diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index ce1a0b1c7..ea6588f54 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -8245,3 +8245,4 @@ Update 224 18/12/24 03:13:12 krakentools_alpha_diversity False Tests failed iuc Update 224 18/12/24 03:26:51 quast False Tests failed iuc a3b35edea53a a3b35edea53a Staging Testing 11/13 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_224/install_log.txt 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 diff --git a/requests/ncbi_fcs_gx.yml b/requests/ncbi_fcs_gx.yml deleted file mode 100644 index e2f8f291d..000000000 --- a/requests/ncbi_fcs_gx.yml +++ /dev/null @@ -1,8 +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 d519c8e51..e995442a5 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,25 +2,25 @@ tools: - name: abricate owner: iuc revisions: - - 6e9aea89e388 - - 3f3e247c053d - - 4efdca267d51 - 78c75f134c16 - c2ef298da409 + - 3f3e247c053d + - 6e9aea89e388 + - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - c45c9dd066e2 - 3f438bf5475d + - c45c9dd066e2 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 @@ -40,16 +40,16 @@ tools: - name: annotatemyids owner: iuc revisions: - - 44018dd6b447 - fe3ca740a485 - - a79ee60b6926 + - 1aae04680c4b - 133f36c29579 - - cd2480f35935 + - 44018dd6b447 - f29602ae449e + - 3e1f6f6d557e + - cd2480f35935 - 4f2967b27e67 - - 1aae04680c4b + - a79ee60b6926 - b5d8e5475247 - - 3e1f6f6d557e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,38 +62,38 @@ tools: - name: augustus_training owner: bgruening revisions: - - 7be22100e5e1 - - 6519ebe25019 - dc027fa56d55 - aada0deea587 + - 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 - - bd0e53f3a891 - 09855551d713 - - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - 92eee5f31117 + - da5f1924bb2e - d77802fe76f7 - 728dacaf08a9 - - da5f1924bb2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - 8fd427007e93 - fe48aa4ccd5e + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -126,9 +126,9 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: + - 9d1fbff733cf - d9c3016f7283 - 63662ae295d6 - - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -158,61 +158,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - b6b5cd37f2a2 + - 9c15ca7e764e - 582fd74dc2a1 + - 9f2455341fac + - b6b5cd37f2a2 - 756376aeb1ae - - 9c15ca7e764e - - 14f588312c56 - 3bbe70fef6df - - 9f2455341fac + - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - 1691af4a0d17 - - a230ea445788 + - 73428a792541 - 8e1ace8f77c6 - 989f7c061f35 + - a230ea445788 - 0ffe5be70caf - - 73428a792541 - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 0418d28136de - - 30f08d74024f + - 494f0bb4a993 - 563a19373357 - - e94187d661df - 5a5ae61da69c - 57c6718cbfcc - - 494f0bb4a993 + - e94187d661df + - 0418d28136de + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 2bba2ff070d9 - - f31125bb85ea - - 1bc5a03faf2e - - 7abc5f6dd595 - - d6c7106b7b2e - 4b96ced19f75 - f77d7b685bb3 + - d6c7106b7b2e + - f31125bb85ea + - 7abc5f6dd595 + - 1bc5a03faf2e + - 2bba2ff070d9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - d77fdcca400e - d3af38b9c7e1 - - 52af33194019 - 54961e026fe4 - - d77fdcca400e - 520e30695ec3 - - b3cf4684e9c7 - fed64e676186 + - b3cf4684e9c7 + - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -225,8 +225,8 @@ tools: owner: iuc revisions: - 07d7991bf205 - - 79261884facd - 2aea122fbd25 + - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -238,10 +238,10 @@ tools: - name: goseq owner: iuc revisions: - - ef2ad746b589 - 602de62d995b - 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: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - c55643c3d813 - - 98cafcbd2578 - 74810db257cc + - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -292,8 +292,8 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker @@ -307,11 +307,11 @@ tools: - name: mitos2 owner: iuc revisions: - - c8ac28e8ac44 + - 033755194fe9 - b815ec682418 - - 624606f7c996 + - c8ac28e8ac44 - e95d52d295d7 - - 033755194fe9 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -353,10 +353,10 @@ tools: - name: prokka owner: crs4 revisions: - - bf68eb663bc3 - - d643e3b03500 - a17498c603ec - eaee459f3d69 + - d643e3b03500 + - bf68eb663bc3 - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -401,23 +401,23 @@ tools: - name: snpeff owner: iuc revisions: + - 8f92c2b26e6d - 6322be79bd8e + - c7275bd8b4d6 + - 5b80f544c67f - cfcf33df7fc0 - - 8f92c2b26e6d - 268d162b9c49 - 5a29ab10dba6 - - c7275bd8b4d6 - - 68693743661e - - 5b80f544c67f - 5c7b70713fb5 + - 68693743661e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - - 2b3e65a4252f - 09d6806c609e + - 2b3e65a4252f + - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -442,18 +442,18 @@ tools: - name: tbprofiler owner: iuc revisions: - - 037a11682176 - - 200c378d85f3 + - d03af1c7002c + - 37213cf56392 + - 45083d070fb8 + - ba6f87115e13 - e1a9d6fd258d + - 51dd22484644 + - ac8250086ac3 + - 037a11682176 + - 8cb134b8c1a5 - 809dfc93d593 - - ba6f87115e13 + - 200c378d85f3 - 4839e590cb26 - - d03af1c7002c - - 8cb134b8c1a5 - - ac8250086ac3 - - 51dd22484644 - - 45083d070fb8 - - 37213cf56392 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 42aeab51f..4064ccd27 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: - - 841084c5fc46 - - fa5259cc561b - - 0124fce4654a + - 8f1b150a2487 - a929ce596a34 - - 553bfe8bd0b5 - - 890b794c997d + - 0124fce4654a - 0e93176640ac - db9b10824c61 - - 8f1b150a2487 - - 7547fcab5d19 + - 553bfe8bd0b5 + - 841084c5fc46 + - fa5259cc561b - d6d5ccc2c581 + - 7547fcab5d19 + - 890b794c997d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b9e31c5c01c7 + - b2860df42e16 + - ddddce450736 - 067592b6b312 - 94fe43e75ddc - 21e491ad532a - - ddddce450736 - - b2860df42e16 + - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -37,48 +37,48 @@ tools: owner: bgruening revisions: - 5258e18bbe23 - - a7f16f24e9a1 - 3371c5bdc17a - - 22286dab5aa1 - faee8629b460 + - 22286dab5aa1 + - a7f16f24e9a1 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: - - 1440ae06552f - - 46ae58b1d792 - - 1e62c28ba91d - 94170eee0ad8 + - 41030a6c03b7 + - bb935709506a + - 0d243f458b53 - 2babe6d5c561 - - ea8146ee148f - - cf13a1e03e5b - - e5c372c91e46 - - 602fb8e63aa7 - - 5ecdeca79a0d + - 1e62c28ba91d + - 46ae58b1d792 + - e824f5d958d0 - 2dd755c1c6ff - - 0d243f458b53 - - e4bd1e99bacf + - 5ecdeca79a0d - 4048d82f0c88 - - e824f5d958d0 - f18f0b887c31 - - bb935709506a - - 41030a6c03b7 + - ea8146ee148f + - 1440ae06552f + - cf13a1e03e5b + - e4bd1e99bacf + - 602fb8e63aa7 + - e5c372c91e46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - 86f150c8019d - - 5732f959936a - c5b7390290b1 + - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -90,46 +90,46 @@ tools: - name: flye owner: bgruening revisions: - - 276f5d8712d5 - - 291923e6f276 - - 8d4f03b5fe9d - - cd11366d92cf - cb8dfd28c16f - - 3ee0ef312022 + - cd11366d92cf + - 3e4f8642c77e + - 1f0769f0b56b + - 8d4f03b5fe9d + - 291923e6f276 - e27815e82dd4 + - 276f5d8712d5 + - 3ee0ef312022 - 1ce9b1d72ec3 - - 1f0769f0b56b - - 3e4f8642c77e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - - 460fad600dce - 01210c4e9144 + - 3169a38c2656 - b2f674562a18 + - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb + - 8b330a577046 - 7348b69e5109 + - 06bcf65179fb - ba88bc5a6446 - - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 764f2516d837 - - 3fba9c77550a - - 3ef480892a9f - f4a3eff8ab85 - - 690c2caa367e + - 3ef480892a9f - 6ec1b853c8fd + - 3fba9c77550a - 5127a713de83 + - 690c2caa367e + - 764f2516d837 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: - - 41cea2aa2dce - - 5161f204ba63 - - 5f625c63b8bc - 60024a528cbd - - ec9e21e9c71b - - 71740308d412 - 6505bd37670d + - 71740308d412 + - 5f625c63b8bc + - 0ee0c3089254 + - 284a1cb82b61 + - ec9e21e9c71b - da9d8bf98802 - - f3c89da3af16 - - 366a11d316a7 - - 045c7c3d8e59 - - 3f7be05a1597 - - df25d4fb79b7 - - 9ef6920c3089 - 2061fb3b81b4 - - 284a1cb82b61 + - df25d4fb79b7 + - 366a11d316a7 - 5bec28269d95 - - 0ee0c3089254 + - 41cea2aa2dce + - 9ef6920c3089 + - 3f7be05a1597 + - 5161f204ba63 + - f3c89da3af16 + - 045c7c3d8e59 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -176,43 +176,43 @@ tools: - name: megahit owner: iuc revisions: - - 7518ee87b53d - 14ddfc8ffb93 - - de387b2b2803 - a96f3ad4e0d8 + - de387b2b2803 + - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - eb7b00ec347d - f8113c25bc6b - - 39edec572bae - d7edbc9c3a07 + - eb7b00ec347d - 09c589057ee8 - 9d79beb19ac3 + - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - - 29dabd8db6f2 - eadfd71dde37 + - 29dabd8db6f2 + - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 99ecfdafc64f - - eb7a370f6588 - - e731ea24e48d - - 3ca2d2a9068c - - f338e9942b27 - 606b09cc9860 + - f338e9942b27 + - 3ca2d2a9068c + - 99ecfdafc64f - fd128c111ab0 - f369ef5f210b + - e731ea24e48d - 2ecf5a570907 + - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -226,9 +226,9 @@ tools: revisions: - 73a3846701e1 - 8b6d0d85252b - - b799a615995d - a7b889b90140 - 8dee0218ac7d + - b799a615995d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -246,9 +246,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - - 7c2f5268d01c - 15200570e926 + - 7c2f5268d01c + - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -261,45 +261,45 @@ tools: owner: iuc revisions: - bbe19ef04a74 + - 02831bf9e95f - d256a51a656b - - dfb8a4497339 + - 2b16ba799da9 - 8fef980d48b5 + - dfb8a4497339 - c6cec5ab35c1 - - 02831bf9e95f - - 2b16ba799da9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - 76d4cbefff85 - - e9bd16ba5ebd - a315c25dc813 + - e9bd16ba5ebd + - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: + - 6fcbee531de6 + - 7594365c546b + - 72472698a2df - 875d0f36d66f - - 342a1d1fed7b - - 675488238c96 - 3061c8b029e5 - - ebb0dcdb621a - - 7594365c546b + - 675488238c96 - 59db8ea8c845 - - 72472698a2df - - 6fcbee531de6 + - ebb0dcdb621a + - 342a1d1fed7b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 78c533842eeb - - d865b62f501c - - 39bed8de8017 - - a199cd7ac344 - cd06929b224b - aa39b19ca11e + - d865b62f501c + - 78c533842eeb + - a199cd7ac344 + - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -317,12 +317,12 @@ tools: - name: raven owner: iuc revisions: - - 33b7d8481a76 - - f11b994b7eb2 - - 5c55448d0f33 - - f8564b2d7f63 - 2b2a352488fa - 3edba9afc9bc + - 5c55448d0f33 + - f8564b2d7f63 + - f11b994b7eb2 + - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -335,11 +335,11 @@ tools: - name: rnaspades owner: iuc revisions: - - 53c2bc8c2ae3 - - 1d06c8b38e77 - - e122f9101584 - 5fc94b3a4704 - 28189050e437 + - 1d06c8b38e77 + - e122f9101584 + - 53c2bc8c2ae3 - ef69617ecb42 - 378e55aeeb25 tool_panel_section_label: Assembly @@ -354,30 +354,30 @@ tools: owner: iuc revisions: - 196a599ec43d - - ad80238462c1 - - ee17a294d3a3 - - f698c7604b3b - d9f6a00b6db7 - - 865119fcb694 + - ad80238462c1 - 83ead2be47b2 + - 865119fcb694 + - f698c7604b3b + - ee17a294d3a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - - 015283de3004 - 24e471d13fe9 + - 015283de3004 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 1bb12736175c - 604782a8a53a - c33a476f4001 - - 904bf932cf78 - 051fd2db8a27 + - 904bf932cf78 + - 1bb12736175c - 1fc82fe7ebef - 7490b213baa9 tool_panel_section_label: Assembly @@ -385,37 +385,37 @@ tools: - name: spades_coronaspades owner: iuc revisions: - - fee85957cebe - - d6e617c4e338 - - ad8b536d1caa - - 9678993ca5bd + - 655fa188c3cc - 34305b013402 + - d6e617c4e338 - 808b3a0a6716 - - 655fa188c3cc + - 9678993ca5bd + - ad8b536d1caa + - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 6b5a5842531e - - 8d4b90bf9caf - b8002c3f7141 + - e5a3b75a271f - 037f9927c4ff - 7e27faaad80e - 21da31ed41a1 - - e5a3b75a271f + - 6b5a5842531e + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 2a10645aeadd - - 86f66ab58e14 - - 9de69775f512 - - 328aa71f0f3c - f1532cb33c75 - 7922870efcca + - 2a10645aeadd + - 328aa71f0f3c - 5b26685e5d3b + - 9de69775f512 + - 86f66ab58e14 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades @@ -425,118 +425,118 @@ tools: - 8cc856b935ee - 340bc17f49cf - e41dcb0e913b - - 1708851f8804 - 6aad515a5270 + - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - b3490b036c5a - - de1260f8a300 - - d5fb354f745d - - 6357b127161e - d159735a6a9f - - 249f6a28c751 - b65a43f70b99 + - d5fb354f745d + - de1260f8a300 + - 249f6a28c751 + - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: + - 7897763d14ec - 33368fec3b70 + - dd7ad84f3943 + - 9006e5836729 + - a90db5dbaaf3 - b7829778729f - d5887ace0dd4 - d2d1df21dfb9 - - 7897763d14ec - - dd7ad84f3943 - - a90db5dbaaf3 - - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 189e837009c9 - - ced385aa976d - - 8f631679571f - 0368ac680e70 + - ced385aa976d - 6f4c8ad6ea01 - 505a9833ab5d + - 8f631679571f + - 189e837009c9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - - a7ed21de23fe - 9ded6109434a + - e59bee4565b3 - 19bdfd1e6fe3 + - d40ed4eb0c0e - 356afed970b4 - - e59bee4565b3 + - a7ed21de23fe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - b23249f81bc4 - - 6dd935e4984b - - 7673a6c920b2 - ebd801e712bc - 80a17897564d + - 7673a6c920b2 + - b23249f81bc4 - 4688ae3b49b5 + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b64696992ee9 - b5e35a2ca4f3 - - 59bd28f6265d - 937ea677d437 - cb1e3db43020 + - 59bd28f6265d + - b64696992ee9 - ed312479d9eb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - b9b0246a2be3 - 05bd7504fdb2 - cb4768eeca3b - 2628f6790eda - 6015aa0303f2 - 383bb5ad32e2 + - b9b0246a2be3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - e92675014ac9 - 3e44ef016b45 + - e92675014ac9 - 0a3a602cd1e3 - - e022dff952df - - 9e3e80cc4ad4 - 8f9f06995f98 + - 9e3e80cc4ad4 - 6e26c9afd301 + - e022dff952df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 5da9a0e2fb2d - 920677cd220f - 08256557922f - 8d09f8be269e - - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: + - 82398ba86ba7 - 0e2b4e3f9ca1 - d81360ea69d8 - 4a53b89fa703 - - 82398ba86ba7 - 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 a240aa0c7..7ca51e8ab 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: + - 1ae00120dd24 - 4768f7f8e93f - - 392f100eebcd - bfd290fe1588 - - 1ae00120dd24 + - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: - - 1f5641a52664 - - ded48b36f3b7 - 8e8dc9a1e3e5 + - 1f5641a52664 - 31812e7a1315 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 17fcac7ddf54 - 24a7a95867b0 + - 17fcac7ddf54 - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 00f458464..da65b51cd 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: - - d1f62024a08b + - d58c27d2c5a7 + - 204a131e47db - a9c9d768b751 - - 1c427e24fb79 + - 0840ba83860c - 159b04e36791 - 7beb76ffbc0f - - 0840ba83860c - - 204a131e47db - - d58c27d2c5a7 + - 1c427e24fb79 + - d1f62024a08b tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge @@ -22,7 +22,7 @@ tools: - name: bbtools_tadpole owner: iuc revisions: - - 0ddf147d1897 - ce13b4678f18 + - 0ddf147d1897 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 1350ff578..9f02f0775 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: - - 07e8b80f278c - - 0a5c785ac6db - - dde39ba9c031 - - a8eabd2838f6 - ce3c7f062223 - - b28e0cfa7ba1 - - a68aa6c1204a + - 07e8b80f278c - 589e7e57fd6d - a1a923cd89e8 - - 64e2edfe7a2c + - a68aa6c1204a + - b28e0cfa7ba1 + - dde39ba9c031 - e19bebe96cd2 + - 64e2edfe7a2c + - 0a5c785ac6db + - a8eabd2838f6 - 87ee588b3d45 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 b35e18d30..ba5b8104f 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -9,9 +9,9 @@ tools: owner: bgruening revisions: - f921014aba5a - - e8ac2b53f262 - 62c9df8382c2 - 54f751e413f4 + - e8ac2b53f262 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: - - 0e3cf9594bb7 - 6f386c5dc4fb - 5edc472ec434 - - acf4e47b734c + - d999e774072a + - 0e3cf9594bb7 - 2889433c7ae1 - - cbf3f518b668 - e25d3acf6e68 - - d999e774072a + - acf4e47b734c - a52d2d93e595 + - cbf3f518b668 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 895b6bed3..29806bdf9 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 - 6ca543ec1bf8 - - f4230f116196 - - 095ad4d096d1 - - 27ee142314a9 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: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -132,72 +132,72 @@ tools: revisions: - 3b8a9d5ced85 - 79cfd9ead848 + - bfb65cb551d8 - 0fac8e2afc13 - 88076940fa94 - - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - 715cd0e87781 - - eb6564a60136 - - f5d979cb4b54 - - 55918daa5651 - d532b7e5f64b + - 55918daa5651 - b46d4b4d995c + - f5d979cb4b54 + - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - f26afd1b7104 - - 5579659312e6 - 97872d87ba80 - d2f955aea23a - fdf2cc80adb5 + - 5579659312e6 + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - - d1d0efda35c0 - 319a28774da9 + - d1d0efda35c0 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - cac1886249a2 - 4da9ee404eab - - 2c349b027a01 - ed736e6eee39 - 070e3ecc3fda + - cac1886249a2 + - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 525ca7c8065f - - da8753545526 - 73008ef1f487 - - f197e34c33a9 - - 2e219a2d9327 - d1f803b5943c - - c0c9a5024177 - 807aa4c9293d + - 525ca7c8065f + - 2e219a2d9327 + - f197e34c33a9 + - da8753545526 + - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - c4fbab8e03c5 + - 61094e01eff9 - 1809414a9454 + - 2c8ed1b52bf7 + - c4fbab8e03c5 - 7568ae18908a - - 61094e01eff9 - 27ea4e1a3f95 - - 2c8ed1b52bf7 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: - - ba83f0923369 - - ccfbd956a2d3 - - d7ec25187599 - 79e8ab8f1e81 - 730ef07b90ae + - d7ec25187599 + - ccfbd956a2d3 + - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 9a3a1f698fc6 - 48d6a6eb438b + - 9a3a1f698fc6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: 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 @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 7672039a0bb0 - 75ee9c410951 + - 7672039a0bb0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -296,8 +296,8 @@ tools: - name: qcxms_neutral_run owner: recetox revisions: - - 8f465c0c3b6c - 33b7a99b6de3 + - 8f465c0c3b6c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_production_run @@ -339,10 +339,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 85fad59f8168 - bf99565cec1f - d4c67ced6abc - 9b48456a96fe - - 85fad59f8168 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 274d4eb60..606e3ec3a 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -3,9 +3,9 @@ tools: owner: bgruening revisions: - c97a786e8fb5 + - fa56d93f7980 - 163688bb8f73 - f907216064f6 - - fa56d93f7980 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -23,17 +23,17 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 86e2413cf3f8 - 640d3af5d833 - - 495a4173006f - f5d67c722d67 + - 495a4173006f + - 86e2413cf3f8 - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -54,8 +54,8 @@ tools: owner: devteam revisions: - 74c9214cc8e6 - - 4a14714649b4 - 5c2cc3b58c7d + - 4a14714649b4 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 2946e26bc..574184099 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -9,17 +9,17 @@ tools: - name: collapse_collections owner: nml revisions: - - 33151a38533a - 90981f86000f - - 830961c48e42 - 25136a2b0cfe + - 33151a38533a + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - - 6cbe2f30c2d7 - baabc30154cd - 2dae863c8f42 + - 0046692724f9 + - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 9c30719f1..d71e05733 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - d6ede73082da - - e7449b2c14bf - abba05ead5d7 + - e7449b2c14bf 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: - - 6ef0b5664c69 - - 3b6f97e7094c - 4a6ee918c13a - - 367b1ed91207 - f3a19509108a - - a3b86937ead6 - 0b3c3ad92827 - - e3cbd2287f63 + - 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: - - 584008e574b2 - - 1b5fc03380d4 - 091bb5922a82 + - 584008e574b2 - e525f9ffb9ac - - bd46669113b9 + - 501c21cce614 - e177a8ea0bf1 - - 54ccb7e1f49a + - 1b5fc03380d4 - d4d4e9febf5c - 33c99804a32f + - 54ccb7e1f49a + - bd46669113b9 - 72ed72122deb - - 501c21cce614 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -60,8 +60,8 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta @@ -75,9 +75,9 @@ tools: - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 43807a65369f - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -151,11 +151,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: + - 26c6706bfb07 - b9b385097f13 + - 19e45916daf9 - 63769c4217a7 - - 26c6706bfb07 - 92ac8e086317 - - 19e45916daf9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -168,17 +168,17 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - 3c6f9e8a4c17 - e9bbe2f71784 + - 3c6f9e8a4c17 - 8067dfa00ed2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: + - fa49730d1d4b - 98704d357ede - a2f83a375bf2 - - fa49730d1d4b tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 5a25e95fc..1cd59d72d 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,205 +2,205 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 29451af70c52 - - e821645ef8fc - - 5f6d123679f4 - - a1ca9bccc7f2 - 268e91e540ee - - c929a006727f + - a1ca9bccc7f2 - de72ba3ed6f2 + - c929a006727f + - 5f6d123679f4 + - 29451af70c52 + - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - 12af64f93288 - - bb1e4f63e0e6 - - 0e143b4c3987 - 2d2cf5c1ea8a - 7a7fd0f5f15d - - 0e49b109abc2 + - 0e143b4c3987 - 5d11599b8a7d + - bb1e4f63e0e6 + - 0e49b109abc2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - 81b1e3e1fc6c - - 195e98217334 - - 7c1beb6d6eca - c06951d10364 - - 1d848bc4585f - dc059492a995 + - 1d848bc4585f + - 195e98217334 + - 7c1beb6d6eca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 3d211717a775 - - 07418a30ed01 - - 93eb012d9eed + - 71aa86af6762 - bfff7454b59a - a67ac707496a - - 71aa86af6762 + - 3d211717a775 + - 07418a30ed01 - 26e7304d6737 + - 93eb012d9eed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 26983857c91a - - dd0b7398bb96 - - b8858746dc1f - - 5be24eba848d - 56d5b797ce84 + - b8858746dc1f + - dd0b7398bb96 - 2bc10a9ca58b - 29fcfd36e90a + - 26983857c91a + - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7e6bcd2e5128 + - e6d0bff01239 - 72bfafe3330b - - ee3a1b0f45f1 - - c3e012dfe21f - 7ef978dc1b8a + - c3e012dfe21f + - 7e6bcd2e5128 - 9384cd033f30 - - e6d0bff01239 + - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fb9cf9c97ec4 - - 9470f29702f8 + - 514fa53b5efb + - b73e213add0c - 167788df3b46 + - 9470f29702f8 - fd1275e01605 - - d9a637e83828 - - b73e213add0c - a60c359ec43c - - 514fa53b5efb + - d9a637e83828 + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - ca0616bb2cdf - a02cfa31e9cb - - 5bffaa8354a1 - - 86febdcc4283 + - e479c7ca5570 - c34d11ea4ba6 + - ca0616bb2cdf + - 86febdcc4283 - 2c37ce318bc3 - - e479c7ca5570 + - 5bffaa8354a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 78f405266706 + - 69a8621ca2f0 - 01fb6a7654e6 - - 1fcb7adc39b8 - 004aea905d4d - - 192ef85c0b0b - - 69a8621ca2f0 - - 78f405266706 - 2d466b530754 + - 1fcb7adc39b8 + - 192ef85c0b0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 137c4beed34b - d9ce4897dbb2 - - 9ecba5e225a6 - - db940c262830 + - 459cfa861f0b - 2f9e4843f480 + - 137c4beed34b - 3c9f0c486cca - - 459cfa861f0b + - db940c262830 + - 9ecba5e225a6 - d580d6acd1df tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 32e451def88c - - bd7db9e2f2cb + - fbe773640707 - fd408d755394 - - f264afa9fa6f + - bd7db9e2f2cb + - 32e451def88c - bad3ca889618 - - fbe773640707 + - f264afa9fa6f - 2c66e43f1c86 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 7e361d147872 - - 4e12ea27f788 - 56bce3c82278 - - 231994413f89 - - 3b9d990a0a0e - 7fda5607e777 - 9368fbc49c8b + - 4e12ea27f788 + - 3b9d990a0a0e + - 231994413f89 + - 7e361d147872 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - c03c3384cd81 + - b1779366c8e9 - 94ca68515826 - e65d16fb2724 - - b1779366c8e9 - - d9114ef1c8a5 - 4431f39ede55 + - c03c3384cd81 + - d9114ef1c8a5 - ce4ce3316f74 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 23f7c5f1fdaf + - d57251071381 + - f8fc4e5aff9d - 2da482e408b8 - b88ebb3672a1 - - 23f7c5f1fdaf - 4ed32329e0ed - - f8fc4e5aff9d - - d57251071381 - 793665fff0f8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 25d830337d31 + - a4dfb122e52b - c60570fa602f - - e4c7985d4585 - - a7849312d328 + - 010e58e9d822 + - 25d830337d31 - 512155688d98 - - a4dfb122e52b - ba6efa77fb79 - - 010e58e9d822 + - e4c7985d4585 + - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - c899e0ccff8c - - 38e3f226248b - - 443d9a9d6d11 - - aa200e4f3939 + - 00d869ea03a1 - 69264da0ce77 + - 443d9a9d6d11 - 4d678170d29b - - 00d869ea03a1 + - 38e3f226248b + - aa200e4f3939 + - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - - 6662b1a8d326 - - c361b12d207a + - 10301d137111 - a2d70c4fd406 + - 6662b1a8d326 + - aac8444d6681 - d806504e96d9 - - 10301d137111 + - 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 baf7c2420..741f56294 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -30,8 +30,8 @@ tools: - name: obi_illumina_pairend owner: iuc revisions: - - 94f412098ac8 - 8cb6bd511879 + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter @@ -51,8 +51,8 @@ tools: - 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 diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index 90586462b..682da2752 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: - - 62f5fab76dfb - - 29bdbc353f20 - - 6da3972210ee - d82648ad25a3 + - 6da3972210ee + - 29bdbc353f20 - cf1322aeb137 + - 62f5fab76dfb 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/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 1edf61a30..5e574dc09 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: - - fe74900d6dc7 - - 48f587c13075 - - c4b82dce8335 - - 135b80fb1ac2 - - 4e5056fefd88 - - c053d4cad713 - - e4691e1589d3 - b1c926deaa2d - - 44e2cc14f75b - - 5915ea1ec9b1 - 8665bcc8b847 - - 660cffd8d92a - - 64172f1c1202 - - 5eb7e84243f2 - - 288f97432497 + - 4e5056fefd88 - 8c0175e03cee - - 093678460093 + - c4b82dce8335 + - e4691e1589d3 + - 288f97432497 + - 