf - - 4805fe3d8fda - - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter @@ -77,17 +77,17 @@ tools: - name: lofreq_indelqual owner: iuc revisions: + - f4473557ffc7 - c27549b9aa1f - 426d707dfc47 - - f4473557ffc7 - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - cdaab621d454 - dbd9f2db9ed8 + - cdaab621d454 - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -108,9 +108,9 @@ tools: - name: snippy owner: iuc revisions: - - d220115f882b - fa016f1eea1a - 5bbf9eada9c2 + - d220115f882b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -146,21 +146,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 3b1e7c170b10 - - e7aff4a85df5 - - 32f14a2723ec - 40f0591deda0 + - e7aff4a85df5 + - 3b1e7c170b10 - ee4a90760848 + - 32f14a2723ec tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - adc0645b945c + - 4934c0ac6197 - 02d81b994ef5 - - 9793bc5d741b - 42818629ec4c - - 4934c0ac6197 - - adc0645b945c + - 9793bc5d741b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/usegalaxy.org.au/vcfbcf.yml b/usegalaxy.org.au/vcfbcf.yml index cb844afb0..71fcf1920 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ b/usegalaxy.org.au/vcfbcf.yml @@ -2,39 +2,39 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - b7ea370b8f5d - - 2c372041ed8c - - 6a88248893c4 - 8a2e296c07ef - - 95815a0bb307 - - ebe5fc018e72 - e075b1be5abb - 265fe0f9ea64 + - b7ea370b8f5d + - 95815a0bb307 + - ebe5fc018e72 + - 6a88248893c4 + - 2c372041ed8c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call owner: iuc revisions: - 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