48f587c13075 - 49370cb85f0f + - 64172f1c1202 + - 660cffd8d92a + - 5915ea1ec9b1 - c5e2e5902201 + - 44e2cc14f75b + - 093678460093 + - fe74900d6dc7 + - c053d4cad713 + - 135b80fb1ac2 - de6cebe3c043 + - 5eb7e84243f2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -45,9 +45,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: - - 9db07fd39f85 - - 8889eb864cef - f666895cbebd + - 8889eb864cef + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -59,9 +59,9 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - de2db1bdfbf8 - 5cbde03c1103 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -86,15 +86,15 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - 8cacfcf96a52 - e626b3ff9922 + - 8cacfcf96a52 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - 9457a20156db + - 859422bcb689 - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -107,16 +107,16 @@ tools: - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - f81d4362b6c1 - ec0b5076173a - f773e98b26cf + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -129,8 +129,8 @@ tools: owner: iuc revisions: - 0dbb995c7d35 - - 56022eb50bbd - cd0874854f51 + - 56022eb50bbd - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -143,14 +143,14 @@ tools: - name: fastp owner: iuc revisions: - - c59d48774d03 - - dbfc505896e9 - 65b93b623c77 - d60c3f704da0 - - dbf9c561ef29 - - ecb9f4854617 + - dbfc505896e9 - a626e8c0e1ba + - ecb9f4854617 - 1d8fe9bc4cb0 + - c59d48774d03 + - dbf9c561ef29 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 @@ -176,9 +176,9 @@ tools: - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - '144275714590' - 10b75444feae + - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -190,9 +190,9 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 47e5dbc3e790 - e9f8633db0a2 - 8611b80a14d6 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -218,9 +218,9 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: + - 4e1d64e6385f - 9dfda4e310ed - 9282652e7234 - - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -232,8 +232,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 523c2aff0376 + - f3936d0632cb - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -247,8 +247,8 @@ tools: owner: devteam revisions: - b41c2c1bcfbf - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -260,9 +260,9 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: + - c885369b207b - 09a2199cd356 - 8d958759cf2a - - c885369b207b 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: - - 397dc333436b - 35e38452bb3f - - 249c8393f2d4 + - 397dc333436b - e39cc71d3ed6 + - 249c8393f2d4 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: - - f86c27295151 - - f0e7deab6518 - b1cea1b2fcd0 + - f0e7deab6518 + - f86c27295151 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -317,8 +317,8 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - 33794bdb7fe0 - b63b2bfb3ea3 + - 33794bdb7fe0 - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -339,9 +339,9 @@ tools: owner: devteam revisions: - 09070cacefd8 - - 567d5b3c52b1 - d5e9e83cd3d8 - 529bccd5e4a1 + - 567d5b3c52b1 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: - - 4bedca26c133 - 8abdedf55101 - 0b7ec11b3c7c + - 4bedca26c133 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: - - 90858c306551 - 736b8f6ee456 - - cb1e251cac37 + - 90858c306551 - bdf1ce174e39 + - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -382,8 +382,8 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 421f0af4ee95 - 7ce1891db6f5 + - 421f0af4ee95 - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -396,10 +396,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 02f8a17a4ebd - f984bb114520 - 3599f5451ee2 - b29d37ca9e41 + - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -411,10 +411,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 177f0621c266 - 0c2907307ba4 - - 6027ef51ef91 - e246088b6e34 + - 177f0621c266 + - 6027ef51ef91 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: - - 547e8d00f11c - - 377ac2829eac - 73194cdd4f57 - 61b4cedc8934 + - 547e8d00f11c + - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -453,10 +453,10 @@ tools: - name: pear owner: iuc revisions: - - f69501361cec + - b4c6f054210a - 2f804526f5fd + - f69501361cec - 037f0acc7830 - - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -468,39 +468,39 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: + - fdc21382376d - 29ef2c5ec205 - 61eb4cfc7313 - - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - 795cd16de38f - - fe1ae2ebf63d - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - a019807f4e67 - 4b494533146a + - a019807f4e67 - 3da72230c066 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - a019807f4e67 - 4b494533146a + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: split_paired_reads @@ -512,8 +512,8 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -533,12 +533,12 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f - - b557acca0b56 + - e654095ab143 + - 71ad4a56c40c - 8250ea3a1501 + - b557acca0b56 - a535cf1e5da4 - - 71ad4a56c40c - - e654095ab143 + - 24013bf85a6f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -550,8 +550,8 @@ tools: - name: umi_tools_dedup owner: iuc revisions: - - c5a2ee07c4e1 - f1d33e4c7bd8 + - c5a2ee07c4e1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -559,12 +559,12 @@ tools: revisions: - 6a675c3aa610 - 7accf7407811 - - 828dba98cdb4 - - 27ac32a22ad2 - 9fa7803d1c51 + - 7a7e33d28f62 - 015cf18f4a15 + - 27ac32a22ad2 + - 828dba98cdb4 - f3759eec3018 - - 7a7e33d28f62 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -576,15 +576,15 @@ tools: - name: umi_tools_group owner: iuc revisions: - - 428735be9764 - d6255614afd7 + - 428735be9764 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist owner: iuc revisions: - 953b4821b183 - - e4e12f0b3af1 - 4c8a1c7d3608 + - e4e12f0b3af1 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 2b255f3a2..9a42333a8 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 - - 7b4468117008 - e41385662e5e + - 7b4468117008 - ce9cd02d5b88 + - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,67 +18,67 @@ tools: - name: fastqc owner: devteam revisions: + - ff9530579d1f + - 2c64fded1286 + - 2b0c9d9fc6ca + - e7b2202befea + - 3d0c7bdf12f5 - f2e8552cf1d0 - 5ec9f6bceaee - - 3d0c7bdf12f5 - 9da02be9c6cc - - e7b2202befea - - ff9530579d1f - - 2b0c9d9fc6ca - - 2c64fded1286 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - ad116ae3f4d9 - b6b54ba71bd8 - 18a51655db17 + - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - 7306ec78632a - - 59003d0543cd - cc0fd298cc17 + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 1f296803dfa3 - a72af9de6bf5 + - 1f296803dfa3 - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 5e33b465d8d5 - - 75c93c70d094 + - f7e2f1eb3a16 - abfd8a6544d7 - - 1c2db0054039 - - f7985e0479b9 - b2f1f75d49c4 - - f7e2f1eb3a16 - - 3d93dd18d9f8 + - 5e33b465d8d5 + - f7985e0479b9 + - 75c93c70d094 - bf675f34b056 + - 3d93dd18d9f8 + - 1c2db0054039 - 9a913cdee30e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 949f01671246 - cd7e644cae1d - 084bbd8ba7b8 + - 949f01671246 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 0dfc5355c..c01999d90 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: - - 19f42b3ea391 - 9e776e7fab4f + - 19f42b3ea391 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 54bbfa7ed..b248d7a64 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 66d369ae7..015c87e6d 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: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -16,58 +16,58 @@ tools: - name: gemini_annotate owner: iuc revisions: - - 8f53b238a360 - - f2f3bc622a16 - 0c8f7322f8fc + - f2f3bc622a16 + - 8f53b238a360 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: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,16 +79,16 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - cf61daf064fe - b2c25142267e - 45296e47d565 + - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -101,15 +101,15 @@ tools: - name: gemini_mendel_errors owner: iuc revisions: - - 61343646155c - 00c2734b3bea + - 61343646155c tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: + - da74170c55c7 - 840fb4850be3 - 666f60a9331a - - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -158,14 +158,14 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 8627a5283..34c4db133 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -9,8 +9,8 @@ tools: - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 45884d847..7c55208a2 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - 983bf725dfc2 - c1b437242fee - e9df53a75f3c - b39347891609 - - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -18,52 +18,52 @@ tools: owner: iuc revisions: - 28587613264f - - e063168e0a81 - 1c58de56d587 + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 1ec814014652 - - 6ea73833cf67 + - 8848455c0270 - 4df8de2d0e48 - - 5e6237d58b0c - - e08a7ad4378b - f8054ea1c365 - - 8848455c0270 - - 1790dcf3c32d + - 9a776b080193 - 69ebb7f46e45 - - e407b9da183a - - 6591f049cf7e - - 4317d3cb6cba - - 734abc7ac21d - - 83c7d564b128 + - e08a7ad4378b + - f5ea3ce9b9b0 - c441583adae5 + - aad3885b3216 + - 6591f049cf7e - 516a54ddf218 - - 7068f48d0ef9 + - e407b9da183a + - 6ea73833cf67 + - 5e6237d58b0c - ba931a59dd59 - - 9a776b080193 - 653e89d73fc4 - - f5ea3ce9b9b0 - - aad3885b3216 + - 83c7d564b128 + - 734abc7ac21d + - 1790dcf3c32d + - 4317d3cb6cba + - 7068f48d0ef9 + - 1ec814014652 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 34758ab8aaa4 - 21a560af5913 - - 9aaa46d45472 - 75b3b3d0adbf + - 9aaa46d45472 + - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - af5eccf83605 + - 054483e27a35 - bfdc6a7ffd3a - 468c71dac78a - - 054483e27a35 + - af5eccf83605 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 3e81f0125..fbe435194 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 + - 7f13dc906cb9 - fd59d783248a - c4bde687c846 - a64dc31ab7f2 - - 740057a5126d - - 7f13dc906cb9 - - df7356989ac1 - - 4b519282a05b - - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -35,8 +35,8 @@ tools: owner: devteam revisions: - 7cf5b1d072b5 - - f95284aa2946 - 867ab348287d + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,24 +48,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 3b37b1b1c3a7 + - 374e9062d874 - ca7cb0eaad62 - - 51c6ccaace7e - 48b42ee61bc5 - - 53460afd5115 - - 374e9062d874 + - 51c6ccaace7e - '566197475670' + - 53460afd5115 + - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - da4c086cff5b - - d3a9e32672ec - - 10515715c940 - 3d059e9c2fba - 1a72f938213e - 391a4cc45fea + - d3a9e32672ec + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -85,12 +85,12 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 5298e06f14f9 - - d0fc8b746d57 + - 5fe1dc76176e - e3a675da7fd0 - 299307abd804 - 1acf88921176 - - 5fe1dc76176e + - d0fc8b746d57 + - 5298e06f14f9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -109,15 +109,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 97e3b735ed22 - 5d6f8f0bef7c + - 97e3b735ed22 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 8f62f666dcb6 - 6e8eb0c0d91f + - 8f62f666dcb6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -136,17 +136,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 667e17248bfe - - 4542035c1075 - - a6e57ff585c0 - - 1cfc579079a6 + - fd5dbf0f732e - ca2def38369c + - a6e57ff585c0 - 17359b808b01 - - fd5dbf0f732e - - 6cd09d7b5f37 + - 667e17248bfe - 836d1aa3e89a - - 2bb2e07a7a21 - 112eb40ba6cf + - 1cfc579079a6 + - 2bb2e07a7a21 + - 4542035c1075 + - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -164,31 +164,31 @@ 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 owner: iuc revisions: - - bd1416eea1f0 - 594b85e4237a + - bd1416eea1f0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plot_ragtag_paf owner: galaxy-australia revisions: - 501dcf66c0ce - - 94e0834ae4ed - 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: - - f234e2e59d76 - 1c5dcef5ce0f + - f234e2e59d76 - 62e3a4e8c54c - 85da91bbdbfb tool_panel_section_label: Graph/Display Data @@ -209,10 +209,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 - 6c571966cfb9 - - 44c66e8d21e6 + - 7c9417381ad5 - 26f2fe7e53a1 + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -224,24 +224,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 14e7c35f3d00 - - 2824d77cd8f8 - - 360df4999907 - 36b848d5f3ec + - 360df4999907 + - 2824d77cd8f8 - a1abfa420d9d - 326a3db8d9d1 - - 4ac4e7083b7e + - 14e7c35f3d00 - 7dd841a32245 + - 4ac4e7083b7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 99ace6c1ff57 + - 44608d0193ed - 83c573f2e73c - - a363ba287b88 + - 99ace6c1ff57 - 73b8cb5bddcd - - 44608d0193ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 @@ -253,7 +252,7 @@ tools: - name: xy_plot owner: devteam revisions: - - 319fa5a9fc1b - ecb437f1d298 + - 319fa5a9fc1b 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 a5c54215f..1975ad826 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -28,9 +28,9 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 7779b9dcf040 - 22bd5861706d - bc9e8de21efb + - 7779b9dcf040 - 6417cccad133 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -38,52 +38,52 @@ tools: owner: ebi-gxa revisions: - e9283529cba1 - - 55ccc0a121bc - - bf1e0bdec1db - 361608369dda + - bf1e0bdec1db + - 55ccc0a121bc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - 474a69c47184 - - da611a744112 - - 23d838d1569d - 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: - - ad6995afd2e6 - fc4b3b46dc9d - - 2ccd9f9e2cd0 - 36735850e461 + - ad6995afd2e6 + - 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 - d8f5224005bb - - 49653e680ea4 - - 81c34e67f262 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 4667fe07bd68 - - 79da59a0b180 - 64dd8bb151e1 + - 4667fe07bd68 - 2861ca3bfe4d + - 79da59a0b180 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - 9d76c3d6dff6 - c9da9192eee5 + - 9d76c3d6dff6 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat @@ -96,8 +96,8 @@ tools: - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - c354af93f567 - 6903bc865d63 + - c354af93f567 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn @@ -111,17 +111,17 @@ tools: - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 70cb0596ffef - 53ce0e336840 + - 70cb0596ffef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 8d9c22419c56 - - 28b1546857b0 - 3027cb62adbd - 6b97ffba31da + - 28b1546857b0 + - 8d9c22419c56 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: - - 35f6611fb8c3 - 7d5c97823f8b - 56d22aa6cb3b - 1be0fc4d8654 + - 35f6611fb8c3 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet @@ -150,8 +150,8 @@ tools: - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x @@ -165,22 +165,22 @@ tools: owner: ebi-gxa revisions: - 36daab33aecf - - 0bab2ae44e7a - d18ed15697bb + - 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 owner: ebi-gxa revisions: - - 03921aa8b29c - 12f67b0c1a94 + - 03921aa8b29c tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_fdg @@ -193,44 +193,44 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - b2768cae00a1 - 6d4f88995e40 + - b2768cae00a1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: - - 3ee74b58c72d - - 4428dba93375 - - 59028945c857 - 0cf90e01d9f8 + - 59028945c857 + - 4428dba93375 + - 3ee74b58c72d 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 - 3fb53f5e46ea - - 8b0d6f6f44c8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - bd4a244faeb8 - - 0f98603d0116 - fe562424a0a6 - 767a675b5254 - ea91cfd0444e + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - - f86b2c3bc459 - 5605f8452eb3 + - e2d0dc8a50ca - 4cc9362782b4 + - f86b2c3bc459 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 c5750d511..d718c0578 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,61 +2,61 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 0f611e7d7858 - - ed2cca6b5de4 + - a4c13ddcc8ee - 9edf8894a22d - - 29f66c353bcb + - ed2cca6b5de4 + - 0f611e7d7858 - d9967770de96 - 921a2da49a0c - - a4c13ddcc8ee + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - d404277cc87a - - 5746d61f0a91 - - 78fb5e286609 - 755df866ad0c - ec4b948dc6f0 + - 78fb5e286609 + - 5746d61f0a91 - 11de0d28ab30 + - d404277cc87a - 478aacfbaa37 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 4d511437b1e5 - 9e357a8b2ec3 - 977dc15add20 - - 4d511437b1e5 - - 03dd3c16ae4e - 9d93c8fbe0a6 - 11fa44ee0603 + - 03dd3c16ae4e - f72063d9426b tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: + - 0ba4f56a3613 + - c3e5e2cf12b7 - 1da5f169b491 - f86ca478c6af - - 41dbf4d162a2 - - 3b5b54ed6392 - 77919cc3618e - - 0ba4f56a3613 - - c3e5e2cf12b7 + - 3b5b54ed6392 + - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - b63363075c2e + - f741330d4a71 + - 025a128652dc - 9939786dd9c9 - - 12d51d7be66f - 7babd8a46fe0 - 5308ca68ef3d - - 025a128652dc - - f741330d4a71 + - 12d51d7be66f tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index b3db742cd..dd9315c67 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,55 +2,55 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 7db4fc31dbee - 0c777d708acc + - 81f0cbca04a7 + - 8bccb36e055a - 3df9f0a4bf34 - - 7db4fc31dbee - 699a5e9146b3 - - 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 - 2436a8807ad1 - - 5791a7f65275 + - 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 - - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - b1c2c210813c - 70316d792fc9 - 77f7159d775a + - b1c2c210813c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: + - f70b215d155c - dba87c4b32d3 - d51310ab328a - - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: + - fcadded98e61 - 10eed33aa9b2 - f3360fbeda64 - - fcadded98e61 - - 85edbb7a436b - b07f4839ca77 + - 85edbb7a436b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -72,39 +72,39 @@ tools: owner: bgruening revisions: - 0e4dccaafef5 - - e917a2424690 - eb6c08714244 + - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - 6070780813d9 - - 670975e92458 - e7273daa5ae2 + - 670975e92458 + - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - 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: - - 5d28ac336861 - - 2484086dee41 - 6a7da2e5f696 + - 2484086dee41 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -118,8 +118,8 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f24c370e5ea4 + - d0178bdcd00e - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -127,64 +127,64 @@ tools: owner: bgruening revisions: - 3245681b2f6d - - ad271f78a87a - 31d195bedf6d + - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: + - b6eec6087271 - 993faa34333b - 87d4d92d7487 - - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - 6100a22bf4f2 - - c09dcda1143f - ff1a86a87364 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - 667a513e67e4 - - 3a05117669cf - b178453ea8d1 + - 3a05117669cf + - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - 2564f461de62 - ac5bea85a391 - a1a961c46d4b + - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: + - a32c3f810ade - 91e03287f285 - 20dbb1f7ec7b - - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - 8536b1ae0254 - - b64af54c5c09 - 5499dc6f8ac1 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - - e972e07c7845 - 6f4715b8540a + - e972e07c7845 + - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -199,16 +199,16 @@ tools: owner: bgruening revisions: - acf3aa487283 - - 79e10d12d90a - d85f11570109 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - 80b200ae516b - b76841ee5560 - 035a58c7f54a - - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -220,17 +220,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - - 8083a87d2fdf - 3a3033222f61 + - 8083a87d2fdf + - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - 33f4fa1413fb - - 4ecf93628f97 - 27edbb90ab2b + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -242,23 +242,23 @@ 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: - - 4b794652dcdc - f92941d1a85e + - 4b794652dcdc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: + - f8b4eada923c - 7b6d9412c7f8 - 236ec78b2e53 - - 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 ab9a0e06e..beb9e628c 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,31 +2,31 @@ tools: - name: ivar_consensus owner: iuc revisions: - - d6e72da3ec35 - - 3a72fede57ce - f362150bef41 - - 78bbd17d0703 - - e4ee04da1c19 - - 3e4f434a69c6 - - 40737febe339 - 1069f6db0a0e - - a38934e303b9 - e319b5b65879 + - 3e4f434a69c6 + - a38934e303b9 + - 40737febe339 + - e4ee04da1c19 + - d6e72da3ec35 + - 3a72fede57ce + - 78bbd17d0703 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 2b95d5c04908 - - 8f8df367470d - - f91cfb73d369 - - 0135f1d487a0 - - 9537184d421f - c88553ec696e - - 7fe36019c073 + - 9537184d421f + - 0135f1d487a0 - 72ddd32392cd - - fcbeda41d0ac - 618297d23022 + - fcbeda41d0ac + - 8f8df367470d + - 7fe36019c073 + - f91cfb73d369 + - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked @@ -41,54 +41,54 @@ tools: - name: ivar_removereads owner: iuc revisions: - - a1c2aecd7a0d - - 6a1515bb0687 + - ee29337f905c + - 43aac8d29685 - ee2beb764a7b - - 7f1cfa4c0e32 + - 9eaadf03e0df - 3d18f8c3c0f6 - - 28a6f1908fcc - - 5dc33613c288 - - bd2a7d1316b9 - 94df24c6bc00 - - 8c05afb547fa - - ee29337f905c - - 43aac8d29685 + - bd2a7d1316b9 + - 28a6f1908fcc + - 6a1515bb0687 - 8d36959b000d - - 9eaadf03e0df + - 7f1cfa4c0e32 + - 8c05afb547fa + - a1c2aecd7a0d + - 5dc33613c288 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - c092052ed673 - - 9f978da6528a - - e3bb03cf207a - - db536ad45f28 - - bcaa0d571ce2 - - 364f4ffec275 - - 5671e1d3d5ee - a250929be21b + - 86a20ae274fc + - 5671e1d3d5ee + - cb903c9dc33d - 8858fa037a15 + - 9f978da6528a + - db536ad45f28 + - c092052ed673 - d37ede8589b2 - - cb903c9dc33d - - 86a20ae274fc - 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 - e1a015876aa9 - - 49236b03e4fd - - 194e3ceee923 + - 584beffa972b + - 38b91a3190cd - c5c9f02b6167 - - f95f403841ad - - abbc8041e8ec - 12d66d0d05ac + - abbc8041e8ec - 3b6a16d82c1b - - 584beffa972b + - 49236b03e4fd - ed28dd32141c - - 38b91a3190cd + - 194e3ceee923 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 de917200b..179237f07 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,9 +2,9 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 0f1724dd59d2 - f198773344e4 - 17e3b698dd52 + - 0f1724dd59d2 - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu @@ -12,9 +12,9 @@ tools: owner: iuc revisions: - 22c2a1ac7ae3 + - a513e3fbb4c5 - ac092723240d - ba0c40780ecf - - a513e3fbb4c5 - 374cb875d38a 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 b56c46e6c..b5665f481 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,27 +2,27 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 522137aaa9c4 - 772e0e89fc68 + - 522137aaa9c4 - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: + - 4d81e3e2fb63 - f22a9297440f - 8a794e6d3388 - - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 2af1346e68c9 - 818f9b69d8a0 - - e1317b5502fa - - b6ef6d0cb6b7 - f1b9a42d6809 + - b6ef6d0cb6b7 + - 2af1346e68c9 + - e1317b5502fa tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex @@ -30,71 +30,71 @@ tools: revisions: - 947c2eacccb8 - 05143043ca13 - - 8334dc98c48e - - c80db5d6fd8c - 1588f9076e32 + - c80db5d6fd8c + - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 29e4122c90de - - 83228baae3c5 - 25b46af53232 + - 29e4122c90de - 9991c4ddde14 + - 83228baae3c5 - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - a07ab242b0b5 + - 53616c8b0865 - 1a53edc4b438 + - 841a6cc5fc58 - f3dfa4bdf87e - - 53616c8b0865 + - a07ab242b0b5 - 060ca94ac049 - - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 - - d4808d5b83da - 927586a18553 - 40f4447733b2 - - dc4b5fd604a6 - 91c4e3331208 + - dc4b5fd604a6 + - 2fc89dcd41c8 + - d4808d5b83da tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - e5a5ad882f1f - - 36e8d6d5d01b + - 25ab6b4e376e - 301e07345c93 - c6ae57f774c6 - - 25ab6b4e376e - 7626ea9c2e1b + - 36e8d6d5d01b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - 4ed102b922cb + - f9639b488779 - 0630258dcf35 - - 02d2be90dedb - - b7c3e9a3b954 - 80852884053f - - f9639b488779 + - b7c3e9a3b954 + - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: + - 61634a87efc7 - 14180f9c831e - - caeb57858702 - ec69cbe34b73 - - 61634a87efc7 + - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 641bb7103..06d276db7 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,16 +2,16 @@ tools: - name: bowtie2 owner: devteam revisions: - - d5ceb9f3c25b - a6d65b0c67af - - 03e9b2fbc005 - - 17062a0decb7 - - 3ba8d4563129 - - 937aa69e715f - - 017aba02828d - 0d4acadabb04 + - 3ba8d4563129 - cd659e8cc5fa - 749c918495f7 + - d5ceb9f3c25b + - 17062a0decb7 + - 017aba02828d + - 03e9b2fbc005 + - 937aa69e715f - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 64f11cf59c6e + - 3fe632431b68 - 2477830927ec + - 64f11cf59c6e - 53646aaaafef - e188dc7a68e6 - dfd8b7f78c37 - - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - 2ff111fac1d7 - - e7f19d6a9af8 - - 60afcc2c1d05 - 37b497aa133f + - 60afcc2c1d05 + - e7f19d6a9af8 - 3e1ea2facca6 + - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 6b1e195506a3 - 11a0d50a54e6 - - 037c6e54df11 - - b3eab4b67562 - 3f4d6399997b - - 09b53c1d4ab1 + - 53c0b7a1a0c3 + - 037c6e54df11 + - be1d967337e4 - f54f5baedfdd - 8c6cd2650d1f - - 6b1e195506a3 - - 53c0b7a1a0c3 - - c0c2d0941de8 + - b3eab4b67562 - 5cc34c3f440d - 77b2770508f6 - - be1d967337e4 + - 09b53c1d4ab1 + - c0c2d0941de8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 5ef7ec16b04f - - 178bdbdb6d24 - - 42ce70172b72 + - 00fbfac99d39 - 13022c3d3076 - - 381a32c51141 + - 178bdbdb6d24 + - ec9cbd6b9a49 - e403d27e8f24 - 9ee34ba73ebf - - 1cd2511a396e - 79b885ce78d7 - - ec9cbd6b9a49 - b8f5f6e87f5c - - 00fbfac99d39 + - 1cd2511a396e + - 381a32c51141 + - 42ce70172b72 + - 5ef7ec16b04f 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 65ad694b9..932622299 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -101,29 +101,29 @@ tools: - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - 83c4b4359ac4 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - - 84af792d3a78 - fd890f162ce6 + - 84af792d3a78 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 owner: recetox revisions: - - f04610d25411 - 8832425b1ff6 + - f04610d25411 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match @@ -167,15 +167,15 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 7ba589b01dbc - 9ff95a1a2705 + - 7ba589b01dbc tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - - 0cf68b536cd1 - ea6c5636c0cf + - 0cf68b536cd1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -256,8 +256,8 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - c53a97599181 - 7b42ee54d757 + - c53a97599181 - ec196e27a61a - 79ad928a0dae tool_panel_section_label: Metabolomics @@ -265,64 +265,64 @@ tools: - name: recetox_aplcms_compute_clusters owner: recetox revisions: + - 59c393d35e0e - 18ec7635bac6 - f3a18e020cdd - 149b9cc7499b - - 59c393d35e0e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: + - dfebc82ba1f0 - 481d769e2f7a - 134be5abb208 - 50b9918aeff2 - - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: + - 51332c2520c7 - 9064aecc78a7 - - 02c772a49998 + - 501a232f3cd5 - 30bf4e35da3e + - 02c772a49998 - a82db010c53e - - 51332c2520c7 - - 501a232f3cd5 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - 89178a72388a - - e7305ba0dd38 - b341cfd4baf8 + - 89178a72388a - b3413f335327 + - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - 17a48d0a80f4 - - cf061712a184 - b7c8a44b9cc1 - dd7bbc2b99d1 + - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: + - d7f5878a98c3 - 99d118321d5f - f92b1b64da93 - - d7f5878a98c3 - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - 7acd11ddc061 - d90187b0f247 + - 7acd11ddc061 - ea0758b41473 - ffbabefbd2e2 tool_panel_section_label: Metabolomics @@ -336,8 +336,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 6b5dec818827 - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -355,8 +355,8 @@ 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/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 04c86dc48..7a00572c8 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -95,50 +95,50 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 3a89c3f99f3d - 63f86089423e - - 76d3d2b10738 - - 7c2100246a2f - 5b5a7af9fbb4 + - 3a89c3f99f3d + - 7c2100246a2f + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 84fd33a60b35 - - 1c35dadbe76f - 96336c6a2bb7 - 00f5005840fa - 18a502a9d287 + - 1c35dadbe76f + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - 34e55239e68b - - f732237754fc - - e8fba04706d3 - addaf9d22850 - a9f4a217dcd6 + - e8fba04706d3 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 0776d824d896 - 04c15826a0b8 - 75403243703a - 5fe3edf19b9c - 8c202e741d68 + - 0776d824d896 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - - e96bbb9e24ea - 8470de786d47 + - e96bbb9e24ea - 43c99742158b + - 1c9b3bcd4261 - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -146,9 +146,9 @@ tools: owner: iuc revisions: - 35176674168c + - 84743da21318 - 1d75bd0595e2 - 5c865a382933 - - 84743da21318 - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -157,39 +157,39 @@ tools: revisions: - 78faebd0879c - 8daf4564ccda - - 32c9ea835770 - - ac72310b038a - 555ccac8a4c5 + - ac72310b038a + - 32c9ea835770 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - d60df8727f59 - - cae017b76acb - 7b8cb2b02978 - a58e4a43f49c + - cae017b76acb + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 7f3b59dee073 - 1770d188f72d - - 1bc3657cd694 - 04144473e59e - - 7f3b59dee073 - 7136e9ab70db + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - d943081510da + - 0a1224c4b781 - 9058d8943303 - 19299bb1c6af + - d943081510da - a7817705348e - - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -202,14 +202,14 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - 5c7ba3d85a01 - - 65d52c693b8e - - 4d9445dff47b - - c4db8c4de66f - - f8f56dd6449f - a68b985913ab - dbf1798c0dcc + - 5c7ba3d85a01 + - 4d9445dff47b - b907a3c0434f + - 65d52c693b8e + - f8f56dd6449f + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -222,9 +222,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - - 6c84982ee6f7 - 6d364c65c946 + - 6c84982ee6f7 + - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -236,25 +236,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - bd7a9c6efb10 - e66ab198ec15 + - bd7a9c6efb10 - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - b084117133af - d77397f09da1 + - b084117133af - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - 7f208f1eb64f - 9704f1a3b32d + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -279,8 +279,8 @@ 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 @@ -294,32 +294,32 @@ tools: owner: iuc revisions: - e88b731dad59 - - c409a495841f - 31c6d107e7a5 - - 79706f10d680 - 8237a0f225db + - 79706f10d680 + - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 714d5a28cc5c - - d24841f5c3d2 + - aabf8cfb8fef - 71ea608ddfa3 - - 172920f67a84 - 094ad9c068af - - aabf8cfb8fef + - 714d5a28cc5c + - 172920f67a84 + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - 4137b492233e - a4d7148ccee4 + - a293a742194f + - 2bdd84912a2b - 12fb63b5f63f - - 4137b492233e - d7e9a3c41657 - - 2bdd84912a2b - - a293a742194f 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: - - e2c71b852aba - - a92c06a3afa7 - 64bc7acc22a9 - 97f7bb0851e7 - - cf87759761eb + - e2c71b852aba - 6fcb8ac37a3e - 75bedfb2078b + - cf87759761eb + - a92c06a3afa7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -356,21 +356,21 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: + - 080ea153677c - 2d35528d2141 - - 4e5e73d03f0d - 4033827c76b8 - - c82508e76ad1 - - 080ea153677c - 5e5a999ffaa9 + - c82508e76ad1 + - 4e5e73d03f0d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - 6b7622dda516 + - 95bf7479d53c - c2803012bbb3 - fc6c328c292f - - 95bf7479d53c - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -396,15 +396,15 @@ tools: - 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: - - 7624945cacd3 - e699e2747356 + - 7624945cacd3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median @@ -417,8 +417,8 @@ 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 @@ -458,17 +458,17 @@ tools: - name: kraken2 owner: iuc revisions: - - cdee7158adf3 + - 4a9da2b6c2e3 - 328c607150ff - 20e2f64aa1fe - - 4a9da2b6c2e3 + - cdee7158adf3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -487,8 +487,8 @@ tools: - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1c677354ab18 + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report @@ -507,8 +507,8 @@ tools: - name: kraken owner: devteam revisions: - - 766d5f63b0f4 - 8ba2174315aa + - 766d5f63b0f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -520,37 +520,37 @@ tools: - name: krakentools_beta_diversity owner: iuc revisions: - - 4505d7643673 - c254d75b8b67 + - 4505d7643673 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 3d2cffa2c4ab + - 073c867c5244 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: - - 02bbace216f2 - 2deaada69b14 - 88d274322340 + - 02bbace216f2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: - - bb96a1e6583d - d33cf727ed94 + - bb96a1e6583d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -580,21 +580,21 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 3cc4a60615c0 - - 327d9f4cc95f - - 0270541aaf46 - 4fd3b5d8706b - 7f5d7b0e9884 - - e073891b2afc - 2cff76cf35c6 + - 0270541aaf46 + - e073891b2afc + - 3cc4a60615c0 - 27250f92a01a + - 327d9f4cc95f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - eb50e7eca3dc - 76bc4efa1aeb + - eb50e7eca3dc - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -661,33 +661,33 @@ 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: - 1a037928504c - - 6dee4abadccb - - ec368db926f4 - - a16313517e55 + - 740fd2d16a28 - a92a632c4d9b - - b89b0765695d - ef65b083bd0c - - 1a6cdf55390f - - ff8f55893e7d - - 2131d7dca455 - 289b3807e80c + - 1a6cdf55390f - fd69c607b43f - - 740fd2d16a28 + - 6dee4abadccb + - 2131d7dca455 + - ff8f55893e7d + - b89b0765695d + - a16313517e55 + - 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 @@ -718,36 +718,36 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda 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 @@ -766,8 +766,8 @@ 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 @@ -785,8 +785,8 @@ 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 @@ -830,13 +830,13 @@ tools: - name: staramr owner: nml revisions: - - aeaa20b96ef2 - - 4d83eccf5f81 - - 2fd4d4c9c5c2 - 141afacabcfa + - 4d83eccf5f81 + - aeaa20b96ef2 - 4b9a8031ab74 - - be818ae858e4 + - 2fd4d4c9c5c2 - 3b22de20bd4b + - be818ae858e4 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: - - 9495df9dd6ef - b3c7199d8786 + - 9495df9dd6ef - 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 0551c3018..8c018af31 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - bdb4a58a2025 - 12e856482d26 + - bdb4a58a2025 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -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 @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 11be7c4e0..d6ae9c075 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: - - cd07731e4434 - - bdfbaf0c10aa - - 098506c54016 - - 94b8c6013083 - - 9baa871cb1d1 - a74dbfee5a86 - 9422c5a87ee2 + - 94b8c6013083 + - 2263989660f5 + - bdfbaf0c10aa - 8b67dd48fec1 + - 9baa871cb1d1 + - 80f03df2e2ce + - cd07731e4434 - 9eeb13a92d79 - - 2263989660f5 - - 48c13389050d - 6ae5a7b5a0a2 - - 80f03df2e2ce + - 098506c54016 + - 48c13389050d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - be78f13134e2 - - 3ff17bad4006 - - c18157c68134 - f0af8936ed41 - - fc2e49f91e52 - - 4a60927aaca5 - - c44f824c051a - bc3831dd65c1 - - aaa0d6a8b808 - - 2e093badc689 - - d7ce0ec78e51 - - d390fe1567dc - 5abf2c2249aa + - 3ff17bad4006 + - c44f824c051a + - d7ce0ec78e51 - '764845535798' + - aaa0d6a8b808 + - 2e093badc689 - f14193ec1f50 + - 4a60927aaca5 + - c18157c68134 + - fc2e49f91e52 + - d390fe1567dc tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -60,19 +60,19 @@ tools: - name: gecko owner: iuc revisions: - - 1de657a3198d - 5efbd15675ca + - 1de657a3198d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - - c5908940967d - f1a5908ea2cb - - f0d493f8f84f - - a65296ffb4a0 - - bf28a8cff401 - 6f28e90db932 + - c5908940967d + - bf28a8cff401 + - a65296ffb4a0 + - f0d493f8f84f - 8e649f27aa0d - 15974dd17515 tool_panel_section_label: Multiple Alignments @@ -80,48 +80,48 @@ tools: - name: mummer_delta_filter owner: iuc revisions: - - e8fdceffea4c - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 + - e8fdceffea4c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - - c9685bc0407c - 5561a1193611 + - c9685bc0407c + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 48823c9635a4 - 57f042937ba7 + - bcd65de9725b 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 4dcb885f5..aedc656c5 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,9 +8,9 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 28928576e1ea - - 18a8d140ec6f - 7c47b3c9e493 + - 18a8d140ec6f + - 28928576e1ea - 9aa9d92c3c51 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,8 +24,8 @@ tools: owner: galaxy-australia revisions: - fc5b6491cf78 - - 6942f170cc43 - 63d8ecfcfab1 + - 6942f170cc43 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -39,17 +39,17 @@ tools: revisions: - fc8804320156 - 72b5e9dda577 - - 0e9e7fcdd543 - - a7228a7ea146 - 79e9a869f40e + - a7228a7ea146 + - 0e9e7fcdd543 - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - d6cddc06aeae - 18505fe2bdb1 + - d6cddc06aeae - fa11aa8103b2 - db25ec99c3ea tool_panel_section_label: Nanopore @@ -63,22 +63,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - eb746fa6f514 - ec699520444c - - 2bf63b38ee9b - - 222669c4afb6 - 19f3b583a9b3 - - 43815fa60f3a - - cc36773a3681 - 0f5f4a208660 - edf6d4003fad + - 43815fa60f3a + - cc36773a3681 + - 222669c4afb6 + - 2bf63b38ee9b + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - c0fb573c1e8d - b833eff63b10 + - c0fb573c1e8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -91,12 +91,12 @@ tools: owner: iuc revisions: - 7b379e98b9a9 - - edbb6c5028f5 + - 0f1c34698076 - 645159bcee2d + - a3c4fe6f49ab + - edbb6c5028f5 - a02b8b3f5a0c - a38bdcec9e4c - - 0f1c34698076 - - a3c4fe6f49ab tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -111,31 +111,31 @@ tools: owner: bgruening revisions: - be95355fef8d - - a8d4be409446 - 90a922f32523 + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: + - d376944466bf - 4857d5bcce52 - 449e9aeded2d - - d376944466bf 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 - 543cbeef3949 + - 5f76b20953e5 - 93d623d9979c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -181,8 +181,8 @@ 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 diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index cf92c3d4d..1ea244375 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - 592ef3959907 - a5921c09b7b7 + - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: annotation_profiler @@ -28,8 +28,8 @@ tools: - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 58341ad4fb42 - 96d2000977ab + - 58341ad4fb42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -67,9 +67,9 @@ tools: revisions: - adfd6bf710bd - 3e73c97f025d - - 97b1b5ad1cda - - baceff842902 - d74850cf4e42 + - baceff842902 + - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder @@ -89,20 +89,20 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 2f27f3b86827 - - edacc4bcd3cb + - e4b4837f06f5 - 8c533e19b697 - 1e34d2e3d285 - - e4b4837f06f5 - - e9ee4d074d5d + - edacc4bcd3cb - ed1518ce2237 + - e9ee4d074d5d + - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 9e993022c762 - 46066df8813d + - 9e993022c762 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -114,23 +114,23 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 472dabcb03bf - 74af283d8ebd + - 472dabcb03bf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: + - 5711fc06a63e - 48a42ca61006 - 38ccd4589990 - - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -150,8 +150,8 @@ 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 @@ -163,16 +163,16 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - 5bcf0e24f42c - - b4b2b284230a - 27a6a256cd23 + - b4b2b284230a - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -199,23 +199,23 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: + - fea85c467896 - 19bbd19b74b3 - 87febc68b45b - - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 4c7ebbad42cf - 15c2fc266540 + - 4c7ebbad42cf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -233,12 +233,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 4ba60cb14cb0 - - 0cb27ea69dc1 - - 9c43baa60906 - 5fe20c915fa6 + - 0cb27ea69dc1 - d8dc037e3c13 + - 9c43baa60906 - 2c61c30a57e7 + - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -251,18 +251,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 9d09724f2bf1 - 0db22932bc39 - aec831b54a5b + - 9d09724f2bf1 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 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: - - 1865e693d8b2 - defd3e9ddd2d - - 3e4d45aca422 - ad90c2da4f38 + - 3e4d45aca422 + - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - d107d20dc6bd - def511e8e005 + - d107d20dc6bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -302,18 +302,18 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 71c994a11f71 - - d63c1442407f - c520a52b5174 - 64deddb6a8ec + - d63c1442407f + - 71c994a11f71 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - 94a50db37d1a - 9946bc39c834 + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1078,8 +1078,8 @@ tools: owner: bgruening revisions: - c362398df83b - - a22969b08177 - e4b7d1507a75 + - a22969b08177 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -1091,10 +1091,10 @@ tools: - name: salsa owner: iuc revisions: + - ba7b0f11e470 - ab5b7f6b7198 - 9a22227bb6d0 - f77f7a7f3b83 - - ba7b0f11e470 - 58a870ef434c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 120157127..94b5e3ab0 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - '841557158611' - b89cac5156ec - - d7c7ef3353fe - - 5a7c56a5cc08 - - a6619171428e - - 6a457678efcb - f73435dc282b - - f04a1264e2a2 - - 26de3a7b1cb9 - - 3f59ebfbfe3d - cce7b18495e4 + - 26de3a7b1cb9 - d033ffc1c161 - - 3b8b5bde0bd9 - 8834daeb9892 + - 6a457678efcb + - 3f59ebfbfe3d - 107d3ba7024a - 81e66674859e + - d7c7ef3353fe + - a6619171428e + - 5a7c56a5cc08 + - f04a1264e2a2 + - 3b8b5bde0bd9 - c78f3d7dd1db + - '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 + - 88c4aa435ded + - 4755f52427c4 + - a185b079b095 - 6a726db04d4b - 5b777002c2de - - a185b079b095 - - 7a2092844346 - 6283babe736e + - b0af57c1a968 + - 6223845127ea - 3b96e92e8ec3 - 5fcd1ece3a6e - - e75442c7f4da - - df47d4845b62 - - 659517798cc4 - - aa8cc71438cf - - 4755f52427c4 - - 6223845127ea - - 88c4aa435ded - - b0af57c1a968 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 24d024316465 - - d1c340a5664b - - 111bd54f6bc4 - 70acec670c30 + - f97743d52b87 - b8476e82ac20 - f87ac61981f0 - - f97743d52b87 + - 24d024316465 + - d1c340a5664b - 524d31add34a + - 111bd54f6bc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 9e10ba792be2 - - feb40665d7cd - - 4f6349228462 - daddf188c13f + - 4f6349228462 + - feb40665d7cd + - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -110,33 +110,33 @@ tools: - name: pangolin owner: iuc revisions: - - 7bb8726be37c - - ca0d8cf80567 - 81804a978fc0 - - 03ed9524dcd1 - - ca337cce3888 - - 2fa9d4f1b48f - - b7e297c2ede6 - - 36912871ccdc - - 9d61d3fa046c - abf6dbe8c9d7 - - 437e28791761 - - b6abccb1f25b - - 42a174224817 + - 03ed9524dcd1 - 8ad84c5753ea + - b7e297c2ede6 - a2099fb98cdb - - 83a69484cb87 - - 2f1019071464 - 5f8727ff21e7 + - b6abccb1f25b + - ca337cce3888 + - 2f1019071464 + - 437e28791761 + - ca0d8cf80567 - 3a43c3982401 - 14ae456b8cc5 + - 7bb8726be37c + - 36912871ccdc + - 42a174224817 + - 83a69484cb87 + - 9d61d3fa046c + - 2fa9d4f1b48f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 2bf47d57ebb5 - 7157a5b34a68 + - 2bf47d57ebb5 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: - - a4b71be30c3c - - ba29b5e2a4be - - 73a469f7dc96 - b1e68bbe4cef + - a4b71be30c3c - ea30d3089354 - 29ff6a849eac + - ba29b5e2a4be + - 73a469f7dc96 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 9b2b122d0415 - - 15ac71df11a0 - - 91887494eb97 - - e88a7de55d6e - 809e42326fc2 - f1ccc8a6eb05 + - 91887494eb97 + - e88a7de55d6e - dbe2b2204555 + - 15ac71df11a0 + - 9b2b122d0415 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 b00b4dd91..905e50afe 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: - - 1aac2a13842a - - b502c227b5e6 - - f6ced08779c4 - - 7d34178f2812 - f9242e01365a - - 881d7645d1bf - a1f0b3f4b781 - 3f254c5ced1d + - 7d34178f2812 + - f6ced08779c4 + - 1aac2a13842a + - b502c227b5e6 - fc288950c3b7 + - 881d7645d1bf tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index 2d9b611da..d88435844 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 + - 3f188450ca4f - 7fbec959cf2b - - 6ab1a261520a - - 2f7702fd0a4c - - e7f1b552a695 - 3bd420ec162d - - e4a053d67e24 - - eb085b3dbaf8 + - 6ab1a261520a - d00e15139065 - - ca90d17ff51b + - eb085b3dbaf8 - c0e71cb2bd1b - - 3f188450ca4f - - 5b85006245f3 + - e4a053d67e24 + - 2f7702fd0a4c + - e7f1b552a695 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 3c5bd0062..9f4e0a401 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,31 +2,31 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - ece627528a78 - - b574b84afc4d - - b18329a8ac14 + - f28ad96b76dc - 277dc652246e - 0a18ac48ac53 - 4c177985028a - - f28ad96b76dc + - b574b84afc4d + - ece627528a78 + - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - a9a28e46d54a - - b41107d8fe89 - bf06d196e23d - e988563cc6e5 - - e215f71d7983 - 525f201b86c1 + - e215f71d7983 + - a9a28e46d54a + - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - bb6397b94018 - 4fbffddde8cd + - bb6397b94018 - 8da3511c9467 - 56da27be956a tool_panel_section_label: Proteomics @@ -34,62 +34,62 @@ tools: - name: cardinal_filtering owner: galaxyp revisions: - - f23d67e28cc8 - 890845926d4b - - a8157342d9a3 + - f23d67e28cc8 - b8c79e70516d - 528fb09022be + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 - - ae304a72db7b - - a69865da6f80 - 80600735685d - - 25b83cbd596a - a95a82eb4d50 + - 25b83cbd596a + - a69865da6f80 + - ae304a72db7b + - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - e0669b1854b1 - - ed9ed1e6cca2 - - 611d80c0e29d - f1897eb07081 - - 798da6bdff3d + - 611d80c0e29d - 83aac7741200 + - ed9ed1e6cca2 + - 798da6bdff3d + - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - 74b61bf5bc4b + - a7fb9b395ddf - 5a35e3a8d013 - d426a9107a6c - - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - 91f0f5922011 - cc430977c8ff - - 82f6c2f4332d - df2187f9013b + - 91f0f5922011 + - 82f6c2f4332d 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 - - ba92b59cd529 - - 1693b2126f30 - - d2483487e077 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -108,9 +108,9 @@ tools: owner: galaxyp revisions: - ff8c9e0e8a7b - - 9fa3dbf06f17 - - ae4dc0c041f9 - bf0728e000cd + - ae4dc0c041f9 + - 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: - - d0ea7589e95f - d263296cd73e + - d0ea7589e95f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify @@ -137,16 +137,16 @@ tools: - name: encyclopedia_searchtolib owner: galaxyp revisions: - - 36880dfd9fa7 - fb192dd6658a + - 36880dfd9fa7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: - 0d2e93e01e68 - - ce1a157a41bd - d6a4dfdad269 + - ce1a157a41bd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -158,16 +158,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - - d286ff4600dd - e66f552a3c47 + - d286ff4600dd + - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -180,15 +180,15 @@ tools: - name: maxquant owner: galaxyp revisions: + - 2133b0be850a + - 37d669de2828 - 1f39c833f65f - - 4d17fcdeb8ff - 9c52362ae7bb - 7f432d87c82c - - f522c08e900c + - 4d17fcdeb8ff - e42225f8a659 + - f522c08e900c - 97a7f34fcb6a - - 2133b0be850a - - 37d669de2828 - 837224ad1694 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -201,54 +201,54 @@ 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: - - 767c1d761aaf - 1974224d63c2 - - 352b37c66d97 - 990b4560ead7 + - 352b37c66d97 + - 767c1d761aaf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - deaf035bbe9f - 35cc7ca0bdc7 + - 4f359549383c - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c1343e3389ca - - e79958768a2c - - c7745841de24 - 06f6826d380c + - c7745841de24 + - e79958768a2c + - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - b9d453dca8d3 + - d46d64e7964d - d2eac53666f0 - da986f83631b - - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - 944b43462104 - - 1199751329b0 - 8bd7734309f6 + - 1199751329b0 - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -285,53 +285,53 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 4e77b8f12cd3 - - 8960fb791701 - f4be248c3d47 - 01dbaf6a57e0 + - 4e77b8f12cd3 + - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 25529df60a81 - - 06cca574e337 - 370141bc0da3 + - 06cca574e337 + - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - 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: - - dff6c756eee5 - 9876bda3ec53 - - ca88bd28f116 - 5e948629bc73 + - ca88bd28f116 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 890025d6e426 + - 1595601708ec - 41859bbdc16e + - 890025d6e426 - 658494a2cb00 - - 1595601708ec tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - 2a93a25f0599 + - 5ad0b5bf1deb - 6634cad7d797 - 9b7977080f6d tool_panel_section_label: Proteomics @@ -339,8 +339,8 @@ tools: - name: openms_filefilter owner: galaxyp revisions: - - fe4e4587d265 - 0bb5056cb775 + - fe4e4587d265 - d6878d27f051 - 05d5e1ddc985 tool_panel_section_label: Proteomics @@ -357,66 +357,66 @@ tools: - name: openms_filemerger owner: galaxyp revisions: - - 27cba4c5fc42 - 92352a475eed - - 39e8fde08881 - b2fc8da99bcc + - 39e8fde08881 + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - d3546bb9fd8e - - 9e26f5c770f8 - 0efbc235f314 + - 9e26f5c770f8 + - d3546bb9fd8e - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - - c28f13cab67a - ca1740533b59 + - c28f13cab67a - 3720e349ba2a + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c55dddc5844a - c427a8628cbe - - ca799a7246e7 - 382cde407f81 + - c55dddc5844a - a5d785af0ad8 + - ca799a7246e7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 8ddb7bab1138 - - adca857b4884 - b5d0905419da + - adca857b4884 - 39caaa778d2e + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 1c5f31b8d632 - - 8d4db262964c - f817513840a9 - - 34e7afee141d - 18f93351f8b6 + - 8d4db262964c + - 1c5f31b8d632 + - 34e7afee141d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a - - 5d9f175dff81 - - 986e03d3201e - 111c3a00136d + - 986e03d3201e + - 5d9f175dff81 + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher @@ -424,41 +424,41 @@ tools: revisions: - 476b5e296979 - 0e52c85f3b15 - - be74a8cd7d66 - 4204882495f2 + - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - e133b5c8878f - 9866e1170611 + - e133b5c8878f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: + - 2b2a7551a857 + - f5ec766d80cf - c18d8efa4474 - a407b6790342 - - f5ec766d80cf - - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - d0304fb829c0 - - 021fdb80f204 - 4e66c4e73909 + - 021fdb80f204 + - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - 8098330f6d91 - - bf32e0bcf554 - ee860980edc6 - 2735db4dd8d9 + - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer @@ -472,25 +472,25 @@ tools: - 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 owner: galaxyp revisions: - - e8f64a7dc470 - - 1bf940c18d93 - c1809c05ae8c + - 1bf940c18d93 + - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - - 496cf619e311 - f861ec9fbe59 + - 496cf619e311 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -504,32 +504,32 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 4bb198c0bd3e - 89254095cbf6 - 8b814eafce2c - - 4bb198c0bd3e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - f9ed7e074900 + - 05ec9fb05ed1 - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 18826fb8e5db - - 6e8cc5ed2a9b - d31426ef20f6 + - 6e8cc5ed2a9b + - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 4a7b96835140 - bc63b4d12779 + - 4a7b96835140 - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -538,57 +538,57 @@ tools: revisions: - 6b01678ec2fc - 3d8d4ada5405 - - 5ae104d0da6e - decc397c3b7e + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - 5182338d5e7c - d6aca689dd48 + - 539a3a4dcc9e - dd173849c3d8 - e039cc5c7aed - - 5182338d5e7c - - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - d426affe977c - - 8a45fd5a608a - 16026cdb1330 + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - dd71e020e2aa - 43b9ed22e8ce - 9c70a651a53e + - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - 1b03536aa3c9 - 9020199dba0a - d063e2fe4ba4 - - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - f036e8cf1a55 - - ad2ba3a95a02 - 78c080d36945 + - ad2ba3a95a02 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 7f6a1f27553e - c8b225c69a7f + - 7f6a1f27553e - 5c2a97a234d6 - fb52e95a370c tool_panel_section_label: Proteomics @@ -596,8 +596,8 @@ tools: - name: pep_pointer owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f 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: - - da885ca16cb2 - - 1beff3ddce58 - - a72c48001f7c - - 07ff622ec007 - 7fdd9119cc4f - - 3ec27b4cee7c - - 943a34df6047 + - 07ff622ec007 + - a72c48001f7c - 3634c90301af + - 943a34df6047 + - da885ca16cb2 + - 3ec27b4cee7c + - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -684,10 +684,10 @@ tools: owner: galaxyp revisions: - a371252a2cf6 - - 12692567c7f9 - 265c35540faa - 4ddc8da62671 - 1a5690a5eedc + - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index ed1a4ed15..a59232894 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 2f1d464ebfd2 + - 110a346daf36 - 289b7d6b69a4 - - cd5f98911089 - 42201b90e3f4 - - 2f1d464ebfd2 + - cd5f98911089 - e345aadf914f - - 110a346daf36 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 42d9087b4789 - - 8501601a118d + - 0345dbaaa79b - fcce77c09289 - c207119ba5f6 - - 0345dbaaa79b + - 42d9087b4789 - 0cd2df8af811 + - 8501601a118d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -37,11 +37,11 @@ tools: owner: iuc revisions: - 33486216eec0 - - 405a212b32ab - 421c33b8bf17 - - 04db7fd6b238 - ad5ab22ffe24 + - 405a212b32ab - 89eb29319bf4 + - 04db7fd6b238 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: - - 1d839ead7ad3 - - 7370bb65bad4 - f6e91108b7b1 + - eb784fa07f80 - 7b72fde3d27e + - 7370bb65bad4 + - 1d839ead7ad3 - fa51dc5e8386 - - eb784fa07f80 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: - - 8a55d29c8fcf - a3e86cd9cac7 + - 1544278c272e + - c9b77ced9a78 + - 8a55d29c8fcf - 3d70c2996730 - d30e36c48c93 - - c9b77ced9a78 - - 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 - - b242deb58952 - - a5969aa9347e - e2db212d64ad - 7b881f5f5ad5 - 564c33e5c3e3 + - a5969aa9347e + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,10 +104,10 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - b4bab607eb05 - 8cff84759bf6 - - bd5ff77e2036 - 9a171f9a450b + - b4bab607eb05 + - bd5ff77e2036 - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -121,11 +121,11 @@ tools: owner: iuc revisions: - 4f65e343ecdf - - 5e10f396979e - - 33f0793edf93 - 6dafad990086 + - 33f0793edf93 - adc7a7610d4f - 887e0991eb24 + - 5e10f396979e 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: - - 17d39bf0a63a + - 97575d01f06b - 4e280b27a831 + - c5d7050e4ad7 - c287418eb288 - - 97575d01f06b + - 17d39bf0a63a - 43e3eeb2e0ec - - c5d7050e4ad7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,11 +154,11 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - a819ec3b362d - - 09b8edb56d80 - 0b8c84a7fdb5 + - 09b8edb56d80 - 9586f08634c0 - d9bf483266a1 + - a819ec3b362d - 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: + - 2645575d1bf2 - 95351dd0fd3f - - 69842dd5aa48 - bf0e43ab0416 - - a9c34a289493 - - 2645575d1bf2 - a4b4bd84f69e + - a9c34a289493 + - 69842dd5aa48 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - bb0475c884ff - cfb504394ae1 - - d1fda11e602f + - 8a35a3bc6752 - 912f904a6e1e - d033e1ccb386 - - 8a35a3bc6752 + - d1fda11e602f + - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - 95286af4139b - d504d945a655 + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index f8cfa166e..3d70d4ef3 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -3,18 +3,18 @@ tools: owner: iuc revisions: - 7acb00fc980a + - 31f8063eedea - 2d4e3aff9dc7 - cf01dd6c6b1f - - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - - 32e542c2a773 - 7a5a2d28c539 - 703a2cb3fb38 + - 125d20cb23d7 + - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -34,8 +34,8 @@ tools: - name: blockclust owner: rnateam revisions: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockclust @@ -92,8 +92,8 @@ tools: owner: devteam revisions: - 6926716bbfb5 - - d080005cffe1 - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -105,11 +105,11 @@ tools: - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - - 04adc9db1581 + - 6a6717a5f421 - 86285ddd4512 + - 04adc9db1581 + - cf747d1bd79a - 22cf48ad7b16 - - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -121,9 +121,9 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 28b94cfbfdb9 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -160,10 +160,10 @@ tools: - name: describe_samples owner: iuc revisions: + - e3b16fd7dd08 + - 8f0181aacb7a - 0693ccd171c4 - 3b36efd62b3e - - 8f0181aacb7a - - e3b16fd7dd08 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 - - 8fe98f7094de - - 0696db066a5b - - 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 - 62adf13b86ea - - 9a7c5b6d8f1e - - b47c006d90c5 - 2872c633f07e - - df929f257179 + - b47c006d90c5 + - 9a7c5b6d8f1e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -209,18 +209,18 @@ tools: - name: edger owner: iuc revisions: - - 070900306913 - - 0cb907a2a810 - - 555659de7321 - - 5bf899c13979 + - a8305cf0c951 - f2843df56434 - 9bdff28ae1b1 - - ae2aad0a6d50 + - 0cb907a2a810 - 334ce9b1bac5 - - 6e53e565fc6a - - 3d89af8a44f0 + - 070900306913 + - 5bf899c13979 - df0c8d0a5992 - - a8305cf0c951 + - 3d89af8a44f0 + - 6e53e565fc6a + - 555659de7321 + - ae2aad0a6d50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -232,8 +232,8 @@ tools: - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -251,18 +251,18 @@ tools: - name: featurecounts owner: iuc revisions: - - a56fbe2d6ba7 + - 90d16db017d7 + - 1b851f87fbe0 + - 6f66ae7c5f7a + - af814359d244 - f3a5f075498f + - a56fbe2d6ba7 - e6a2a912677a - - 6f66ae7c5f7a - - 90d16db017d7 - - ea04b737afa0 - - a37612abf7f9 - f9d49f5cb597 + - a37612abf7f9 - 38b6d12edc68 + - ea04b737afa0 - 7db9d3ea71c9 - - af814359d244 - - 1b851f87fbe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -292,9 +292,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 0f710191a66d - 3c97c841a443 - 3c5e024a18cf - - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -312,13 +312,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 6c19daec423d - - 3fb01a8c902d - - d4b55e2beb12 - - a86e80d3c09c - 26371a1df031 - - f4af63aaf57a - 6ab42baa56e9 + - a86e80d3c09c + - 3fb01a8c902d + - f4af63aaf57a + - 6c19daec423d + - d4b55e2beb12 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -356,10 +356,10 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - ce5d418183c5 + - 87c11c05d238 - 5ae5c312d718 - 1c75aa5de15e - - 87c11c05d238 + - ce5d418183c5 - 01247aaf0a10 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -373,9 +373,9 @@ tools: owner: iuc revisions: - 40985510cd98 - - 10c98fab6c5a - - 4f9c4e6566e5 - c971db6f0fe5 + - 4f9c4e6566e5 + - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -387,14 +387,14 @@ tools: - name: limma_voom owner: iuc revisions: - - 119b069fc845 - - 58c35179ebf0 - - d6f5fa4ee473 - 708348a17fa1 - - 32511f586472 + - d6f5fa4ee473 - e827f9aae031 + - 32511f586472 + - 58c35179ebf0 - 0921444c832d - 97e06a4c7c75 + - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -443,8 +443,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -462,21 +462,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 99b17b74a8cd - - e132e7d02a3e - - 4df95e2d7f61 - - 3ea5a2a63fa2 - - c772497b2c32 - - 5ec75f5dae3c - - b0f2be869d6d - - b9e04854e2bb - 79de45b5069b + - c772497b2c32 + - c7c55b694974 - 4074fc1940e2 + - 5ec75f5dae3c + - 4df95e2d7f61 + - 980d2a2e1180 - 0a563fd2f22e - - 53255f6eecfc - - c7c55b694974 + - 3ea5a2a63fa2 + - b9e04854e2bb + - e132e7d02a3e + - 99b17b74a8cd + - b0f2be869d6d - 7ed2edc1337f - - 980d2a2e1180 + - 53255f6eecfc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -500,14 +500,14 @@ tools: - name: salmon owner: bgruening revisions: - - 49121db48873 - 15cd64d7c58b - - 53e9709776a0 - - ebab418107f5 - - cc05793bb896 - f4d5237a84f6 - - e3d32471da11 - 2c0ca397d302 + - ebab418107f5 + - e3d32471da11 + - 49121db48873 + - 53e9709776a0 + - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -528,14 +528,14 @@ tools: - name: stringtie owner: iuc revisions: - - 1ebd14235b92 - - ae618321f34a - - dd4df992d93d - - cef79931dda5 - cbf488da3b2c - - 258d696dbd7e - 914cfcba0ec8 + - ae618321f34a + - 1ebd14235b92 + - cef79931dda5 - 76d290331481 + - dd4df992d93d + - 258d696dbd7e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -571,10 +571,10 @@ tools: - name: transdecoder owner: iuc revisions: + - c6334cb383ff - ffd1300599a1 - d0d4cef4f967 - 0db979fead3a - - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -586,10 +586,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - 74217fbfba4d - - d6a479fd4281 - ba3720d7e68b + - d6a479fd4281 + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -601,10 +601,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - 2fb4ee002432 - - c2b82a94493e - 56162e446004 + - c2b82a94493e + - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -616,9 +616,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: + - fab23c3b5258 - 3f4094b6a565 - 9ff3765e7172 - - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -630,10 +630,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e - - 34a018cbee9c - - be3f26533209 - 4687ecf0eb2d + - be3f26533209 + - 34a018cbee9c + - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -645,11 +645,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 5192f657f305 - 33406f5a445c + - 65e7dea767ea - c5fbddcac63a - 05ab8d5e04a2 - - 65e7dea767ea - - 5192f657f305 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -661,10 +661,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - a35cba31d904 - - e406ac71165d - 6f0fb35b799c + - 1fdb25a8384d + - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -676,10 +676,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: + - c2c039e421af + - 37a1129c89d2 - 7c7fbf13aadd - 964b7efe2639 - - 37a1129c89d2 - - c2c039e421af tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -691,9 +691,9 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 24e94d84adc9 - - eafea3083352 - 047c22569787 + - eafea3083352 + - 24e94d84adc9 - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -734,14 +734,14 @@ tools: owner: iuc revisions: - 32b86cd8eb50 - - d2bc35f3d1c5 - - 9fa24d5aac68 - - cee61b3fcf78 - 48636f857c4b + - 9fa24d5aac68 - 8f1c3df4dd49 - - db1f362cca3e + - d2bc35f3d1c5 - c9cfec002f71 + - db1f362cca3e - d84caa5a98ad + - cee61b3fcf78 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -753,10 +753,10 @@ tools: - name: trinotate owner: iuc revisions: - - 6fd16fad465d - - 9e61bc67866f - 2b093007fab9 + - 9e61bc67866f - 4383070d29ed + - 6fd16fad465d 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 e601372c1..f931924b3 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: - - 27e16a30667a - - 1a052c827e88 - - 473382134e56 - 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 44a22dc11..a4cf08ec3 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -16,10 +16,10 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 993b19f20c76 - - 108db6635177 - cb20f99fd45b + - 108db6635177 - 1dfd95ee241e + - 993b19f20c76 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - 9c1c0b947e46 - ef11139d4545 + - 9c1c0b947e46 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - 19ece8afbaab - - e7fd6754d093 + - 5f8e69cc4c6e - 30a201c9c310 + - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -110,8 +110,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -130,8 +130,8 @@ tools: - name: sam_to_bam owner: devteam revisions: - - cf1ffd88f895 - 0e60e2dd20af + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -149,9 +149,9 @@ tools: - name: samtool_filter2 owner: devteam revisions: + - 56c31114ad4a - dc6ff68ea5e8 - 649a225999a5 - - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -163,8 +163,8 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 6856f8a01905 - 9149ad20699a + - 6856f8a01905 - 46c6639921f1 - 12749212f61b tool_panel_section_label: SAM/BAM @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: + - 06dc50b7b711 - 92ec40abcdcf - 26b4f9f98aca - 33208952b99d - - 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 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -221,18 +221,18 @@ tools: - name: samtools_fixmate owner: iuc revisions: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: + - cc61ade70eb8 - 22970df7a40e + - fefd89ab563c - db17d5321bad - fe34990e5ce7 - - cc61ade70eb8 - - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,11 +244,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: + - 7def34e6cf4d + - fa5d3e61e429 - 88b8c2916784 - 7a6034296ae9 - 811fc2d75ad4 - - fa5d3e61e429 - - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -267,21 +267,21 @@ tools: - name: samtools_merge owner: iuc revisions: - - 740ce0a18f0d - - cae2794d2deb + - 36677f429310 - 65a38e8c8e2a - b40e2d865d52 - - 36677f429310 + - 740ce0a18f0d + - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - 583abf29fc8e - - fa7ad9b89f4a + - 9da0311ab1dd - 329deb17a9f7 - b61f5d6a7f25 - - 9da0311ab1dd + - fa7ad9b89f4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -306,8 +306,8 @@ tools: - name: samtools_reheader owner: devteam revisions: - - 30388d878f81 - 85e38b31e8b3 + - 30388d878f81 - db000c6007a0 - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM @@ -327,9 +327,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: + - 344fc91e1bfd - b8beef827165 - a4a10c7924d1 - - 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: - - 6c2c1836728b + - e613c1ad4c4c - cab3f8d35989 - d54a4df48867 - - e613c1ad4c4c + - 6c2c1836728b 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: - - 818030fa6bbf - - bd850490c7f1 - b7f7826ef1cd - - 135c85f4cfaf + - 818030fa6bbf - 5d9ae78f34d3 - bcedabb53ddf + - bd850490c7f1 + - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - 24c5d43cb545 - - 145f6d74ff5e - - 1cc79f49b8d5 - - 3a0efe14891f - 541082d03bef + - 3a0efe14891f + - 1cc79f49b8d5 + - 24c5d43cb545 - 5a08c09b9311 + - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - b01db2684fa5 - - c370440f901e - - 32dc5f781059 + - 350bbc5c2ffd + - 5826298f6a73 + - bf328cec6a42 + - 0dbf49c414ae - 2dce91e11ca7 + - 32dc5f781059 - 6be888be75f9 + - c370440f901e + - b01db2684fa5 - b72793637686 - - 0dbf49c414ae - - 350bbc5c2ffd - - bf328cec6a42 - - 5826298f6a73 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.gvl.org.au/send_data.yml b/staging.gvl.org.au/send_data.yml index d57bba352..42dbb53bc 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 - - 5cb6146337d8 - - a62c4a11a67d - - d147d6455873 + - ea5e944f447d - 59bb6d34fca6 - - 4aab5ae907b6 + - a62c4a11a67d - 480d9e9d156b - - ea5e944f447d + - d147d6455873 + - 5cb6146337d8 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 eb93acebe..0f6d5ad9c 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: - - f2000bc73102 - - b0fe3e482cb7 - - e32b215b7c04 - e4c01dcece8b + - f2000bc73102 - ecb9ea6269ee + - e32b215b7c04 + - b0fe3e482cb7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - 7a6655aa6eb2 - - c0b037b12765 - e1c3c2f2a834 - 707023fa62fe + - 7a6655aa6eb2 + - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 6f143dfe902a - - 32e547223c9e + - fb9e030ffae4 - cfc3f5a57dc6 + - 55e35e9203cf + - 6f143dfe902a - 93dd15e13e6a + - 32e547223c9e - 00712416fdaa - - 55e35e9203cf - - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -49,8 +49,8 @@ tools: - 038e32885fec - b9fac48532eb - 14c576ea6148 - - 6f0d0c784f09 - ee98d611afc6 + - 6f0d0c784f09 - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -63,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 43cb7b5a6fe7 - - ed4996a16f7f + - b85871dd69f9 - d4af736e7b83 + - 43cb7b5a6fe7 - c4209ea387d4 - - 9bd945a03d7b - 3d748954434b - - b85871dd69f9 + - ed4996a16f7f + - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -82,46 +82,46 @@ tools: owner: ebi-gxa revisions: - 890fb06a2893 - - fe75d2414dc0 - - 2e8022f1923c - - 7ebc22f77d86 - a4774b7b2e85 + - 7ebc22f77d86 + - 2e8022f1923c + - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 0e70b2dfe4be - - 02b1fe7aed76 - 769d815e4b0d - 4fff5a293013 + - 02b1fe7aed76 + - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - a90f8efe08b4 - - 344c2af50552 - c29e7bb492bf - aa4a6f0916b4 + - a90f8efe08b4 + - 344c2af50552 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 5b7c81b35b89 - - 050cf43887d3 - b13d3e4c48e1 + - 5b7c81b35b89 - c32347702e12 + - 050cf43887d3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: + - 02fc39c8610d - 1d77986f9ddc - - 239193b96d72 - ae969fdb8442 - - 02fc39c8610d + - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -157,11 +157,11 @@ tools: - name: dropletutils owner: iuc revisions: + - a9caad671439 - cdf4443d5625 - 2c1200fba922 - 8855361fcfc5 - cfe1e6c28d95 - - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -197,71 +197,71 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e + - 952abbc4b1de - fb7068d30ec9 - c3ffb2c1e314 - - 952abbc4b1de + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 57aeaf6b237d - f1c35f3f310d - 9d42a6133690 - 45828071edc3 + - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - - 1a31e75e979e - 163fd744e235 + - 1a31e75e979e - cab616fe7e64 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - b9ab56aecd18 + - f47ac4a0b337 - '920526260066' + - b9ab56aecd18 - 013e53ccc7ac - - f47ac4a0b337 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - f6a169b5e43b - - b892fa1fcaec - 9ea228a9afc8 - a63e9713c39d + - b892fa1fcaec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 640e0e45518a - - f8320df1866b - 45a386d18509 - ff1af7bac1cb + - f8320df1866b + - 640e0e45518a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: + - f963c251ac77 - c354255ff705 - - 6f8debcf2ac9 - 9d02f1819e81 - - f963c251ac77 + - 6f8debcf2ac9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - 37125838e360 - f881c94fb3b3 + - 37125838e360 - 40fee49bc6c3 - c4ed35f4f77f tool_panel_section_label: Single-cell @@ -269,143 +269,143 @@ tools: - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - 782bdcb775fb - e06265d204f6 - 2dccb6bb0add + - 782bdcb775fb - e8760fc0e29b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - 63c8377c58b3 - f0216498a666 - - b05f662f9f35 + - 63c8377c58b3 - 30677e95bc89 + - b05f662f9f35 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: + - c72fa6cb8817 - 3240e8a7c54f - 8a11d70b6cd8 - - c72fa6cb8817 - 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 - - 3ee5332bf57c - - 5dd1aae12f03 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - - 87eb9c58cd19 - a315574104c6 + - 87eb9c58cd19 + - 4401ed529d2c - 3a6a5381db36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - a83732c79949 - - 2ba6cee8e4db - c0737631eea1 - 574f295b5ba4 + - a83732c79949 + - 2ba6cee8e4db tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - 30d7390bc918 - - 937b7b9832d0 - 62b720dceb56 - ea19190ce5e0 + - 937b7b9832d0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - cd40ca76865a - - 2b4d6a8dab36 - 2786a931cad2 + - 2b4d6a8dab36 - 0f5786ffa10d + - cd40ca76865a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - ffc33339cd3e - - 4375e25de06a - 0410b6aada45 + - 4375e25de06a - bf9379529c3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 5dfba24d7bdd - 4977f65da0ff - 77d8e0fd162a + - 5dfba24d7bdd - 07dd436ea686 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - f1b3902f8baf - 972dcccb5bbc - - f0b1bd38745a + - f1b3902f8baf - 6c5097f6d41e + - f0b1bd38745a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 409396ea5cf0 - - bb8849fca57c - 3e5c86c2f80d + - bb8849fca57c + - 409396ea5cf0 - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - b0f33533181d - 7fbd6feba1ca - - e4f8fceab96a - 51e40e9b6c3c + - b0f33533181d + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 32173084d53f - - 908fa330b93b - - c261b6b05ee3 - 55b013e59018 + - c261b6b05ee3 + - 908fa330b93b + - 32173084d53f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b376ef118807 - - 4b194e675916 - febfddb0b3e8 - b6b8c8672756 + - b376ef118807 + - 4b194e675916 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1511a8ebe906 - 1d9799f4b854 + - 1511a8ebe906 - 910c6a1c3a27 - ed900cd4a0a9 tool_panel_section_label: Single-cell @@ -413,10 +413,10 @@ tools: - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - - 5e83c077e31d - 6d042c96aceb + - 5e83c077e31d - 2aa5b6b65197 + - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -431,27 +431,27 @@ tools: - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 6326cd29c1c3 - - 06ced663d24f - 11f39d7f6c64 + - 06ced663d24f - 89cfe7de541b + - 6326cd29c1c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: + - 337705015ee8 - 1602cc5b673c - - beb5b5917d2f - b4e780e93c91 - - 337705015ee8 + - beb5b5917d2f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: + - a10fce08c2dc - 8d203e74869b - 58de3c7c8e89 - - a10fce08c2dc - e285920f8585 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -460,8 +460,8 @@ tools: revisions: - b13e7a200525 - 21d859ad4502 - - 5cbd7a902a8d - ea8fb5e899e8 + - 5cbd7a902a8d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices @@ -489,29 +489,29 @@ tools: owner: bgruening revisions: - 1de2276f633f - - df64cc4dfb4d - - f36828ebdc54 - 27fe5cd1729c + - f36828ebdc54 + - df64cc4dfb4d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - 1d201e8378b3 - - cef9fb4ece1c - d890828ab02a + - cef9fb4ece1c + - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: + - db575b4c8b22 + - 59be31ac9dc3 - eeab712b0b99 + - 7784821452ac - 4b0adaa31c95 - e98619de2776 - - db575b4c8b22 - - 7784821452ac - - 59be31ac9dc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -523,9 +523,9 @@ 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 @@ -557,11 +557,11 @@ tools: - name: raceid_clustering owner: iuc revisions: + - c4f39bf4a068 - a4b734cd253b - - 7e014059a88d - f911a64454fb - - c4f39bf4a068 - 49776718ae90 + - 7e014059a88d 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: - - 8b917923f7d4 - d45f092caf24 - - 43c146e25a43 - 7608d5faee41 + - 8b917923f7d4 + - 43c146e25a43 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: - - 2b0d3e2f402a - c7ddb719554d - 37a47c4fd84d + - 2b0d3e2f402a 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 - - 6e90c8adf84f - df8e4e54d367 + - 6e90c8adf84f + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -618,9 +618,9 @@ tools: revisions: - 2bfd55b87af3 - 44b935f2271b - - 72979cac22b2 - - c92d0f9338c5 - e93b008c637a + - c92d0f9338c5 + - 72979cac22b2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -644,17 +644,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - b2df381a6004 - 6acb08931836 + - 6f83f8fd381f - 4d8f983cd751 - - 8983e7a04ba7 - - cb43c5d3acd3 - 38db3fef7aad - - f9353ee6a0d4 - aaa5da8e73a9 - - b2df381a6004 - - 77b91b9bdf52 - - 6f83f8fd381f + - cb43c5d3acd3 + - 8983e7a04ba7 - edec35114f72 + - 77b91b9bdf52 + - f9353ee6a0d4 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: - - fc0321c000a3 - - d636ce5cde16 - - 3c86f71498bc - - 8cb783c81905 - 64388be6d510 + - 72a6bebab2a5 + - d636ce5cde16 - 277313130da5 - a03ff8633507 - - a97abb8cd15b - - 72a6bebab2a5 + - 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 - c0a80a16560f - - d86cb2ce311b - - c5d3684f7c4c - cc0deb593fc8 - - 6bd82ed14acd + - 5c3ebe2adc77 - f54f0f0598ad - 5e9171dc8244 - - 18262103fa61 - - 5c3ebe2adc77 + - c5d3684f7c4c - 3081ff5c84a3 - - 6c145a6868cc + - d86cb2ce311b + - 18262103fa61 + - 6bd82ed14acd 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 - - d844935c906c - - a407e7f8bdc1 - - 9f354c7c8c92 - - 146ae5d70b47 - 4bda4412b8c2 + - ab55fe8030b6 - 56c0d4acef02 + - a407e7f8bdc1 + - 9f354c7c8c92 - 7b9fafe32c86 - - 3bcd5445cd7a - - ab55fe8030b6 + - 146ae5d70b47 + - d844935c906c 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 + - dbbe1ea8ecb1 - f7446fd8d5e7 - aa0c474463c2 - - 95777145cb92 - 62acdd96d4a0 - - dbbe1ea8ecb1 - - 6f5349dd5c49 + - 1072ce66b426 + - 95777145cb92 - 40812a65a78b - - 0185bd174ea0 - 9b0cdb8cf6be - - 6adf98e782f3 - - 1072ce66b426 + - 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: - - d18e7a6e5cd4 - - 9fb627495ec2 - - bf2017df9837 - - c5541bfb8feb + - a39040ae0a38 - 215733a383f2 - - f2f6c703da06 - - c65fce500915 + - 9fb627495ec2 - 73ab2ac53d06 - - a39040ae0a38 + - c5541bfb8feb - fe8f16c594ec + - f2f6c703da06 + - bf2017df9837 + - d18e7a6e5cd4 - 458e8f43a775 + - c65fce500915 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -777,8 +777,8 @@ tools: owner: iuc revisions: - b834074a9aff - - fd808de478b1 - 8f333f90d8d6 + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -790,9 +790,9 @@ tools: - name: scater_filter owner: iuc revisions: - - 652923ce664f - 7a365ec81b52 - b7ea9f09c02f + - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -830,9 +830,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - c99ba278dfa9 - 46fc6751d746 - 9e5c0bb18d08 + - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -1061,8 +1061,8 @@ tools: - name: sinto_fragments owner: iuc revisions: - - 29e6bfb2cf49 - 6f66f523a9b7 + - 29e6bfb2cf49 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image @@ -1074,15 +1074,15 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - 8f8bef61fd0b - d3ea0ba3d066 + - 8f8bef61fd0b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -1095,8 +1095,8 @@ tools: - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - c5c94e01a1b5 + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy @@ -1108,8 +1108,8 @@ 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/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index c0f823030..fddb0bd9a 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,11 +32,11 @@ tools: - name: datamash_ops owner: iuc revisions: - - 562f3c677828 + - 2f3c6f2dcf39 + - 4c07ddedc198 - 419027d822d6 - 746e8e4bf929 - - 4c07ddedc198 - - 2f3c6f2dcf39 + - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,29 +49,29 @@ 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 owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 7a15159140d1 - cb1c59d69557 + - 7a15159140d1 - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -121,19 +121,19 @@ tools: owner: bgruening revisions: - 7442b94d6a1e - - 9c3e1d3235c8 - - 4c4ec859c31a - 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: - - d0352e8b4c10 - 9fda0b82f419 - 30d21a6041f6 + - d0352e8b4c10 - 07843f917990 - 375bbd555f4a tool_panel_section_label: Statistics @@ -141,22 +141,22 @@ tools: - name: sklearn_nn_classifier owner: bgruening revisions: - - 7ae443e6217d - - 2c58b83c9bad - - 4cc980df6265 - 8b1b2b91f8d0 + - 2c58b83c9bad - cd02bf168d23 + - 4cc980df6265 + - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - e10e776f2109 + - bb9fc9d46ea4 - 4bbaf77573ef + - ad7e0b4291ee + - e10e776f2109 - 7dd3fb35904f - 1dd433d2c92c - - bb9fc9d46ea4 - - ad7e0b4291ee 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 b698c6044..0e7164428 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -34,15 +34,15 @@ tools: - name: column_maker owner: devteam revisions: - - 626658afe4cb - - 9cd341095afd - 02026300aa45 - - 6e8d94597139 - - 13b6f0007d9e + - 626658afe4cb - be25c075ed54 - - 6595517c2dd8 + - 9cd341095afd - 464b9305180e - aff5135563c6 + - 6595517c2dd8 + - 6e8d94597139 + - 13b6f0007d9e tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -80,10 +80,10 @@ tools: owner: iuc revisions: - 9cc411a62277 + - 37cde8134c6a - 90f657745fea - 557ec8d7087d - 34d29339abab - - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,22 +107,22 @@ 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: - - 3a6b78c39dca - - cf4397560712 - - 83069b38aa85 - - 33d61c89fb8d - 2e8f945f7285 + - 623f3eb7aa48 + - cf4397560712 + - 3a6b78c39dca - cf34c344508d + - 33d61c89fb8d - 1ea4e668bf73 - - 623f3eb7aa48 + - 83069b38aa85 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace @@ -142,8 +142,8 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - bce29ec10b78 - b722161a845a + - bce29ec10b78 - c4d18aa4ec4a - f768f6183386 tool_panel_section_label: Text Manipulation @@ -151,22 +151,22 @@ tools: - 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: - - d698c222f354 - - 74a8bef53a00 - - 86755160afbf - - fbf99087e067 + - 0a8c6b61f0f4 - ddf54b12c295 - - 9ff72e942410 + - 86755160afbf + - 74a8bef53a00 + - f46f0e4f75c4 - a6f147a050a2 + - 9ff72e942410 + - d698c222f354 + - fbf99087e067 - 12615d397df7 - - 0a8c6b61f0f4 - - 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 6c5a7a186..e76986af4 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -14,8 +14,8 @@ tools: - name: breseq owner: iuc revisions: - - 82fb5e3bb93e - 0d18a3ba2d1c + - 82fb5e3bb93e - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -28,40 +28,40 @@ 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: - - 3e954e7125bf - - 04fa42777df9 - - 57def2d7c093 - a5937157062f + - 3e954e7125bf - ef2c525bd8cd - 156b60c1530f + - 57def2d7c093 + - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 791f73caa0c8 - 09d6e4693887 - e61c9ac190ad - 435b157bed6d + - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - e1461b5c52a0 - dfadc322b065 - - 03627f24605f + - 4805fe3d8fda - b11e8e9c23bf + - e1461b5c52a0 - 3b4b2121842f - - 4805fe3d8fda + - 03627f24605f - 074d44697036 - 65432c3abf6c tool_panel_section_label: Variant Calling @@ -69,26 +69,26 @@ tools: - name: lofreq_filter owner: iuc revisions: - - 9cb929f21cfa - 7dfca164d2e3 - 701d134358ad + - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 971e07ca4456 - - c27549b9aa1f - - f4473557ffc7 - 426d707dfc47 + - f4473557ffc7 + - c27549b9aa1f + - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - aa35ee7f3ab2 - - cdaab621d454 - dbd9f2db9ed8 + - cdaab621d454 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -100,19 +100,19 @@ tools: - name: sniffles owner: iuc revisions: - - ceff2f6a5368 - - 93c4b04a0769 - 43fffeed243f + - 93c4b04a0769 + - ceff2f6a5368 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: + - d220115f882b + - c9a8ef2aa380 + - 5bbf9eada9c2 - 9bccc8404a3c - fa016f1eea1a - - 5bbf9eada9c2 - - c9a8ef2aa380 - - d220115f882b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -154,9 +154,9 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - 3b1e7c170b10 - ee4a90760848 - 40f0591deda0 - - 3b1e7c170b10 - 32f14a2723ec - e7aff4a85df5 tool_panel_section_label: Variant Calling @@ -165,10 +165,10 @@ tools: owner: iuc revisions: - 02d81b994ef5 - - 42818629ec4c + - 9793bc5d741b - adc0645b945c - 4934c0ac6197 - - 9793bc5d741b + - 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 f59c273e2..f3c594fbd 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: - - 95815a0bb307 - - 2c372041ed8c - - 6a88248893c4 - - 8a2e296c07ef - - e075b1be5abb - b7ea370b8f5d - ebe5fc018e72 + - 6a88248893c4 + - 95815a0bb307 - 265fe0f9ea64 + - 2c372041ed8c + - e075b1be5abb + - 8a2e296c07ef 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: - - c37b684e7f4e - 1001172b5089 - - 544cb432072b - - 21687e35f066 - 0fba2c15b40d - 22637b1a55bf + - 544cb432072b + - 21687e35f066 - b03984136ce4 + - c37b684e7f4e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,15 +39,15 @@ tools: - name: bcftools_cnv owner: iuc revisions: + - ccb83bf54de0 + - 01d6b7d6365e - bf1f4994f104 - 143796b504eb - - 01d6b7d6365e - - 0238f68ad641 - 3a7084316a6e - - 8ca3647c90fd - - ccb83bf54de0 - 8627b2b383b4 + - 8ca3647c90fd - 8408bffd5616 + - 0238f68ad641 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -60,13 +60,13 @@ tools: owner: iuc revisions: - 03e0645395d2 - - d144af39073a - - abd489215f73 - 81426b3cf18b + - abd489215f73 - 6b6c992d3a14 - - 9b5abbf50d23 - 62ca6da715bf + - 9b5abbf50d23 - f430a1ec7ee4 + - d144af39073a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - 8aa352093d73 + - 1171446da5db + - d3081540d175 + - d37e313a41be - 95c6f3f4c77f - 2363ef414c9b - - d37e313a41be - - 1829900b5dcd - e522022137f6 - - d3081540d175 - - 1171446da5db + - 8aa352093d73 + - 1829900b5dcd 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 - - 9b29129fb491 - 1137ce8efc1e - - 348cd212dbad - - 92c0aff8b53e - 012656fd329f + - 9b29129fb491 + - 348cd212dbad + - d58d2e8c7a57 - 09f37afb3621 + - 92c0aff8b53e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -117,12 +117,12 @@ tools: owner: iuc revisions: - ecc9192912b8 + - 7291189e98b4 - 55c0e906c14c - 367ba501b6eb + - de68c11034f6 - cfd81f17580b - 1f2183a23823 - - 7291189e98b4 - - de68c11034f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,13 +134,13 @@ tools: - name: bcftools_csq owner: iuc revisions: + - 039ea3f1dea9 - d237eaef451f - - 6c790a091c7c - 7cbf3c66d4ad - 64a8f7dae3ad - - 039ea3f1dea9 - - e6f4badbe6f3 - ae68ceb4cca3 + - 6c790a091c7c + - e6f4badbe6f3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -153,13 +153,13 @@ tools: owner: iuc revisions: - 6ea7170a016d - - cdb7b4927742 - - 277719af4dd7 + - 33bd9301568c - 5d6653c989cb - - 46fcafba49ec - e7452697afd9 + - cdb7b4927742 + - 46fcafba49ec - 963a3635b2e1 - - 33bd9301568c + - 277719af4dd7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 91c1e57d5c7f - - a1213a0b7b66 - - a29a2f40b665 - 26d97cdd5410 - - b7f0f59baa7e - - 5a321fab1fe4 - 501bfb078342 + - a1213a0b7b66 + - b7f0f59baa7e + - 91c1e57d5c7f + - a29a2f40b665 - 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: - - 97d19c008d15 - - 81e4014fa809 - - 5f27e814a119 - 39bca000353d + - 5f27e814a119 - 709dd8291b83 - - d7d1663559e9 - - 15da1ddcfeff - - 768d04526638 - c803c34361e0 + - 768d04526638 + - 15da1ddcfeff + - 81e4014fa809 + - d7d1663559e9 + - 97d19c008d15 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -211,13 +211,13 @@ tools: owner: iuc revisions: - 7ba36babba2d - - 85ee7e6c4204 - - 5b006286a458 - 86296490704e - b84fda8ebef0 - - 2215287d5cc9 - - b931e65638b8 - b1eba148b35b + - b931e65638b8 + - 5b006286a458 + - 2215287d5cc9 + - 85ee7e6c4204 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -229,15 +229,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 31ea13dfe5e6 + - 56556e1267de + - 0a5dcc9a8ec2 - f506df85c652 + - 37757ffb4c5f + - 5660b21a0dbd + - 31ea13dfe5e6 - 9c711df3258d - - ce9396ddcb2b - cf06b44624c7 - - 0a5dcc9a8ec2 - - 56556e1267de - - 5660b21a0dbd - - 37757ffb4c5f + - ce9396ddcb2b - 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: - - 021693fdadaa - - 48291658fdf6 - - 1ca7418e46ee - - 19905c025d2a - 6deb4d549bc9 - - a404f786a94c + - 19905c025d2a - 271965b55437 + - a404f786a94c + - 1ca7418e46ee + - 48291658fdf6 + - 021693fdadaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: + - 97e8145d7e30 - f7879f1e77f9 - 3f6fadf8b8ff - - 69d8b7567281 + - dadbd61dc4cf - 71c78e0eea52 - - 97e8145d7e30 - c450406f722b - - dadbd61dc4cf - 5ad5d4243987 + - 69d8b7567281 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,14 +287,14 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 2514e684f8a3 - - 283911fe7e1a - - 52f9e4a660e3 - 79f7a1acc2cd - - cc7f9a4e186b - 6cf13a657cf6 - - 0fe007201caf + - 283911fe7e1a + - 52f9e4a660e3 - d31a2e310a52 + - 0fe007201caf + - cc7f9a4e186b + - 2514e684f8a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,13 +306,13 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: + - 0a62420cb9cd - 75ddd081f608 - - 230e424bde67 - 6963a6841d22 - 80e6e399ccd0 - - 0a62420cb9cd - a12844ca467a - 1411bef27a75 + - 230e424bde67 - 026a989b7cee tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - bca7ce81688f - e493702b19eb - - 5acfca5a76af - b10d1510fa84 - 5808f77b2bb6 - 450a265f92e8 - - 444e6a756c35 + - bca7ce81688f - ba20340426fe + - 444e6a756c35 + - 5acfca5a76af 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 + - d52b8947b269 - c43399f161f4 - - dd72ff87cfd0 - - 68fec03a63b7 - f2482aa4862e - - d52b8947b269 - 157ffcdd3fa7 + - dd72ff87cfd0 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: - - 0e5d11004815 - - cbe39e530cbf + - 29ba253e2e05 - 8dbce095986c - - 75becf493cd3 - 6f8e223f78f3 - - 29ba253e2e05 + - 75becf493cd3 + - 0e5d11004815 - 8f2fc0ab30fb + - cbe39e530cbf 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 - - a8630d4fbaf8 - 3ff5654b4e7d - - e0a856def0b0 - - f544f71adb73 - - 9708e3086f32 - 88bb477f45f7 + - a8630d4fbaf8 - a367a15c6de5 + - e0a856def0b0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -400,14 +400,14 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 6ce175385dd9 - - 34dc0bbc7e93 - 96d0145c041a - - 03e30f06f15f - - 4ed46189d6c6 + - 6ce175385dd9 - 31c096c6b156 - 5c9729d54721 - 8b260d252ff4 + - 4ed46189d6c6 + - 34dc0bbc7e93 + - 03e30f06f15f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -419,14 +419,14 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: + - a1aad8b559c6 - a730269af659 + - 11af7fce71cf + - 40daf124be88 + - 09f5e45a8212 - 46eb13bc2c73 - 2c4941386820 - 681bdf1e22ff - - a1aad8b559c6 - - 40daf124be88 - - 11af7fce71cf - - 09f5e45a8212 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 - - b74b8cbfc1f1 - - 743cd1472aeb - 8cb121b6a1d2 - - 0594ea1417c8 - - 12038f59c0f4 + - 743cd1472aeb - f272b8ba0983 + - b74b8cbfc1f1 - 3897eaadfbff - 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: - - adee7e8b746f - a9826db86d9a - dba06328556a - - 238f78e38a8b - eccb508bb678 - - cced6715f926 + - adee7e8b746f + - 238f78e38a8b - 18cf9de1cf73 + - cced6715f926 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -477,12 +477,12 @@ tools: owner: iuc revisions: - f64e7ca2efd2 - - e0ad88dec40d - - e53501abf992 - - 3ce32adc55b2 - - 31a1b89eab9b - fdec14f69010 - 9f36041495a3 + - e53501abf992 + - 31a1b89eab9b + - e0ad88dec40d + - 3ce32adc55b2 - c9935c9e8a24 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - 2331ddcbd5aa + - 4db0695a6fc7 + - 79489d5685dd + - fd3539749127 - 3b7b1fe7b937 - - d68c43202172 - d43eb39b989e - - fd3539749127 - b7be725976b6 - - 79489d5685dd - - 4db0695a6fc7 + - d68c43202172 + - 2331ddcbd5aa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,13 +514,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 6a636d58dfc2 + - b0d39ef600a7 - 1a989b4110da - - 5296d26b0373 - 78cd8b69da4c + - 5296d26b0373 - 58091e1be01b - 1ccf0e7fb4f6 - - b0d39ef600a7 + - 6a636d58dfc2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: - - e8af591435d1 - - b641062a2587 - - b17394940c7a - - baa8823f8073 - - 591cc8518033 - '388983871932' + - 591cc8518033 + - baa8823f8073 - 4d3ce9dc1525 - bf8325a07ce7 + - b17394940c7a + - e8af591435d1 + - b641062a2587 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -552,13 +552,13 @@ tools: owner: iuc revisions: - c2ab91a0d506 - - 3a233c8eb814 - - 38d75661c235 - e6b5cbbf449b + - 3a233c8eb814 + - 3ca3de4e5291 - 59fa8742285e + - 38d75661c235 - 1a2ef636f48e - d1f8f55f564d - - 3ca3de4e5291 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -591,15 +591,15 @@ tools: - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes owner: devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -619,8 +619,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -633,8 +633,8 @@ tools: - name: vcfcommonsamples owner: devteam revisions: - - 254f285dbaaa - f1852ecef841 + - 254f285dbaaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance @@ -647,16 +647,16 @@ tools: - name: vcffilter owner: devteam revisions: + - eae7c08ebb6f - 4bdc111b2470 - 6b935ab36d7b - - eae7c08ebb6f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -718,8 +718,8 @@ tools: - name: vcfsort owner: devteam revisions: - - ee60203e68d9 - 5b7120c66efc + - ee60203e68d9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index a1de80b39..1bed75e74 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: + - 6e9aea89e388 + - 78c75f134c16 - 3f3e247c053d - c2ef298da409 - - 78c75f134c16 - 4efdca267d51 - - 6e9aea89e388 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 @@ -33,30 +33,30 @@ tools: - name: aegean_parseval owner: iuc revisions: - - d6c074a93c51 - 1b52f0c8ad7f + - d6c074a93c51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - 133f36c29579 - - 1aae04680c4b - - 44018dd6b447 - - b5d8e5475247 - - a79ee60b6926 - cd2480f35935 + - fe3ca740a485 - 4f2967b27e67 - - f29602ae449e + - b5d8e5475247 + - a79ee60b6926 + - 133f36c29579 + - 44018dd6b447 + - 1aae04680c4b - 3e1f6f6d557e - - fe3ca740a485 + - f29602ae449e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training @@ -72,27 +72,27 @@ tools: - name: augustus owner: bgruening revisions: - - 0fc0f9cf035a - - bd0e53f3a891 - 09855551d713 - - 28433faa6e42 + - bd0e53f3a891 - ca6d970d931c + - 0fc0f9cf035a + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - d77802fe76f7 - - da5f1924bb2e - 728dacaf08a9 + - d77802fe76f7 - 92eee5f31117 + - da5f1924bb2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - 8fd427007e93 + - 7355bbf5e05f - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -118,16 +118,16 @@ tools: - name: cpat owner: bgruening revisions: - - 7ccc6234b54e - - 8e9e228c54c4 - 1ac12c0cc7a0 + - 8e9e228c54c4 + - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf - 63662ae295d6 + - 9d1fbff733cf - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -158,61 +158,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - b6b5cd37f2a2 - - 9c15ca7e764e - - 3bbe70fef6df - 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: - - 989f7c061f35 - - 8e1ace8f77c6 - - a230ea445788 - - 73428a792541 - 30fb23d4c31c - - 0ffe5be70caf + - 73428a792541 + - a230ea445788 - 1691af4a0d17 + - 8e1ace8f77c6 + - 0ffe5be70caf + - 989f7c061f35 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 563a19373357 - 30f08d74024f - - 5a5ae61da69c - - 494f0bb4a993 - - 0418d28136de + - 563a19373357 - e94187d661df + - 0418d28136de - 57c6718cbfcc + - 494f0bb4a993 + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f77d7b685bb3 - - d6c7106b7b2e - 2bba2ff070d9 - - 4b96ced19f75 - - 1bc5a03faf2e - 7abc5f6dd595 + - f77d7b685bb3 + - 4b96ced19f75 - f31125bb85ea + - d6c7106b7b2e + - 1bc5a03faf2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - d77fdcca400e + - 54961e026fe4 + - b3cf4684e9c7 - fed64e676186 - - 520e30695ec3 + - d77fdcca400e - 52af33194019 - d3af38b9c7e1 - - b3cf4684e9c7 - - 54961e026fe4 + - 520e30695ec3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -240,8 +240,8 @@ tools: revisions: - 602de62d995b - 43798b4caee0 - - ef2ad746b589 - 8b3e3657034e + - ef2ad746b589 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 - - 98cafcbd2578 - c55643c3d813 + - 98cafcbd2578 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -300,18 +300,18 @@ tools: owner: iuc revisions: - 3c1a01127868 - - d46d803ca6cc - 370c210d9541 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - c8ac28e8ac44 - - b815ec682418 - 624606f7c996 - - 033755194fe9 - e95d52d295d7 + - 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: - - d643e3b03500 - bf68eb663bc3 - - a17498c603ec - 8a22554cdde2 + - a17498c603ec + - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -381,8 +381,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -406,23 +406,23 @@ tools: - name: snpeff owner: iuc revisions: - - 68693743661e + - 268d162b9c49 - 8f92c2b26e6d - 5b80f544c67f - - 5c7b70713fb5 - - 268d162b9c49 - c7275bd8b4d6 - - cfcf33df7fc0 - 6322be79bd8e + - cfcf33df7fc0 + - 68693743661e + - 5c7b70713fb5 - 5a29ab10dba6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - 5fab4f81391d - 09d6806c609e + - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna @@ -441,25 +441,25 @@ tools: - name: tbprofiler owner: iuc revisions: + - ac8250086ac3 + - 037a11682176 - e1a9d6fd258d - - 51dd22484644 + - 200c378d85f3 + - 45083d070fb8 + - d03af1c7002c - 4839e590cb26 - - 037a11682176 - - ac8250086ac3 + - 8cb134b8c1a5 + - ba6f87115e13 - 37213cf56392 - 809dfc93d593 - - ba6f87115e13 - - 45083d070fb8 - - 8cb134b8c1a5 - - d03af1c7002c - - 200c378d85f3 + - 51dd22484644 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/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 5bb78423f..19340ed67 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,28 +2,28 @@ tools: - name: abyss owner: iuc revisions: - - 890b794c997d - - 841084c5fc46 - - 8f1b150a2487 - - 0e93176640ac - - 553bfe8bd0b5 - - a929ce596a34 + - d6d5ccc2c581 - 0124fce4654a + - 841084c5fc46 + - 890b794c997d + - 7547fcab5d19 - db9b10824c61 + - a929ce596a34 - fa5259cc561b - - d6d5ccc2c581 - - 7547fcab5d19 + - 0e93176640ac + - 553bfe8bd0b5 + - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 21e491ad532a + - b9e31c5c01c7 - b2860df42e16 - - ddddce450736 - 067592b6b312 + - 21e491ad532a + - ddddce450736 - 94fe43e75ddc - - b9e31c5c01c7 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: - - 5258e18bbe23 - - 3371c5bdc17a - - faee8629b460 - - a7f16f24e9a1 - 22286dab5aa1 + - a7f16f24e9a1 + - faee8629b460 + - 3371c5bdc17a + - 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: - - 1e62c28ba91d + - e4bd1e99bacf - 2babe6d5c561 - - 94170eee0ad8 - - 2dd755c1c6ff - - bb935709506a - 1440ae06552f - - ea8146ee148f - - cf13a1e03e5b - e824f5d958d0 - - e4bd1e99bacf + - bb935709506a + - 2dd755c1c6ff + - 94170eee0ad8 + - cf13a1e03e5b - 602fb8e63aa7 - - 41030a6c03b7 - - 46ae58b1d792 + - ea8146ee148f - e5c372c91e46 + - 46ae58b1d792 - 4048d82f0c88 - - 5ecdeca79a0d + - 1e62c28ba91d - 0d243f458b53 + - 5ecdeca79a0d + - 41030a6c03b7 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 @@ -89,46 +89,46 @@ tools: - name: flye owner: bgruening revisions: + - 276f5d8712d5 - 1ce9b1d72ec3 - - cd11366d92cf - - e27815e82dd4 - 1f0769f0b56b - - 276f5d8712d5 - 8d4f03b5fe9d - 3ee0ef312022 - - 3e4f8642c77e - cb8dfd28c16f + - 3e4f8642c77e - 291923e6f276 + - e27815e82dd4 + - cd11366d92cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - 01210c4e9144 - - 460fad600dce - b2f674562a18 + - 3169a38c2656 + - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - - 7348b69e5109 - ba88bc5a6446 + - 06bcf65179fb - 8b330a577046 + - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - f4a3eff8ab85 - - 6ec1b853c8fd - - 3ef480892a9f - 5127a713de83 - - 690c2caa367e + - 6ec1b853c8fd - 3fba9c77550a + - 690c2caa367e - 764f2516d837 + - 3ef480892a9f + - f4a3eff8ab85 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: - - 366a11d316a7 - - 5bec28269d95 - - 2061fb3b81b4 - - 3f7be05a1597 - - da9d8bf98802 + - 5161f204ba63 + - 9ef6920c3089 - ec9e21e9c71b - - 71740308d412 - 60024a528cbd - - 045c7c3d8e59 + - f3c89da3af16 + - 3f7be05a1597 + - 2061fb3b81b4 - 41cea2aa2dce - - 0ee0c3089254 - - 284a1cb82b61 + - 366a11d316a7 + - 71740308d412 + - da9d8bf98802 - 5f625c63b8bc - - f3c89da3af16 - 6505bd37670d - df25d4fb79b7 - - 9ef6920c3089 - - 5161f204ba63 + - 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: - - eb7b00ec347d - - 39edec572bae - - 9d79beb19ac3 - - f8113c25bc6b - 09c589057ee8 + - 9d79beb19ac3 - d7edbc9c3a07 + - 39edec572bae + - eb7b00ec347d + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 29dabd8db6f2 - - 51c2360aa807 - eadfd71dde37 + - 51c2360aa807 + - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - fd128c111ab0 - 99ecfdafc64f - - 2ecf5a570907 - eb7a370f6588 - - 606b09cc9860 - e731ea24e48d - - f369ef5f210b - - 3ca2d2a9068c - - fd128c111ab0 - f338e9942b27 + - 3ca2d2a9068c + - f369ef5f210b + - 2ecf5a570907 + - 606b09cc9860 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 - b799a615995d - 8b6d0d85252b - - 73a3846701e1 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 - - 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: - - dfb8a4497339 + - bbe19ef04a74 - 02831bf9e95f - - 2b16ba799da9 + - dfb8a4497339 - 8fef980d48b5 - - c6cec5ab35c1 - - bbe19ef04a74 - d256a51a656b + - 2b16ba799da9 + - c6cec5ab35c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - a315c25dc813 - 76d4cbefff85 + - a315c25dc813 - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 675488238c96 - - ebb0dcdb621a - - 3061c8b029e5 - - 342a1d1fed7b - - 72472698a2df - 6fcbee531de6 - - 875d0f36d66f - 7594365c546b + - 675488238c96 + - 72472698a2df - 59db8ea8c845 + - 342a1d1fed7b + - ebb0dcdb621a + - 875d0f36d66f + - 3061c8b029e5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - - 78c533842eeb + - a199cd7ac344 - 39bed8de8017 - d865b62f501c - - a199cd7ac344 + - 78c533842eeb - aa39b19ca11e + - cd06929b224b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -317,30 +317,30 @@ tools: owner: iuc revisions: - f8564b2d7f63 - - f11b994b7eb2 - - 2b2a352488fa - 3edba9afc9bc - - 33b7d8481a76 - 5c55448d0f33 + - 2b2a352488fa + - 33b7d8481a76 + - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - 8e66f695d859 - f73ab5187eed + - 8e66f695d859 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - e122f9101584 + - 378e55aeeb25 + - ef69617ecb42 - 5fc94b3a4704 - 53c2bc8c2ae3 - - 28189050e437 - - ef69617ecb42 - 1d06c8b38e77 - - e122f9101584 - - 378e55aeeb25 + - 28189050e437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -352,158 +352,158 @@ tools: - name: shovill owner: iuc revisions: - - ee17a294d3a3 - - d9f6a00b6db7 - - 196a599ec43d - - ad80238462c1 - 865119fcb694 - - f698c7604b3b - 83ead2be47b2 + - ad80238462c1 + - 196a599ec43d + - d9f6a00b6db7 + - f698c7604b3b + - ee17a294d3a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 015283de3004 - 24e471d13fe9 - 5e0825476fb7 + - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 7490b213baa9 + - 051fd2db8a27 + - 904bf932cf78 - c33a476f4001 - - 1fc82fe7ebef - 604782a8a53a - 1bb12736175c - - 051fd2db8a27 - - 904bf932cf78 + - 1fc82fe7ebef + - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 9678993ca5bd - - 808b3a0a6716 - - 655fa188c3cc + - d6e617c4e338 - ad8b536d1caa + - 9678993ca5bd - fee85957cebe - - d6e617c4e338 + - 655fa188c3cc - 34305b013402 + - 808b3a0a6716 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: + - 6b5a5842531e - e5a3b75a271f - - 037f9927c4ff - 21da31ed41a1 - b8002c3f7141 - - 8d4b90bf9caf - 7e27faaad80e - - 6b5a5842531e + - 037f9927c4ff + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 7922870efcca - - 328aa71f0f3c - - 9de69775f512 - - 2a10645aeadd - 86f66ab58e14 - - f1532cb33c75 + - 9de69775f512 + - 328aa71f0f3c + - 7922870efcca - 5b26685e5d3b + - f1532cb33c75 + - 2a10645aeadd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 6aad515a5270 - - e41dcb0e913b - - 340bc17f49cf - 8cc856b935ee - 85fb02c43042 + - 340bc17f49cf + - 6aad515a5270 + - e41dcb0e913b - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - de1260f8a300 - - b65a43f70b99 - - b3490b036c5a - d159735a6a9f - 249f6a28c751 - d5fb354f745d + - b65a43f70b99 + - b3490b036c5a + - de1260f8a300 - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 9006e5836729 - - b7829778729f - - dd7ad84f3943 - d5887ace0dd4 - - d2d1df21dfb9 + - dd7ad84f3943 - a90db5dbaaf3 - - 7897763d14ec - 33368fec3b70 + - 7897763d14ec + - b7829778729f + - 9006e5836729 + - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - ced385aa976d - - 0368ac680e70 + - 8f631679571f - 505a9833ab5d - - 189e837009c9 - 6f4c8ad6ea01 - - 8f631679571f + - 0368ac680e70 + - 189e837009c9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: + - e59bee4565b3 + - 19bdfd1e6fe3 - a7ed21de23fe - d40ed4eb0c0e - - 9ded6109434a - 356afed970b4 - - e59bee4565b3 - - 19bdfd1e6fe3 + - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - b23249f81bc4 - 4688ae3b49b5 + - b23249f81bc4 - 6dd935e4984b - - 80a17897564d - - 7673a6c920b2 - ebd801e712bc + - 7673a6c920b2 + - 80a17897564d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - ed312479d9eb - 937ea677d437 - - cb1e3db43020 - b5e35a2ca4f3 - 59bd28f6265d - b64696992ee9 + - cb1e3db43020 + - ed312479d9eb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - 6015aa0303f2 - - cb4768eeca3b - - b9b0246a2be3 - 383bb5ad32e2 + - b9b0246a2be3 + - cb4768eeca3b - 05bd7504fdb2 - 2628f6790eda tool_panel_section_label: Assembly @@ -511,30 +511,30 @@ tools: - name: unicycler owner: iuc revisions: + - 6e26c9afd301 + - 0a3a602cd1e3 + - e022dff952df + - 8f9f06995f98 - 3e44ef016b45 - 9e3e80cc4ad4 - - 8f9f06995f98 - e92675014ac9 - - e022dff952df - - 0a3a602cd1e3 - - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 8d09f8be269e - 08256557922f - 5da9a0e2fb2d - - 8d09f8be269e - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: + - 82398ba86ba7 - 37d88f41c810 - 4a53b89fa703 - - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko @@ -546,8 +546,8 @@ tools: - name: yahs owner: iuc revisions: - - ff4031bfaa22 - 425e63adcc5d - 39495e107274 + - ff4031bfaa22 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 0df238dfe..b8e74aa6f 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 - - 4768f7f8e93f - - 1ae00120dd24 - bfd290fe1588 + - 1ae00120dd24 + - 4768f7f8e93f + - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 + - ded48b36f3b7 - 1f5641a52664 - 31812e7a1315 - - ded48b36f3b7 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 17fcac7ddf54 - - 24a7a95867b0 - 5c8ff92e38a9 + - 24a7a95867b0 + - 17fcac7ddf54 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 357c56af0..a6ea10902 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,14 +2,14 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 7beb76ffbc0f - - d1f62024a08b - 159b04e36791 - a9c9d768b751 - - 0840ba83860c - d58c27d2c5a7 - - 204a131e47db + - 0840ba83860c - 1c427e24fb79 + - 7beb76ffbc0f + - 204a131e47db + - d1f62024a08b tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index 029115354..aad7eab53 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: + - 589e7e57fd6d - 0a5c785ac6db - - 64e2edfe7a2c - - 07e8b80f278c - a68aa6c1204a - - a8eabd2838f6 + - 64e2edfe7a2c + - b28e0cfa7ba1 - dde39ba9c031 - 87ee588b3d45 - - b28e0cfa7ba1 - - a1a923cd89e8 - - ce3c7f062223 + - 07e8b80f278c - e19bebe96cd2 - - 589e7e57fd6d + - ce3c7f062223 + - a8eabd2838f6 + - a1a923cd89e8 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 0c8745c8a..c73f29817 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,24 +8,24 @@ tools: - name: diamond owner: bgruening revisions: - - 54f751e413f4 - e8ac2b53f262 - - 62c9df8382c2 + - 54f751e413f4 - f921014aba5a + - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - 0e3cf9594bb7 - - acf4e47b734c - - 6f386c5dc4fb - - d999e774072a - - a52d2d93e595 - - e25d3acf6e68 - cbf3f518b668 + - e25d3acf6e68 + - 6f386c5dc4fb + - acf4e47b734c - 2889433c7ae1 - 5edc472ec434 + - d999e774072a + - a52d2d93e595 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 5386745de..73163f6eb 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 095ad4d096d1 - - c8cdde00b105 - 710301bc46fa - - 27ee142314a9 - f4230f116196 - 6ca543ec1bf8 - da6bd1975a71 + - 27ee142314a9 + - c8cdde00b105 + - 095ad4d096d1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -132,72 +132,72 @@ tools: revisions: - 88076940fa94 - bfb65cb551d8 - - 0fac8e2afc13 - 3b8a9d5ced85 - 79cfd9ead848 + - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - f5d979cb4b54 + - d532b7e5f64b + - eb6564a60136 - 715cd0e87781 + - f5d979cb4b54 - b46d4b4d995c - - eb6564a60136 - - d532b7e5f64b - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a - - 5579659312e6 - - fdf2cc80adb5 - dae135dfd519 - f26afd1b7104 + - d2f955aea23a + - fdf2cc80adb5 + - 5579659312e6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - 319a28774da9 - - bc31d02be922 - d1d0efda35c0 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 070e3ecc3fda - cac1886249a2 - - 2c349b027a01 - 4da9ee404eab + - 2c349b027a01 + - 070e3ecc3fda - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - 2e219a2d9327 + - f197e34c33a9 + - 73008ef1f487 - 807aa4c9293d + - 525ca7c8065f + - da8753545526 - d1f803b5943c - c0c9a5024177 - - 73008ef1f487 - - da8753545526 - - f197e34c33a9 - - 525ca7c8065f - - 2e219a2d9327 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - - 61094e01eff9 + - 27ea4e1a3f95 - 7568ae18908a - 2c8ed1b52bf7 + - 1809414a9454 + - 61094e01eff9 - c4fbab8e03c5 - - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: - - ba83f0923369 - - 79e8ab8f1e81 + - ccfbd956a2d3 - 730ef07b90ae + - ba83f0923369 - d7ec25187599 - - ccfbd956a2d3 + - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e6011617c748 - e2c36f62e22f - - b59c91adeac1 + - e6011617c748 - 4242b4d68e9c + - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -296,8 +296,8 @@ tools: - name: qcxms_neutral_run owner: recetox revisions: - - 8f465c0c3b6c - 33b7a99b6de3 + - 8f465c0c3b6c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_production_run @@ -351,10 +351,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - bf99565cec1f - - d4c67ced6abc - 85fad59f8168 + - d4c67ced6abc - 9b48456a96fe + - bf99565cec1f 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 3284e4115..c1639187e 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: - - fa56d93f7980 - - c97a786e8fb5 - 163688bb8f73 + - c97a786e8fb5 - 2605cbdaa7d8 + - fa56d93f7980 - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,11 +25,11 @@ tools: - name: macs2 owner: iuc revisions: - - 424aefbd7777 - - f5d67c722d67 - - 640d3af5d833 - 495a4173006f - 86e2413cf3f8 + - 424aefbd7777 + - 640d3af5d833 + - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator @@ -42,7 +42,7 @@ tools: - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index ab2722c81..161c19e92 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,8 +9,8 @@ tools: - name: collapse_collections owner: nml revisions: - - 25136a2b0cfe - 830961c48e42 + - 25136a2b0cfe - 90981f86000f - 33151a38533a tool_panel_section_label: Collection Operations @@ -33,8 +33,8 @@ tools: revisions: - 0046692724f9 - baabc30154cd - - 2dae863c8f42 - 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 75a117a1e..8db015a5b 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,9 +2,9 @@ tools: - name: agat owner: bgruening revisions: - - e7449b2c14bf - d6ede73082da - abba05ead5d7 + - e7449b2c14bf 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: - - ab9350a8ab4d - - 367b1ed91207 - 3b6f97e7094c - 4a6ee918c13a + - f3a19509108a - 6ef0b5664c69 + - 5e1240a87bcb + - ab9350a8ab4d + - 367b1ed91207 - a3b86937ead6 - - e3cbd2287f63 - - f3a19509108a - 0b3c3ad92827 - - 5e1240a87bcb + - e3cbd2287f63 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - d4d4e9febf5c - 33c99804a32f + - d4d4e9febf5c + - e177a8ea0bf1 + - 72ed72122deb + - e525f9ffb9ac - 54ccb7e1f49a + - 091bb5922a82 - 1b5fc03380d4 - - 72ed72122deb - 584008e574b2 - 501c21cce614 - - e525f9ffb9ac - - 091bb5922a82 - bd46669113b9 - - e177a8ea0bf1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -66,17 +66,17 @@ tools: - name: fastq_to_fasta owner: devteam revisions: + - 77b41c89d856 - 186b8d913e6c - 8979c288aefb - - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - - 4b347702c4aa - 43807a65369f + - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa @@ -95,9 +95,9 @@ tools: - name: gffread owner: devteam revisions: + - 4dea02886337 - 154d00cbbf2d - 3e436657dcd0 - - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -115,15 +115,15 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - f5c632894818 - 705821bf30d2 + - f5c632894818 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bam_to_cram owner: iuc revisions: - - b9ea85dfaf45 - 18dbde5680c0 + - b9ea85dfaf45 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -135,34 +135,34 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - - 2dcfbbf9071a - 78fb18899c99 + - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - 26c6706bfb07 - - 92ac8e086317 - 19e45916daf9 - - b9b385097f13 + - 92ac8e086317 - 63769c4217a7 + - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf owner: iuc revisions: - - a40dd4fd3096 - 3c19c84fbce2 + - a40dd4fd3096 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_twobittofa owner: iuc revisions: + - 8067dfa00ed2 - 3c6f9e8a4c17 - e9bbe2f71784 - - 8067dfa00ed2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 55af7acd2..9d30d193a 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,23 +2,23 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 29451af70c52 - de72ba3ed6f2 - c929a006727f + - e821645ef8fc - 5f6d123679f4 - 268e91e540ee - - e821645ef8fc + - 29451af70c52 - a1ca9bccc7f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - bb1e4f63e0e6 - 5d11599b8a7d - - 0e143b4c3987 - - 12af64f93288 - 2d2cf5c1ea8a + - 12af64f93288 + - 0e143b4c3987 + - bb1e4f63e0e6 - 7a7fd0f5f15d - 0e49b109abc2 tool_panel_section_label: DeepTools @@ -26,24 +26,24 @@ tools: - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 195e98217334 - c06951d10364 - 1d848bc4585f + - 195e98217334 + - dc059492a995 - 7c1beb6d6eca - 81b1e3e1fc6c - - dc059492a995 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 07418a30ed01 - - bfff7454b59a - - 26e7304d6737 - 93eb012d9eed + - 71aa86af6762 - a67ac707496a + - bfff7454b59a + - 26e7304d6737 + - 07418a30ed01 - 3d211717a775 - - 71aa86af6762 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 - - 2bc10a9ca58b - - dd0b7398bb96 + - 29fcfd36e90a - 26983857c91a - 5be24eba848d - - 29fcfd36e90a + - 2bc10a9ca58b + - dd0b7398bb96 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7e6bcd2e5128 - - ee3a1b0f45f1 - 9384cd033f30 - - c3e012dfe21f - 72bfafe3330b - - e6d0bff01239 - 7ef978dc1b8a + - e6d0bff01239 + - 7e6bcd2e5128 + - ee3a1b0f45f1 + - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - b73e213add0c - - 9470f29702f8 - - fd1275e01605 - 514fa53b5efb + - 9470f29702f8 + - a60c359ec43c - d9a637e83828 - fb9cf9c97ec4 - - a60c359ec43c + - b73e213add0c - 167788df3b46 + - fd1275e01605 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - e479c7ca5570 - - ca0616bb2cdf - - c34d11ea4ba6 - 86febdcc4283 - a02cfa31e9cb - - 2c37ce318bc3 - 5bffaa8354a1 + - e479c7ca5570 + - c34d11ea4ba6 + - ca0616bb2cdf + - 2c37ce318bc3 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 69a8621ca2f0 + - 78f405266706 - 192ef85c0b0b - - 004aea905d4d - - 01fb6a7654e6 - 2d466b530754 - - 78f405266706 - - 69a8621ca2f0 + - 01fb6a7654e6 - 1fcb7adc39b8 + - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - d9ce4897dbb2 - - 2f9e4843f480 - - 3c9f0c486cca - - 9ecba5e225a6 - 137c4beed34b - - d580d6acd1df + - 2f9e4843f480 + - d9ce4897dbb2 - 459cfa861f0b - db940c262830 + - 9ecba5e225a6 + - d580d6acd1df + - 3c9f0c486cca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - bd7db9e2f2cb + - 32e451def88c + - 2c66e43f1c86 - f264afa9fa6f - - fbe773640707 - - bad3ca889618 + - bd7db9e2f2cb - fd408d755394 - - 2c66e43f1c86 - - 32e451def88c + - bad3ca889618 + - fbe773640707 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 4e12ea27f788 - - 7fda5607e777 - - 3b9d990a0a0e - - 56bce3c82278 - 7e361d147872 - 231994413f89 + - 56bce3c82278 + - 3b9d990a0a0e - 9368fbc49c8b + - 4e12ea27f788 + - 7fda5607e777 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: + - ce4ce3316f74 - 4431f39ede55 - - b1779366c8e9 + - e65d16fb2724 + - d9114ef1c8a5 - 94ca68515826 + - b1779366c8e9 - c03c3384cd81 - - d9114ef1c8a5 - - ce4ce3316f74 - - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 793665fff0f8 - - b88ebb3672a1 - - 4ed32329e0ed - 23f7c5f1fdaf + - b88ebb3672a1 - 2da482e408b8 - f8fc4e5aff9d + - 793665fff0f8 - d57251071381 + - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 010e58e9d822 - - a4dfb122e52b - - 25d830337d31 - e4c7985d4585 - - a7849312d328 + - 25d830337d31 + - ba6efa77fb79 - c60570fa602f - 512155688d98 - - ba6efa77fb79 + - a4dfb122e52b + - a7849312d328 + - 010e58e9d822 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 38e3f226248b - - 443d9a9d6d11 - - c899e0ccff8c - 69264da0ce77 - aa200e4f3939 + - 443d9a9d6d11 + - 38e3f226248b - 4d678170d29b - 00d869ea03a1 + - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - - c361b12d207a - - 6662b1a8d326 - 10301d137111 - d806504e96d9 - a2d70c4fd406 + - aac8444d6681 + - c361b12d207a + - 6662b1a8d326 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 5b3a11614..e21626217 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -44,22 +44,22 @@ tools: - name: obi_sort owner: iuc revisions: - - 12b9e285ca1c - b6d9ea2fb41b + - 12b9e285ca1c tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: iuc revisions: - - 3299c7d5268f - 4cf47c504672 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 8f17492a3..208286509 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - cf1322aeb137 + - 6da3972210ee - 29bdbc353f20 - 62f5fab76dfb - d82648ad25a3 - - 6da3972210ee 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: - - d6787bab7b11 - 183cb55b1729 + - d6787bab7b11 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 2ffe63bbc..5c36150ee 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 49370cb85f0f - - 44e2cc14f75b - - e4691e1589d3 - - fe74900d6dc7 - - de6cebe3c043 - - 288f97432497 - - b1c926deaa2d - 5915ea1ec9b1 + - c4b82dce8335 + - de6cebe3c043 + - 49370cb85f0f - 48f587c13075 - - 8c0175e03cee - 8665bcc8b847 - - 64172f1c1202 - - 135b80fb1ac2 - - 5eb7e84243f2 - - 4e5056fefd88 - - 660cffd8d92a - c053d4cad713 - - c4b82dce8335 + - 44e2cc14f75b + - 660cffd8d92a + - 4e5056fefd88 + - b1c926deaa2d - c5e2e5902201 + - 288f97432497 + - 5eb7e84243f2 + - 64172f1c1202 + - fe74900d6dc7 + - e4691e1589d3 - 093678460093 + - 8c0175e03cee + - 135b80fb1ac2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: falco @@ -40,16 +40,16 @@ tools: owner: devteam revisions: - 8889eb864cef - - f666895cbebd - 9db07fd39f85 + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - - de2db1bdfbf8 - 5cbde03c1103 + - de2db1bdfbf8 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -67,8 +67,8 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 9457a20156db - 516b97a23d7e + - 9457a20156db - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -82,71 +82,71 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f81d4362b6c1 - f773e98b26cf - ec0b5076173a + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - 0dbb995c7d35 - - cd0874854f51 - 56022eb50bbd - 9c620a950d3a + - 0dbb995c7d35 + - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: + - dbfc505896e9 + - 1d8fe9bc4cb0 - a626e8c0e1ba + - d60c3f704da0 - dbf9c561ef29 - - ecb9f4854617 - - dbfc505896e9 - c59d48774d03 - 65b93b623c77 - - d60c3f704da0 - - 1d8fe9bc4cb0 + - ecb9f4854617 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - 9115b978ce10 + - b05e39b9c170 - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - '144275714590' - 81a9090d6df3 + - '144275714590' - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - - e9f8633db0a2 - 8611b80a14d6 + - e9f8633db0a2 - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - - e30352e889fe - - 5b87038565bb - 7861f3b10c68 + - 5b87038565bb + - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: + - 9282652e7234 - 4e1d64e6385f - 9dfda4e310ed - - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -160,17 +160,17 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 2ccb8dcabddc - - b41c2c1bcfbf - 3e396e702cea + - b41c2c1bcfbf + - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - c885369b207b - 8d958759cf2a - 09a2199cd356 + - c885369b207b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -186,72 +186,72 @@ tools: owner: devteam revisions: - 74db4cffab1f - - 045f0e1043f7 - 54053ea6c77e + - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - b1cea1b2fcd0 - - f0e7deab6518 - f86c27295151 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: + - f0b18efb97f1 - 33794bdb7fe0 - b63b2bfb3ea3 - - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 529bccd5e4a1 - 09070cacefd8 - - d5e9e83cd3d8 + - 529bccd5e4a1 - 567d5b3c52b1 + - d5e9e83cd3d8 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 - - bdf1ce174e39 - 736b8f6ee456 - - cb1e251cac37 + - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - 7ce1891db6f5 - - 421f0af4ee95 - 07497255281e + - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 - 02f8a17a4ebd + - b29d37ca9e41 - 3599f5451ee2 - f984bb114520 tool_panel_section_label: FASTA/FASTQ @@ -268,10 +268,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 547e8d00f11c - - 377ac2829eac - 73194cdd4f57 - 61b4cedc8934 + - 377ac2829eac + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -284,66 +284,66 @@ tools: owner: iuc revisions: - 037f0acc7830 + - f69501361cec - b4c6f054210a - 2f804526f5fd - - f69501361cec tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: - - 61eb4cfc7313 - - fdc21382376d - 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: - - 4b494533146a - - a019807f4e67 - 3da72230c066 + - a019807f4e67 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - d3f58a0dc09d - bf04bd405d5b + - d3f58a0dc09d - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f + - b557acca0b56 - 8250ea3a1501 - 71ad4a56c40c - a535cf1e5da4 - - b557acca0b56 - e654095ab143 + - 24013bf85a6f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -357,13 +357,13 @@ tools: owner: iuc revisions: - 6a675c3aa610 - - 27ac32a22ad2 - - 828dba98cdb4 - - 7a7e33d28f62 - - f3759eec3018 - 9fa7803d1c51 + - 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 2ad5d1b28..35dd35987 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: - - ce9cd02d5b88 - 64e9a6afdd0c - 7b4468117008 + - ce9cd02d5b88 - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - 3d0c7bdf12f5 - ff9530579d1f + - e7b2202befea + - 5ec9f6bceaee + - 3d0c7bdf12f5 - 9da02be9c6cc + - 2b0c9d9fc6ca - f2e8552cf1d0 - - 5ec9f6bceaee - - e7b2202befea - 2c64fded1286 - - 2b0c9d9fc6ca tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - 89d299153577 - - c1a33f603da2 - a252d8415583 + - 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 - 59003d0543cd - - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - a72af9de6bf5 - - 8880fb74ef56 - 1f296803dfa3 + - 8880fb74ef56 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 9a913cdee30e - - bf675f34b056 - - b2f1f75d49c4 - - 1c2db0054039 - 75c93c70d094 + - f7e2f1eb3a16 + - 9a913cdee30e + - 5e33b465d8d5 - 3d93dd18d9f8 - - abfd8a6544d7 - c1a4b5f3b432 - - 5e33b465d8d5 - - f7e2f1eb3a16 + - b2f1f75d49c4 + - abfd8a6544d7 + - 1c2db0054039 + - bf675f34b056 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - - cd7e644cae1d - 949f01671246 + - cd7e644cae1d + - 084bbd8ba7b8 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 08819c5b5..b329fac45 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -16,8 +16,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: + - 85ef5f5a0562 - 141612f8c3e3 - 83a19df00eab - - 85ef5f5a0562 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index c660c1f58..e121c021a 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -16,16 +16,16 @@ tools: - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - 0c8f7322f8fc - 8f53b238a360 + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,8 +59,8 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -79,16 +79,16 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 2550239feed5 - 184aa4e686e2 + - 2550239feed5 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - 45296e47d565 - - cf61daf064fe - b2c25142267e + - cf61daf064fe + - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,22 +108,22 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - 666f60a9331a - da74170c55c7 + - 666f60a9331a - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -144,8 +144,8 @@ tools: - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -158,8 +158,8 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 83b9cd11e..ba4164156 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,8 +2,8 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea @@ -23,14 +23,14 @@ tools: - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 47767fead..65bae993e 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - c1b437242fee - - b39347891609 - 983bf725dfc2 - e9df53a75f3c + - c1b437242fee + - b39347891609 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: - - e063168e0a81 - - 28587613264f - 1c58de56d587 + - 28587613264f + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - 653e89d73fc4 - - 5e6237d58b0c - - c441583adae5 - - 69ebb7f46e45 - - 1ec814014652 - - 4317d3cb6cba - - f8054ea1c365 - - 8848455c0270 + - 6591f049cf7e - aad3885b3216 - 9a776b080193 - - 516a54ddf218 + - e08a7ad4378b + - 1ec814014652 + - 4317d3cb6cba - e407b9da183a - - 734abc7ac21d - - 4df8de2d0e48 - - 1790dcf3c32d - - 7068f48d0ef9 + - 83c7d564b128 - ba931a59dd59 - - 6591f049cf7e + - 5e6237d58b0c + - 69ebb7f46e45 - 6ea73833cf67 - - e08a7ad4378b + - f8054ea1c365 + - 7068f48d0ef9 + - 4df8de2d0e48 - f5ea3ce9b9b0 - - 83c7d564b128 + - 1790dcf3c32d + - 8848455c0270 + - c441583adae5 + - 734abc7ac21d + - 516a54ddf218 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 - 21a560af5913 - - 34758ab8aaa4 - 75b3b3d0adbf + - 34758ab8aaa4 + - 9aaa46d45472 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 95fb5712344f - af5eccf83605 - - 054483e27a35 - 468c71dac78a - bfdc6a7ffd3a + - 054483e27a35 + - 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 aea0ba8c9..849cc3962 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: - - 740057a5126d - - df7356989ac1 + - c4bde687c846 - 7f13dc906cb9 - - a64dc31ab7f2 + - 290a11559985 - fd59d783248a - - c4bde687c846 - 4b519282a05b - - 290a11559985 - ae9994cf526f + - 740057a5126d + - a64dc31ab7f2 + - df7356989ac1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -29,8 +29,8 @@ tools: owner: devteam revisions: - 867ab348287d - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,23 +42,23 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - - '566197475670' - - 51c6ccaace7e - - 374e9062d874 - - 3b37b1b1c3a7 - 48b42ee61bc5 + - 3b37b1b1c3a7 - ca7cb0eaad62 + - '566197475670' + - 53460afd5115 + - 374e9062d874 + - 51c6ccaace7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 1a72f938213e - 391a4cc45fea - - d3a9e32672ec - - 3d059e9c2fba - 10515715c940 - - 1a72f938213e + - 3d059e9c2fba + - d3a9e32672ec - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -79,10 +79,10 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 5298e06f14f9 - e3a675da7fd0 - 1acf88921176 - 5fe1dc76176e + - 5298e06f14f9 - 299307abd804 - d0fc8b746d57 tool_panel_section_label: Graph/Display Data @@ -90,8 +90,8 @@ tools: - name: ggplot2_violin owner: iuc revisions: - - 0e7290688b50 - 17b666467c32 + - 0e7290688b50 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -129,17 +129,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 2bb2e07a7a21 - - a6e57ff585c0 + - 112eb40ba6cf - 17359b808b01 - - 667e17248bfe - - ca2def38369c + - 836d1aa3e89a + - fd5dbf0f732e - 4542035c1075 - - 112eb40ba6cf + - 2bb2e07a7a21 - 1cfc579079a6 - - 836d1aa3e89a + - a6e57ff585c0 + - ca2def38369c + - 667e17248bfe - 6cd09d7b5f37 - - fd5dbf0f732e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -158,31 +158,31 @@ tools: owner: iuc revisions: - 03c13085aecc - - fe154a7af404 - f1691de443a7 + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - 594b85e4237a - bd1416eea1f0 + - 594b85e4237a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plot_ragtag_paf owner: galaxy-australia revisions: - - c1bed78b9ed5 - 501dcf66c0ce + - c1bed78b9ed5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - f234e2e59d76 - - 1c5dcef5ce0f - - 85da91bbdbfb - 62e3a4e8c54c + - 85da91bbdbfb + - 1c5dcef5ce0f + - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -201,10 +201,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 + - 26f2fe7e53a1 - 6c571966cfb9 + - 44c66e8d21e6 - 7c9417381ad5 - - 26f2fe7e53a1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -216,24 +216,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 14e7c35f3d00 - 2824d77cd8f8 - 326a3db8d9d1 - - 360df4999907 - - 4ac4e7083b7e - a1abfa420d9d + - 14e7c35f3d00 + - 360df4999907 - 7dd841a32245 - 36b848d5f3ec + - 4ac4e7083b7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed + - 73b8cb5bddcd - 83c573f2e73c + - 44608d0193ed - 99ace6c1ff57 - - ab01e379d29e - - 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 98ebbbd3f..e5b212b1c 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -28,84 +28,84 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: - - bc9e8de21efb - - 6417cccad133 - 7779b9dcf040 - 22bd5861706d + - bc9e8de21efb + - 6417cccad133 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: - - e9283529cba1 - - bf1e0bdec1db - 55ccc0a121bc + - bf1e0bdec1db + - e9283529cba1 - 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 - - 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 - - fc4b3b46dc9d - 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: - - 0a8e527d1517 - 81c34e67f262 - - d8f5224005bb - 49653e680ea4 + - 0a8e527d1517 + - d8f5224005bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 + - 79da59a0b180 - 2861ca3bfe4d + - 64dd8bb151e1 - 4667fe07bd68 - - 79da59a0b180 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - c9da9192eee5 - 9d76c3d6dff6 + - c9da9192eee5 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 3c47bc560688 - 352cdf3b2f75 + - 3c47bc560688 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: + - 94697510d55f - 9a2f72d7dbd2 - ff6decc0f432 - - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -118,33 +118,33 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 8d9c22419c56 - 28b1546857b0 - - 3027cb62adbd + - 8d9c22419c56 - 6b97ffba31da + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 0387a2179f88 - 73d43034c860 + - 0387a2179f88 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 35f6611fb8c3 - - 56d22aa6cb3b - 1be0fc4d8654 + - 56d22aa6cb3b + - 35f6611fb8c3 - 7d5c97823f8b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 4a74b45c1ce4 - 6f5509cf3176 + - 4a74b45c1ce4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory @@ -157,23 +157,23 @@ tools: - 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 owner: ebi-gxa revisions: - - d18ed15697bb - - 36daab33aecf - 0bab2ae44e7a + - 36daab33aecf + - d18ed15697bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 6a6364b488db - 79cc06a557b0 + - 6a6364b488db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -193,44 +193,44 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - 6d4f88995e40 - b2768cae00a1 + - 6d4f88995e40 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: - 3ee74b58c72d - - 4428dba93375 - - 59028945c857 - 0cf90e01d9f8 + - 59028945c857 + - 4428dba93375 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - 3fb53f5e46ea - - 181d61d2f3cd - abdb61e4afa3 - 8b0d6f6f44c8 + - 181d61d2f3cd 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 - - 0f98603d0116 - 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 - 5605f8452eb3 - - 4cc9362782b4 - 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 7016a4d4d..66c65ee5a 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -3,21 +3,21 @@ tools: owner: bgruening revisions: - d9967770de96 + - ed2cca6b5de4 + - a4c13ddcc8ee - 0f611e7d7858 - 29f66c353bcb - - a4c13ddcc8ee - - 921a2da49a0c - 9edf8894a22d - - ed2cca6b5de4 + - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - 78fb5e286609 - 755df866ad0c - ec4b948dc6f0 - 11de0d28ab30 - - 78fb5e286609 - d404277cc87a - 5746d61f0a91 - 478aacfbaa37 @@ -26,37 +26,37 @@ tools: - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 9d93c8fbe0a6 + - 11fa44ee0603 - 03dd3c16ae4e - - 9e357a8b2ec3 - f72063d9426b - - 977dc15add20 - - 9d93c8fbe0a6 + - 9e357a8b2ec3 - 4d511437b1e5 - - 11fa44ee0603 + - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 1da5f169b491 - - f86ca478c6af + - 77919cc3618e - 3b5b54ed6392 - - 0ba4f56a3613 - 41dbf4d162a2 - c3e5e2cf12b7 - - 77919cc3618e + - 0ba4f56a3613 + - 1da5f169b491 + - f86ca478c6af tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e - - 5308ca68ef3d + - 025a128652dc - 7babd8a46fe0 - - 12d51d7be66f - - 9939786dd9c9 - f741330d4a71 - - 025a128652dc + - 5308ca68ef3d + - 9939786dd9c9 + - b63363075c2e + - 12d51d7be66f 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 b394a90bb..8a9b13728 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,37 +2,37 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 3df9f0a4bf34 - 0c777d708acc - - 81f0cbca04a7 - - 7db4fc31dbee - 699a5e9146b3 + - 7db4fc31dbee + - 3df9f0a4bf34 - 8bccb36e055a + - 81f0cbca04a7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - - 2436a8807ad1 - 0a53256b48c6 + - 5791a7f65275 - 5bc8cdc17fd0 + - 2436a8807ad1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - 6ad1d3cfdea1 - - e576b73a2e2f - 9d47aabda459 + - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - 77f7159d775a - - 70316d792fc9 - b1c2c210813c + - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter @@ -53,10 +53,10 @@ tools: owner: imgteam revisions: - f3360fbeda64 - - 85edbb7a436b + - fcadded98e61 - b07f4839ca77 + - 85edbb7a436b - 10eed33aa9b2 - - fcadded98e61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -70,16 +70,16 @@ tools: owner: imgteam revisions: - 5bf8eb50b280 - - 664232d2a3f7 - b58447a2eed2 + - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - eb6c08714244 - 0e4dccaafef5 + - e917a2424690 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 @@ -108,41 +108,41 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: + - 5d28ac336861 - 2484086dee41 - 6a7da2e5f696 - - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - f2ed92b011a9 - 11f177b1a59e + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - f8fa0f6718a3 - - d0178bdcd00e - f24c370e5ea4 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - 3245681b2f6d - ad271f78a87a + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - - 87d4d92d7487 - 993faa34333b + - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -156,33 +156,33 @@ tools: - name: cp_mask_image owner: bgruening revisions: + - 667a513e67e4 - 3a05117669cf - b178453ea8d1 - - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - 2564f461de62 - a1a961c46d4b - ac5bea85a391 + - 2564f461de62 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: - - 5499dc6f8ac1 - - 8536b1ae0254 - b64af54c5c09 + - 8536b1ae0254 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality @@ -205,8 +205,8 @@ tools: owner: bgruening revisions: - d85f11570109 - - 79e10d12d90a - acf3aa487283 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture @@ -227,17 +227,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - - 8083a87d2fdf - 3a3033222f61 + - 8083a87d2fdf + - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 4ecf93628f97 - 33f4fa1413fb - 27edbb90ab2b + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -256,15 +256,15 @@ tools: - name: idr_download_by_ids owner: iuc revisions: - - 4b794652dcdc - f92941d1a85e + - 4b794652dcdc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - f8b4eada923c - 7b6d9412c7f8 + - f8b4eada923c - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 9b1e8c563..d8357bdfc 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 78bbd17d0703 + - 40737febe339 + - 3e4f434a69c6 - 1069f6db0a0e - - d6e72da3ec35 - 3a72fede57ce - - a38934e303b9 - - e4ee04da1c19 + - 78bbd17d0703 - e319b5b65879 - - 40737febe339 + - d6e72da3ec35 - f362150bef41 - - 3e4f434a69c6 + - a38934e303b9 + - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 9537184d421f - - f91cfb73d369 - - 618297d23022 - - 8f8df367470d - - 7fe36019c073 - - fcbeda41d0ac - 0135f1d487a0 + - fcbeda41d0ac - c88553ec696e - - 72ddd32392cd + - 8f8df367470d + - 9537184d421f - 2b95d5c04908 + - 72ddd32392cd + - 618297d23022 + - 7fe36019c073 + - f91cfb73d369 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: - - 8d36959b000d - - bd2a7d1316b9 - - 28a6f1908fcc - - 43aac8d29685 - 6a1515bb0687 - - 5dc33613c288 + - 3d18f8c3c0f6 - a1c2aecd7a0d + - ee29337f905c + - 8d36959b000d + - ee2beb764a7b + - bd2a7d1316b9 - 9eaadf03e0df - - 94df24c6bc00 + - 5dc33613c288 - 8c05afb547fa - - ee29337f905c - - 3d18f8c3c0f6 - 7f1cfa4c0e32 - - ee2beb764a7b + - 28a6f1908fcc + - 94df24c6bc00 + - 43aac8d29685 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - bcaa0d571ce2 - - d37ede8589b2 + - 86a20ae274fc - a250929be21b - 364f4ffec275 - - 86a20ae274fc - - 5671e1d3d5ee + - 5d6ed46cc101 - 9f978da6528a + - db536ad45f28 + - c092052ed673 - cb903c9dc33d - 8858fa037a15 - - 5d6ed46cc101 - - c092052ed673 + - 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 - - 12d66d0d05ac - - e1a015876aa9 - - 3b6a16d82c1b - - 584beffa972b + - c5c9f02b6167 + - abbc8041e8ec - ed28dd32141c - 49236b03e4fd + - 12d66d0d05ac + - 3b6a16d82c1b - 230b05597996 - - 38b91a3190cd - - abbc8041e8ec - - c5c9f02b6167 - - 194e3ceee923 + - e1a015876aa9 + - 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 b1f0c4e14..8169d9cf6 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,10 +2,10 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 17e3b698dd52 - - f198773344e4 - b8a457820315 - 0f1724dd59d2 + - 17e3b698dd52 + - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 6bd292412..0f500eede 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,9 +2,9 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - - 522137aaa9c4 - 772e0e89fc68 + - 522137aaa9c4 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config @@ -19,30 +19,30 @@ tools: owner: bgruening revisions: - 818f9b69d8a0 - - b6ef6d0cb6b7 - - e1317b5502fa - f1b9a42d6809 - 2af1346e68c9 + - e1317b5502fa + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - c80db5d6fd8c - - 05143043ca13 + - 947c2eacccb8 - 1588f9076e32 - 8334dc98c48e - - 947c2eacccb8 + - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 25b46af53232 + - 29e4122c90de - 83228baae3c5 - - 9991c4ddde14 + - 25b46af53232 - 1552b8cb4a94 - - 29e4122c90de + - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble @@ -60,21 +60,21 @@ tools: owner: bgruening revisions: - dc4b5fd604a6 - - 927586a18553 - - d4808d5b83da - - 91c4e3331208 - 40f4447733b2 - 2fc89dcd41c8 + - d4808d5b83da + - 91c4e3331208 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - e5a5ad882f1f - - 7626ea9c2e1b + - 36e8d6d5d01b - 301e07345c93 + - 7626ea9c2e1b + - e5a5ad882f1f - 25ab6b4e376e - - 36e8d6d5d01b - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -82,10 +82,10 @@ tools: owner: bgruening revisions: - 0630258dcf35 - - 80852884053f - - f9639b488779 - - 4ed102b922cb - 02d2be90dedb + - 4ed102b922cb + - f9639b488779 + - 80852884053f - b7c3e9a3b954 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -93,8 +93,8 @@ tools: owner: bgruening revisions: - caeb57858702 - - 61634a87efc7 - ec69cbe34b73 - 14180f9c831e + - 61634a87efc7 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 ef42394bb..cb98520c0 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - cd659e8cc5fa - - 03e9b2fbc005 - d5ceb9f3c25b - - 017aba02828d - - f6877ad76b00 - 749c918495f7 + - f6877ad76b00 - 0d4acadabb04 - - 3ba8d4563129 - - 937aa69e715f - a6d65b0c67af + - 03e9b2fbc005 - 17062a0decb7 + - 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: - - 64f11cf59c6e + - 2477830927ec + - e188dc7a68e6 - dfd8b7f78c37 - - 53646aaaafef + - 64f11cf59c6e - 3fe632431b68 - - e188dc7a68e6 - - 2477830927ec + - 53646aaaafef tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,29 +48,29 @@ tools: - name: lastz owner: devteam revisions: - - e7f19d6a9af8 - 3e1ea2facca6 - - 37b497aa133f - 2ff111fac1d7 + - 37b497aa133f + - e7f19d6a9af8 - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 037c6e54df11 - - 6b1e195506a3 + - f54f5baedfdd + - 77b2770508f6 + - 3f4d6399997b - 11a0d50a54e6 - - be1d967337e4 - - 09b53c1d4ab1 - 5cc34c3f440d - - 77b2770508f6 - b3eab4b67562 + - 6b1e195506a3 + - 09b53c1d4ab1 - c0c2d0941de8 + - be1d967337e4 - 53c0b7a1a0c3 - - 3f4d6399997b - - f54f5baedfdd - 8c6cd2650d1f + - 037c6e54df11 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo @@ -78,16 +78,16 @@ tools: revisions: - 5ef7ec16b04f - ec9cbd6b9a49 - - b8f5f6e87f5c - - 00fbfac99d39 - - e403d27e8f24 - 79b885ce78d7 - - 381a32c51141 + - 00fbfac99d39 - 13022c3d3076 - - 178bdbdb6d24 + - 381a32c51141 + - e403d27e8f24 - 1cd2511a396e - - 42ce70172b72 + - 178bdbdb6d24 + - b8f5f6e87f5c - 9ee34ba73ebf + - 42ce70172b72 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metabolomics.yml b/usegalaxy.org.au/metabolomics.yml index f76369484..b68850522 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -57,8 +57,8 @@ tools: - name: isolib owner: recetox revisions: - - 6b0fef8a77c0 - 2b1118bce0b1 + - 6b0fef8a77c0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -76,8 +76,8 @@ tools: - name: matchms_convert owner: recetox revisions: - - b9cc12600553 - 9e83636da9d3 + - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering @@ -90,8 +90,8 @@ tools: - name: matchms_fingerprint_similarity owner: recetox revisions: - - 84af792d3a78 - fd890f162ce6 + - 84af792d3a78 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter @@ -104,8 +104,8 @@ tools: - name: matchms_metadata_export owner: recetox revisions: - - 8832425b1ff6 - f04610d25411 + - 8832425b1ff6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match @@ -149,8 +149,8 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 7ba589b01dbc - 9ff95a1a2705 + - 7ba589b01dbc tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -169,8 +169,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - 90745ecc5e9f - b5467dead5b1 + - 90745ecc5e9f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -218,87 +218,87 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - f2c1d0bbb074 - 5f2b58dadb39 + - f2c1d0bbb074 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr owner: recetox revisions: - - da7722f665f4 - 9b716db0a786 + - da7722f665f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - 7b42ee54d757 - - c53a97599181 - 79ad928a0dae - ec196e27a61a + - 7b42ee54d757 + - c53a97599181 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - f3a18e020cdd - - 18ec7635bac6 - 59c393d35e0e + - f3a18e020cdd - 149b9cc7499b + - 18ec7635bac6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - 50b9918aeff2 - 481d769e2f7a - - dfebc82ba1f0 - 134be5abb208 + - 50b9918aeff2 + - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 501a232f3cd5 - - 30bf4e35da3e - 9064aecc78a7 - a82db010c53e + - 501a232f3cd5 - 51332c2520c7 - 02c772a49998 + - 30bf4e35da3e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b341cfd4baf8 - - e7305ba0dd38 - 89178a72388a - b3413f335327 + - b341cfd4baf8 + - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - b7c8a44b9cc1 - - dd7bbc2b99d1 - cf061712a184 - 17a48d0a80f4 + - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - 24278c6b6d1c - - d7f5878a98c3 - 99d118321d5f + - 24278c6b6d1c - f92b1b64da93 + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - 7acd11ddc061 - ffbabefbd2e2 + - 7acd11ddc061 - ea0758b41473 - d90187b0f247 tool_panel_section_label: Metabolomics diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 20a740823..2b3e4f37d 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,23 +2,23 @@ tools: - name: bracken owner: iuc revisions: - - 1d4bd12f01cf - 0c7b6eb7e752 + - 1d4bd12f01cf 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 owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -91,99 +91,99 @@ tools: owner: iuc revisions: - 3a89c3f99f3d - - 76d3d2b10738 - - 63f86089423e - 5b5a7af9fbb4 + - 63f86089423e - 7c2100246a2f + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 96336c6a2bb7 + - 18a502a9d287 - 1c35dadbe76f - - 84fd33a60b35 - 00f5005840fa - - 18a502a9d287 + - 96336c6a2bb7 + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - e8fba04706d3 - f732237754fc + - a9f4a217dcd6 + - e8fba04706d3 - 34e55239e68b - addaf9d22850 - - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 0776d824d896 + - 5fe3edf19b9c + - 8c202e741d68 - 75403243703a + - 0776d824d896 - 04c15826a0b8 - - 8c202e741d68 - - 5fe3edf19b9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 75c8945b0da2 - - 43c99742158b - 1c9b3bcd4261 - - e96bbb9e24ea - 8470de786d47 + - 75c8945b0da2 + - e96bbb9e24ea + - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 306a40d4bb8f - - 35176674168c - 1d75bd0595e2 - - 84743da21318 - 5c865a382933 + - 84743da21318 + - 306a40d4bb8f + - 35176674168c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: + - 8daf4564ccda - ac72310b038a - - 32c9ea835770 - 555ccac8a4c5 - - 8daf4564ccda + - 32c9ea835770 - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: + - d60df8727f59 - f947b4bb5107 - - 7b8cb2b02978 - cae017b76acb - - d60df8727f59 + - 7b8cb2b02978 - a58e4a43f49c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7136e9ab70db - 04144473e59e - - 1770d188f72d - - 7f3b59dee073 + - 7136e9ab70db - 1bc3657cd694 + - 7f3b59dee073 + - 1770d188f72d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: + - a7817705348e - d943081510da - - 9058d8943303 - 19299bb1c6af - - a7817705348e + - 9058d8943303 - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -192,35 +192,34 @@ tools: revisions: - c7e73acfa3eb - bc939965ce41 - - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - dbf1798c0dcc - - 65d52c693b8e + - f8f56dd6449f + - a68b985913ab - 5c7ba3d85a01 - - 4d9445dff47b - c4db8c4de66f - - a68b985913ab - - f8f56dd6449f + - dbf1798c0dcc + - 65d52c693b8e - b907a3c0434f + - 4d9445dff47b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 213df31ba341 - 15dbb444df71 + - 213df31ba341 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: + - 6d364c65c946 - 654548ae1357 - 6c84982ee6f7 - - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -233,24 +232,24 @@ tools: owner: iuc revisions: - e66ab198ec15 - - 6aad8ca3918b - bd7a9c6efb10 + - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - c6676a890f50 - - d77397f09da1 - b084117133af + - d77397f09da1 + - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - 9704f1a3b32d - 7f208f1eb64f + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -275,8 +274,8 @@ tools: - name: humann_join_tables owner: iuc revisions: - - 6bf703133209 - f01ca38fb6c5 + - 6bf703133209 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table @@ -289,33 +288,33 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 79706f10d680 - e88b731dad59 - - 31c6d107e7a5 - c409a495841f + - 79706f10d680 + - 31c6d107e7a5 - 8237a0f225db 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 - - aabf8cfb8fef - - 094ad9c068af - 714d5a28cc5c + - 094ad9c068af + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a293a742194f - - d7e9a3c41657 - 4137b492233e - - 2bdd84912a2b + - d7e9a3c41657 + - a293a742194f - 12fb63b5f63f - a4d7148ccee4 + - 2bdd84912a2b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -327,20 +326,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: + - a92c06a3afa7 - 6fcb8ac37a3e - - 97f7bb0851e7 - cf87759761eb - - a92c06a3afa7 + - 97f7bb0851e7 - e2c71b852aba - - 75bedfb2078b - 64bc7acc22a9 + - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -352,22 +351,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c + - 5e5a999ffaa9 + - 4e5e73d03f0d + - 2d35528d2141 - 4033827c76b8 + - 080ea153677c - c82508e76ad1 - - 2d35528d2141 - - 4e5e73d03f0d - - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - 95bf7479d53c - - 2cd76b089570 - fc6c328c292f - - 6b7622dda516 - c2803012bbb3 + - 6b7622dda516 + - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: itsx @@ -386,8 +385,8 @@ tools: - 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 @@ -407,8 +406,8 @@ tools: - name: khmer_extract_partitions owner: iuc revisions: - - adb3dd5a899f - 1061711538c6 + - adb3dd5a899f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance @@ -428,8 +427,8 @@ tools: - name: khmer_normalize_by_median owner: iuc revisions: - - b1fe2ef3d244 - 4d23ab83ea29 + - b1fe2ef3d244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -448,10 +447,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 + - cdee7158adf3 - 328c607150ff + - 4a9da2b6c2e3 - 20e2f64aa1fe - - cdee7158adf3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -470,8 +469,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 67236d921e83 - 5bee9adae474 + - 67236d921e83 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -484,8 +483,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - bfae8da6082c - 27d65c78863c + - bfae8da6082c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -517,8 +516,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 3d2cffa2c4ab + - 073c867c5244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -531,16 +530,16 @@ tools: - 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: - - d33cf727ed94 - bb96a1e6583d + - d33cf727ed94 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -570,22 +569,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 4fd3b5d8706b - - e073891b2afc - 27250f92a01a - 3cc4a60615c0 - - 0270541aaf46 + - e073891b2afc + - 4fd3b5d8706b - 327d9f4cc95f - 7f5d7b0e9884 - 2cff76cf35c6 + - 0270541aaf46 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - - eb50e7eca3dc - 76bc4efa1aeb + - eb50e7eca3dc + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -658,19 +657,19 @@ tools: - name: metaphlan owner: iuc revisions: - - 289b3807e80c - a16313517e55 - - ff8f55893e7d - - 2131d7dca455 - - b89b0765695d - 740fd2d16a28 - - ec368db926f4 - - fd69c607b43f - 6dee4abadccb - - 1a6cdf55390f + - 2131d7dca455 - a92a632c4d9b + - 289b3807e80c + - b89b0765695d - 1a037928504c - ef65b083bd0c + - 1a6cdf55390f + - fd69c607b43f + - ff8f55893e7d + - ec368db926f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -701,8 +700,8 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 2f47a294ef49 - 6034c3f3ecf0 + - 2f47a294ef49 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp @@ -715,29 +714,29 @@ tools: - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -756,8 +755,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 8e2ac1b8f70a + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -801,27 +800,27 @@ tools: - name: recentrifuge owner: iuc revisions: - - 591175c0f051 - d4fbfd31696c + - 591175c0f051 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - 4b9a8031ab74 - - aeaa20b96ef2 - - 3b22de20bd4b - - be818ae858e4 - - 4d83eccf5f81 - 141afacabcfa - 2fd4d4c9c5c2 + - 4d83eccf5f81 + - be818ae858e4 + - 4b9a8031ab74 + - 3b22de20bd4b + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - 576963db5f1b - - 9495df9dd6ef - b3c7199d8786 + - 9495df9dd6ef 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 15401e631..a43ddad63 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: - - 12e856482d26 - bdb4a58a2025 + - 12e856482d26 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 4e790d8d8..736db1f62 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -4,37 +4,37 @@ tools: revisions: - 6ae5a7b5a0a2 - 9baa871cb1d1 - - bdfbaf0c10aa - - 9422c5a87ee2 - - cd07731e4434 + - 80f03df2e2ce - 098506c54016 + - cd07731e4434 - 2263989660f5 - - 9eeb13a92d79 - a74dbfee5a86 - - 8b67dd48fec1 + - bdfbaf0c10aa + - 9422c5a87ee2 - 94b8c6013083 + - 8b67dd48fec1 - 48c13389050d - - 80f03df2e2ce + - 9eeb13a92d79 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f14193ec1f50 - - d7ce0ec78e51 - - fc2e49f91e52 - - 3ff17bad4006 - - f0af8936ed41 - 2e093badc689 - - be78f13134e2 - bc3831dd65c1 - '764845535798' + - c18157c68134 - aaa0d6a8b808 - d390fe1567dc - - c18157c68134 - - c44f824c051a + - f0af8936ed41 - 4a60927aaca5 + - d7ce0ec78e51 - 5abf2c2249aa + - f14193ec1f50 + - fc2e49f91e52 + - c44f824c051a + - be78f13134e2 + - 3ff17bad4006 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,42 +46,42 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: - - 1de657a3198d - 5efbd15675ca + - 1de657a3198d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - - 8e649f27aa0d - - bf28a8cff401 + - c5908940967d - 15974dd17515 - - f1a5908ea2cb - a65296ffb4a0 + - bf28a8cff401 + - 8e649f27aa0d - f0d493f8f84f - 6f28e90db932 - - c5908940967d + - f1a5908ea2cb tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - b3acbb3a6af0 + - fbca557a4847 - e8fdceffea4c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -96,16 +96,16 @@ tools: - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - - 57f042937ba7 - 48823c9635a4 + - 57f042937ba7 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - fb43e8887350 + - 4fc0cb2ac8ae - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,8 +120,8 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - - cf3c9489c088 - b4124df98b26 + - cf3c9489c088 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 77c2bf892..50eb7fa22 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 - - 9aa9d92c3c51 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -25,28 +25,28 @@ tools: revisions: - 63d8ecfcfab1 - 6942f170cc43 - - fc5b6491cf78 - 99c9427219d3 + - fc5b6491cf78 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - 0e9e7fcdd543 - - a7228a7ea146 - cb34f00cc10f - - fc8804320156 - - 79e9a869f40e - 72b5e9dda577 + - 79e9a869f40e + - fc8804320156 + - a7228a7ea146 + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - d6cddc06aeae - 18505fe2bdb1 - db25ec99c3ea - fa11aa8103b2 + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -58,22 +58,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - 222669c4afb6 - - 2bf63b38ee9b - - edf6d4003fad - - eb746fa6f514 - - cc36773a3681 - - 19f3b583a9b3 - ec699520444c + - edf6d4003fad - 43815fa60f3a + - 19f3b583a9b3 + - eb746fa6f514 + - 222669c4afb6 + - 2bf63b38ee9b - 0f5f4a208660 + - cc36773a3681 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - c0fb573c1e8d - b833eff63b10 + - c0fb573c1e8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -85,60 +85,60 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab + - 0f1c34698076 + - 645159bcee2d + - edbb6c5028f5 - 7b379e98b9a9 - a38bdcec9e4c - - edbb6c5028f5 + - a3c4fe6f49ab - a02b8b3f5a0c - - 645159bcee2d - - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - d219b6d8158a - - 85a394edc247 - 3b6f94fc7e1d + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - a8d4be409446 - - 90a922f32523 - be95355fef8d + - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: + - 4857d5bcce52 - 449e9aeded2d - d376944466bf - - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - de5b3d8f5b90 - a3afc5f0a96c + - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - 5f76b20953e5 - 93d623d9979c + - 543cbeef3949 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 @@ -163,8 +163,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 0433aad600e9 + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -176,8 +176,8 @@ 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 @@ -214,8 +214,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - c5c5a3e84989 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index cf5aa95d7..01516b776 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -27,19 +27,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: + - 97b1b5ad1cda + - baceff842902 - adfd6bf710bd - 3e73c97f025d - - 97b1b5ad1cda - d74850cf4e42 - - baceff842902 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - 83da94c0e4a6 - 9dd107db92c2 + - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -51,14 +51,14 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - 2f27f3b86827 + - 1e34d2e3d285 - e9ee4d074d5d + - 13851aefa67a - 19b6a2f0dbe2 - - e4b4837f06f5 - 8c533e19b697 - - 1e34d2e3d285 - ed1518ce2237 - - 2f27f3b86827 - - 13851aefa67a + - e4b4837f06f5 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -84,37 +84,37 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - 48a42ca61006 + - 38ccd4589990 - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 5a0d0bee4f8d - 4a08b7b76b78 + - 5a0d0bee4f8d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - 81a286e4c5a2 - fcb8bdd124f4 + - 81a286e4c5a2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - b1bc53e9bbc5 - 4d3eff1bc421 + - b1bc53e9bbc5 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -126,15 +126,15 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 9a40272f56d0 - 6287d0ee459e + - 9a40272f56d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 - 52b6a4d98009 + - 27a6a256cd23 - 172815da3d41 - b4b2b284230a tool_panel_section_label: None @@ -161,8 +161,8 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 87febc68b45b - 19bbd19b74b3 + - 87febc68b45b - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -176,8 +176,8 @@ 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 @@ -195,19 +195,19 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - d8dc037e3c13 + - 9c43baa60906 - 0cb27ea69dc1 - 4ba60cb14cb0 - 2c61c30a57e7 - - 9c43baa60906 - - d8dc037e3c13 - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite @@ -222,9 +222,9 @@ tools: owner: iuc revisions: - df30a2f1db55 - - 6e24e79d3d69 - - ed7a967cb11b - 29c738066906 + - ed7a967cb11b + - 6e24e79d3d69 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -244,8 +244,8 @@ tools: revisions: - 3e4d45aca422 - ad90c2da4f38 - - defd3e9ddd2d - 1865e693d8b2 + - defd3e9ddd2d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -265,9 +265,9 @@ tools: owner: iuc revisions: - c520a52b5174 - - d63c1442407f - - 71c994a11f71 - 64deddb6a8ec + - 71c994a11f71 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder @@ -799,11 +799,11 @@ tools: - name: salsa owner: iuc revisions: - - 9a22227bb6d0 - 58a870ef434c - - ba7b0f11e470 - ab5b7f6b7198 - f77f7a7f3b83 + - ba7b0f11e470 + - 9a22227bb6d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index f430ac53e..7b1ec6d28 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,66 +33,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: + - b89cac5156ec - 3f59ebfbfe3d - - 26de3a7b1cb9 - - a6619171428e - - f04a1264e2a2 - - 3b8b5bde0bd9 + - '841557158611' + - 81e66674859e + - d033ffc1c161 - c78f3d7dd1db - 107d3ba7024a - - d033ffc1c161 - - '841557158611' - - cce7b18495e4 + - f04a1264e2a2 + - f73435dc282b - 5a7c56a5cc08 - - b89cac5156ec + - 3b8b5bde0bd9 + - 26de3a7b1cb9 - d7c7ef3353fe - - 6a457678efcb - - 81e66674859e + - cce7b18495e4 + - a6619171428e - 8834daeb9892 - - f73435dc282b + - 6a457678efcb tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: + - 659517798cc4 + - 4755f52427c4 - 6a726db04d4b - - 5fcd1ece3a6e - 88c4aa435ded + - a185b079b095 + - 6283babe736e - b0af57c1a968 - - 6223845127ea + - 5fcd1ece3a6e - df47d4845b62 - - 659517798cc4 + - aa8cc71438cf + - 6223845127ea + - 7a2092844346 - 5b777002c2de + - 3b96e92e8ec3 - e75442c7f4da - 02b8758214b0 - - 4755f52427c4 - - 3b96e92e8ec3 - - aa8cc71438cf - - 6283babe736e - - 7a2092844346 - - a185b079b095 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: + - 70acec670c30 - d1c340a5664b - f97743d52b87 - - 70acec670c30 + - b8476e82ac20 + - 24d024316465 - f87ac61981f0 - c1d53e95327f - - 24d024316465 - 111bd54f6bc4 - - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - feb40665d7cd - - 9e10ba792be2 - 4f6349228462 + - daddf188c13f + - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -104,33 +104,33 @@ tools: - name: pangolin owner: iuc revisions: - - 42a174224817 - - ca337cce3888 - 36912871ccdc + - a2099fb98cdb + - ca337cce3888 + - ca0d8cf80567 - 3a43c3982401 - - 2fa9d4f1b48f - 81804a978fc0 - - 7bb8726be37c + - 9d61d3fa046c + - abf6dbe8c9d7 - b6abccb1f25b - 8ad84c5753ea - - ca0d8cf80567 - - 83a69484cb87 - - abf6dbe8c9d7 - - a2099fb98cdb - - 03ed9524dcd1 + - 5f8727ff21e7 - 14ae456b8cc5 + - 2fa9d4f1b48f + - 03ed9524dcd1 - 2f1019071464 - b7e297c2ede6 - - 5f8727ff21e7 + - 7bb8726be37c + - 83a69484cb87 - 437e28791761 - - 9d61d3fa046c + - 42a174224817 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 2bf47d57ebb5 - 7157a5b34a68 + - 2bf47d57ebb5 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - ea30d3089354 + - 29ff6a849eac + - 73a469f7dc96 - ba29b5e2a4be - a4b71be30c3c - - 29ff6a849eac - b1e68bbe4cef - - 73a469f7dc96 + - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 9b2b122d0415 + - dbe2b2204555 - e88a7de55d6e + - f1ccc8a6eb05 - 91887494eb97 - 809e42326fc2 - - dbe2b2204555 - - f1ccc8a6eb05 + - 9b2b122d0415 - 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 22c93df83..b8545ec3e 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - a1f0b3f4b781 - 1aac2a13842a - - 7d34178f2812 - b502c227b5e6 - - f6ced08779c4 - 881d7645d1bf - - fc288950c3b7 - - 3f254c5ced1d + - a1f0b3f4b781 - f9242e01365a + - 3f254c5ced1d + - f6ced08779c4 + - fc288950c3b7 + - 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 7e079798f..672b46a1a 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: - - e4a053d67e24 - - 5b85006245f3 - - d00e15139065 + - e7f1b552a695 + - 3f188450ca4f + - ca90d17ff51b - 6ab1a261520a - - 2f7702fd0a4c - c0e71cb2bd1b - - 3bd420ec162d - - ca90d17ff51b - - e7f1b552a695 - 7fbec959cf2b + - 3bd420ec162d + - 5b85006245f3 - eb085b3dbaf8 - - 3f188450ca4f + - e4a053d67e24 + - d00e15139065 - a58f7eb0df2c + - 2f7702fd0a4c 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 c64080861..e0cf2c6c0 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,54 +2,54 @@ tools: - name: cardinal_classification owner: galaxyp revisions: + - ece627528a78 + - 277dc652246e + - 4c177985028a - 0a18ac48ac53 + - b574b84afc4d - f28ad96b76dc - - 4c177985028a - - ece627528a78 - b18329a8ac14 - - b574b84afc4d - - 277dc652246e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - a9a28e46d54a - bf06d196e23d - - e215f71d7983 - 525f201b86c1 - - b41107d8fe89 - - a9a28e46d54a - e988563cc6e5 + - e215f71d7983 + - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: + - bb6397b94018 + - 4fbffddde8cd - 8da3511c9467 - 56da27be956a - - 4fbffddde8cd - - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - 528fb09022be - - a8157342d9a3 - - b8c79e70516d - f23d67e28cc8 + - a8157342d9a3 - 890845926d4b + - b8c79e70516d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - ae304a72db7b - - 25b83cbd596a - - 59e85306eae5 - - a69865da6f80 - a95a82eb4d50 + - 25b83cbd596a - 80600735685d + - a69865da6f80 + - 59e85306eae5 + - ae304a72db7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing @@ -57,39 +57,39 @@ tools: revisions: - f1897eb07081 - ed9ed1e6cca2 - - 611d80c0e29d + - 83aac7741200 - e0669b1854b1 + - 611d80c0e29d - 798da6bdff3d - - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - - 5a35e3a8d013 - - d426a9107a6c - 74b61bf5bc4b + - d426a9107a6c + - 5a35e3a8d013 + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - 82f6c2f4332d - - df2187f9013b - cc430977c8ff - 91f0f5922011 + - 82f6c2f4332d + - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - c5aa9fca18c6 - - 043f9c91f686 - ba92b59cd529 - 10566783d718 - 1693b2126f30 + - c5aa9fca18c6 - d2483487e077 + - 043f9c91f686 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 - - ff8c9e0e8a7b - bf0728e000cd - - 9fa3dbf06f17 + - ff8c9e0e8a7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,17 +122,17 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - eac99effe86f - - d0ea7589e95f - d263296cd73e + - d0ea7589e95f + - eac99effe86f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: + - 0fa397f4f40b - 1c5cbf8f79ce - 4081e4faa4ab - - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -146,8 +146,8 @@ tools: owner: galaxyp revisions: - ce1a157a41bd - - 0d2e93e01e68 - d6a4dfdad269 + - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -159,9 +159,9 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - d286ff4600dd - 160538a890a6 - e66f552a3c47 + - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -181,16 +181,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - f522c08e900c + - 4d17fcdeb8ff + - e42225f8a659 - 837224ad1694 - 1f39c833f65f - 2133b0be850a - - 4d17fcdeb8ff - - e42225f8a659 - - 7f432d87c82c + - 9c52362ae7bb + - f522c08e900c - 37d669de2828 + - 7f432d87c82c - 97a7f34fcb6a - - 9c52362ae7bb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,10 +202,10 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 + - 85b8866f06d7 - a72ac2c7cc5b - e63db1aa82ee - - 85b8866f06d7 + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand @@ -220,19 +220,19 @@ tools: - name: metaquantome_filter owner: galaxyp revisions: - - 99450519d727 - - 35cc7ca0bdc7 - deaf035bbe9f + - 35cc7ca0bdc7 - 4f359549383c + - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - c1343e3389ca - - c7745841de24 - - 06f6826d380c - e79958768a2c + - 06f6826d380c + - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat @@ -248,8 +248,8 @@ tools: owner: galaxyp revisions: - 944b43462104 - - 8bd7734309f6 - 9bf325045235 + - 8bd7734309f6 - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -270,78 +270,78 @@ tools: - name: msstats owner: galaxyp revisions: - - de7593c29499 - - 28434abe6c5c - - 593839e1f2c3 - 8212e342e482 + - 593839e1f2c3 + - 28434abe6c5c + - de7593c29499 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - bd1535813cfe - a5e394b36d87 + - bd1535813cfe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - 4e77b8f12cd3 - 01dbaf6a57e0 - - 8960fb791701 + - 4e77b8f12cd3 - f4be248c3d47 + - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: + - 25529df60a81 - 06cca574e337 - 370141bc0da3 - - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - f7fef900f5b2 - - c9eff69a7c62 - - 518b1730cf2a - 6ccbf9a2072c + - c9eff69a7c62 - 9cdf15d3cfc8 + - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: + - 5e948629bc73 - dff6c756eee5 - 9876bda3ec53 - - 5e948629bc73 - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: + - 890025d6e426 - 41859bbdc16e - 1595601708ec - - 890025d6e426 - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - - 2a93a25f0599 - 6634cad7d797 + - 2a93a25f0599 + - 5ad0b5bf1deb - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - d6878d27f051 - 0bb5056cb775 + - d6878d27f051 - 05d5e1ddc985 - fe4e4587d265 tool_panel_section_label: Proteomics @@ -349,8 +349,8 @@ tools: - name: openms_fileinfo owner: galaxyp revisions: - - 52ba9695e752 - 4af67edd5aef + - 52ba9695e752 - 5ad830edc021 - febd569ad26f tool_panel_section_label: Proteomics @@ -358,10 +358,10 @@ tools: - name: openms_filemerger owner: galaxyp revisions: - - b2fc8da99bcc - 39e8fde08881 - 92352a475eed - 27cba4c5fc42 + - b2fc8da99bcc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector @@ -385,19 +385,19 @@ tools: - name: openms_idfilter owner: galaxyp revisions: - - a5d785af0ad8 - - c427a8628cbe - - c55dddc5844a - ca799a7246e7 - 382cde407f81 + - c427a8628cbe + - a5d785af0ad8 + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 39caaa778d2e - - b5d0905419da - 8ddb7bab1138 + - b5d0905419da + - 39caaa778d2e - adca857b4884 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -405,70 +405,70 @@ tools: owner: galaxyp revisions: - 34e7afee141d - - 1c5f31b8d632 - - 8d4db262964c - 18f93351f8b6 + - 8d4db262964c + - 1c5f31b8d632 - f817513840a9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a + - 986e03d3201e - 5d9f175dff81 + - c69f69d7867a - 111c3a00136d - - 986e03d3201e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - - 476b5e296979 - be74a8cd7d66 - 4204882495f2 + - 476b5e296979 + - 0e52c85f3b15 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - c18d8efa4474 + - f5ec766d80cf - 2b2a7551a857 - a407b6790342 - - f5ec766d80cf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - d0304fb829c0 - 4e66c4e73909 - 021fdb80f204 + - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - 8098330f6d91 + - ee860980edc6 - 2735db4dd8d9 - bf32e0bcf554 - - ee860980edc6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - a2a6e9551046 - - 08488066d588 - 0ced5bc9f4dd + - 08488066d588 + - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - de7a553552a6 - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -482,9 +482,9 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 496cf619e311 - - 9f505cd4428f - f861ec9fbe59 + - 9f505cd4428f + - 496cf619e311 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -498,25 +498,25 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 8b814eafce2c - - 4bb198c0bd3e - 89254095cbf6 + - 4bb198c0bd3e + - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - f9ed7e074900 - f82b320ceb90 + - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - 18826fb8e5db - d31426ef20f6 + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -530,10 +530,10 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - - 3d8d4ada5405 - 6b01678ec2fc + - 3d8d4ada5405 - 5ae104d0da6e + - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer @@ -541,25 +541,25 @@ tools: revisions: - 539a3a4dcc9e - 5182338d5e7c + - dd173849c3d8 - d6aca689dd48 - e039cc5c7aed - - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - d426affe977c - - 16026cdb1330 - 8a45fd5a608a + - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 43b9ed22e8ce - dd71e020e2aa - 9c70a651a53e + - 43b9ed22e8ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter @@ -581,17 +581,17 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - - c8b225c69a7f - - 7f6a1f27553e - 5c2a97a234d6 + - 7f6a1f27553e + - c8b225c69a7f + - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -612,12 +612,12 @@ tools: revisions: - 07ff622ec007 - 1beff3ddce58 - - a72c48001f7c - - 3634c90301af - - 943a34df6047 - da885ca16cb2 - 3ec27b4cee7c + - a72c48001f7c - 7fdd9119cc4f + - 943a34df6047 + - 3634c90301af 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: - - 265c35540faa + - 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 52697721b..bf015d3f9 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 60398d367..65a7c0234 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,10 +2,10 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 289b7d6b69a4 - - cd5f98911089 - 2f1d464ebfd2 - 42201b90e3f4 + - cd5f98911089 + - 289b7d6b69a4 - e345aadf914f - 110a346daf36 tool_panel_section_label: RAD-seq @@ -13,96 +13,96 @@ tools: - name: stacks2_cstacks owner: iuc revisions: + - 0345dbaaa79b - 42d9087b4789 - 0cd2df8af811 - - 8501601a118d - fcce77c09289 - c207119ba5f6 - - 0345dbaaa79b + - 8501601a118d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 405a212b32ab - 33486216eec0 + - 405a212b32ab - ad5ab22ffe24 + - 89eb29319bf4 - 04db7fd6b238 - 421c33b8bf17 - - 89eb29319bf4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - 7370bb65bad4 - - fa51dc5e8386 - - 7b72fde3d27e - eb784fa07f80 - - f6e91108b7b1 - 1d839ead7ad3 + - 7b72fde3d27e + - fa51dc5e8386 + - f6e91108b7b1 + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - 1544278c272e - - c9b77ced9a78 - 3d70c2996730 - - d30e36c48c93 + - c9b77ced9a78 - a3e86cd9cac7 - 8a55d29c8fcf + - d30e36c48c93 + - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - b242deb58952 + - 887cf585cafc - a5969aa9347e + - b242deb58952 - e2db212d64ad - 564c33e5c3e3 - - 887cf585cafc - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - bd5ff77e2036 + - e897c74a48bb - 9a171f9a450b + - bd5ff77e2036 - b4bab607eb05 - - e897c74a48bb - 8cff84759bf6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 887e0991eb24 - - 33f0793edf93 - - adc7a7610d4f - - 5e10f396979e - 4f65e343ecdf + - 5e10f396979e + - 33f0793edf93 - 6dafad990086 + - adc7a7610d4f + - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 97575d01f06b - 17d39bf0a63a - 4e280b27a831 - - c287418eb288 + - 97575d01f06b - 43e3eeb2e0ec + - c287418eb288 - c5d7050e4ad7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: + - 0b8c84a7fdb5 - cd034465d4a4 - 9586f08634c0 - - 0b8c84a7fdb5 - a819ec3b362d - d9bf483266a1 - 09b8edb56d80 @@ -111,23 +111,23 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - bf0e43ab0416 - 95351dd0fd3f - - a4b4bd84f69e - 2645575d1bf2 - - 69842dd5aa48 - a9c34a289493 + - 69842dd5aa48 + - bf0e43ab0416 + - a4b4bd84f69e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - 912f904a6e1e - - bb0475c884ff - - cfb504394ae1 - d033e1ccb386 + - cfb504394ae1 - 8a35a3bc6752 + - bb0475c884ff - d1fda11e602f + - 912f904a6e1e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - - 95286af4139b - d504d945a655 + - 95286af4139b + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index da699cd2f..a4a1d2452 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,27 +2,27 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - cf01dd6c6b1f - 2d4e3aff9dc7 - 31f8063eedea - - cf01dd6c6b1f - 7acb00fc980a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - - 32e542c2a773 - 7a5a2d28c539 - 125d20cb23d7 + - 703a2cb3fb38 + - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 - 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: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cemitool @@ -90,34 +90,34 @@ tools: owner: devteam revisions: - e66b9b5b8580 - - ad5d061fbdf2 - f648e5180e40 + - ad5d061fbdf2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - d080005cffe1 - 6926716bbfb5 - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - 22cf48ad7b16 - - cf747d1bd79a - - 86285ddd4512 - 04adc9db1581 - 6a6717a5f421 + - cf747d1bd79a + - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 28b94cfbfdb9 - 9a854107dbb2 - 6cbfede05833 + - 28b94cfbfdb9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -142,49 +142,49 @@ tools: - name: describe_samples owner: iuc revisions: - - 8f0181aacb7a - - e3b16fd7dd08 - 3b36efd62b3e + - e3b16fd7dd08 - 0693ccd171c4 + - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - cd9874cb9019 - - 9a882d108833 + - 0696db066a5b + - d027d1f4984e - 8fe98f7094de + - 9a882d108833 + - cd9874cb9019 - 24a09ca67621 - - d027d1f4984e - 6a3a025714d3 - - 0696db066a5b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: + - 9a7c5b6d8f1e + - 62adf13b86ea + - b47c006d90c5 - 2872c633f07e - df929f257179 - - b47c006d90c5 - - 62adf13b86ea - - 9a7c5b6d8f1e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 3d89af8a44f0 - - 5bf899c13979 - - ae2aad0a6d50 - - 070900306913 - - 555659de7321 - 334ce9b1bac5 - - df0c8d0a5992 - 9bdff28ae1b1 - - 0cb907a2a810 - f2843df56434 + - 5bf899c13979 + - df0c8d0a5992 + - 555659de7321 + - 0cb907a2a810 + - 3d89af8a44f0 + - ae2aad0a6d50 - a8305cf0c951 - 6e53e565fc6a + - 070900306913 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -203,18 +203,18 @@ tools: - name: featurecounts owner: iuc revisions: - - a37612abf7f9 - - 6f66ae7c5f7a - - 38b6d12edc68 - - f3a5f075498f - - 1b851f87fbe0 - - ea04b737afa0 - - e6a2a912677a - - f9d49f5cb597 + - 7db9d3ea71c9 - 90d16db017d7 + - f3a5f075498f - a56fbe2d6ba7 - - 7db9d3ea71c9 + - e6a2a912677a - af814359d244 + - 38b6d12edc68 + - ea04b737afa0 + - 1b851f87fbe0 + - 6f66ae7c5f7a + - f9d49f5cb597 + - a37612abf7f9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -238,9 +238,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 3c97c841a443 - 3c5e024a18cf - 0f710191a66d - - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -252,21 +252,21 @@ tools: - name: hisat2 owner: iuc revisions: - - 6c19daec423d + - f4af63aaf57a - 26371a1df031 + - 3fb01a8c902d - 6ab42baa56e9 - - f4af63aaf57a + - 6c19daec423d - a86e80d3c09c - d4b55e2beb12 - - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 4418229c501e - - 916cb26bd9d3 - 67b0b160903a + - 916cb26bd9d3 + - 4418229c501e 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: + - ce5d418183c5 - 1c75aa5de15e - 01247aaf0a10 - - 87c11c05d238 - - ce5d418183c5 - 5ae5c312d718 + - 87c11c05d238 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 10c98fab6c5a - 4f9c4e6566e5 - 40985510cd98 - c971db6f0fe5 + - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: + - e827f9aae031 + - 97e06a4c7c75 + - 119b069fc845 - 32511f586472 - 0921444c832d - 708348a17fa1 - d6f5fa4ee473 - 58c35179ebf0 - - 97e06a4c7c75 - - e827f9aae031 - - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -341,8 +341,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -362,18 +362,18 @@ tools: revisions: - c7c55b694974 - 980d2a2e1180 - - 3ea5a2a63fa2 - - 99b17b74a8cd - - b9e04854e2bb - 7ed2edc1337f - - 4df95e2d7f61 - - 5ec75f5dae3c - b0f2be869d6d + - 5ec75f5dae3c + - b9e04854e2bb + - 99b17b74a8cd - 53255f6eecfc - 0a563fd2f22e + - c772497b2c32 + - 4df95e2d7f61 + - 3ea5a2a63fa2 - e132e7d02a3e - 79de45b5069b - - c772497b2c32 - 4074fc1940e2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -386,36 +386,36 @@ tools: - name: salmon owner: bgruening revisions: + - 49121db48873 - f4d5237a84f6 - - cc05793bb896 - 53e9709776a0 - - 49121db48873 + - cc05793bb896 + - ebab418107f5 - e3d32471da11 - 2c0ca397d302 - 15cd64d7c58b - - ebab418107f5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: + - 56242ff81c84 + - c0fd285eb553 - fab6ff46e019 - 8c28affc7c48 - - c0fd285eb553 - - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 1ebd14235b92 - - ae618321f34a - - dd4df992d93d - 914cfcba0ec8 + - cbf488da3b2c - cef79931dda5 - - 76d290331481 + - ae618321f34a - 258d696dbd7e - - cbf488da3b2c + - 76d290331481 + - 1ebd14235b92 + - dd4df992d93d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -445,19 +445,19 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - ffd1300599a1 - - d0d4cef4f967 - c6334cb383ff + - 0db979fead3a + - 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 - - 74217fbfba4d - d6a479fd4281 - ba3720d7e68b + - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -472,17 +472,17 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - 9ff3765e7172 - - 3f4094b6a565 - fab23c3b5258 + - 3f4094b6a565 + - 9ff3765e7172 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - be3f26533209 - - 4687ecf0eb2d - 870ac06dff8e + - 4687ecf0eb2d + - be3f26533209 - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -501,35 +501,35 @@ tools: revisions: - 1fdb25a8384d - a35cba31d904 - - 6f0fb35b799c - e406ac71165d + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - 964b7efe2639 - - 37a1129c89d2 - - 7c7fbf13aadd - 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 - 1d689e4e1caf - - 24e94d84adc9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 3a4ac03d1266 - 04bb8bb7c198 - - 9871104ea630 + - 3a4ac03d1266 - 1812dbc5bb7b + - 9871104ea630 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: - - 8f1c3df4dd49 - - c9cfec002f71 - 9fa24d5aac68 - - 32b86cd8eb50 - - 48636f857c4b - - cee61b3fcf78 - d2bc35f3d1c5 + - 8f1c3df4dd49 - db1f362cca3e + - c9cfec002f71 - d84caa5a98ad + - 32b86cd8eb50 + - cee61b3fcf78 + - 48636f857c4b 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 0693de33b..a3d6f6f22 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 - - 080fd5739bb4 - 27e16a30667a - - 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 9d37938eb..0438886af 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -3,17 +3,17 @@ tools: owner: devteam revisions: - 10184eaa85fc - - 3c661e57a88f - 88eedb4abea0 + - 3c661e57a88f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: + - 1dfd95ee241e + - 108db6635177 - 993b19f20c76 - cb20f99fd45b - - 108db6635177 - - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -75,17 +75,17 @@ tools: - name: qualimap_bamqc owner: iuc revisions: + - 19ece8afbaab - 5f8e69cc4c6e - - 30a201c9c310 - e7fd6754d093 - - 19ece8afbaab + - 30a201c9c310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam2interval @@ -110,8 +110,8 @@ tools: - name: sam_to_bam owner: devteam revisions: - - cf1ffd88f895 - 0e60e2dd20af + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -130,10 +130,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 46c6639921f1 - 6856f8a01905 - 9149ad20699a - 12749212f61b + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -160,11 +160,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 66e23b11feae - - b3d99709fe1a + - 720217c23995 - b906586a6596 + - b3d99709fe1a + - 66e23b11feae - a8d69aee190e - - 720217c23995 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate @@ -177,48 +177,48 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - cc61ade70eb8 + - fefd89ab563c - 22970df7a40e + - cc61ade70eb8 - db17d5321bad - fe34990e5ce7 - - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - - 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: - - 40fa6c240105 - a389f74c3630 + - 40fa6c240105 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - cae2794d2deb - 65a38e8c8e2a - - b40e2d865d52 - 36677f429310 + - b40e2d865d52 + - cae2794d2deb - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 + - 8da515fbc1bf + - b61f5d6a7f25 - 583abf29fc8e + - 329deb17a9f7 - 9da0311ab1dd - - b61f5d6a7f25 - - 8da515fbc1bf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -231,10 +231,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - 85e38b31e8b3 - - bb8cfc6f6e0c - 30388d878f81 - db000c6007a0 + - 85e38b31e8b3 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -247,17 +247,17 @@ tools: owner: devteam revisions: - 344fc91e1bfd - - a4a10c7924d1 - b8beef827165 + - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - d54a4df48867 - cab3f8d35989 - - e613c1ad4c4c - 6c2c1836728b + - d54a4df48867 + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -265,35 +265,35 @@ tools: revisions: - bd850490c7f1 - 5d9ae78f34d3 - - bcedabb53ddf - - 818030fa6bbf - 135c85f4cfaf - b7f7826ef1cd + - bcedabb53ddf + - 818030fa6bbf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: + - 5a08c09b9311 - 1cc79f49b8d5 - 145f6d74ff5e - 24c5d43cb545 - 3a0efe14891f - - 5a08c09b9311 - 541082d03bef tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - 32dc5f781059 - - 5826298f6a73 - - b01db2684fa5 + - b72793637686 + - 350bbc5c2ffd - 6be888be75f9 - - 2dce91e11ca7 - c370440f901e - bf328cec6a42 + - b01db2684fa5 + - 5826298f6a73 + - 32dc5f781059 + - 2dce91e11ca7 - 0dbf49c414ae - - 350bbc5c2ffd - - b72793637686 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/send_data.yml b/usegalaxy.org.au/send_data.yml index 6b5201318..415c14a35 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: - - 480d9e9d156b - - 5cb6146337d8 - - 6f6537780379 - - 4aab5ae907b6 - 59bb6d34fca6 - - a62c4a11a67d - ea5e944f447d + - 4aab5ae907b6 + - 6f6537780379 + - 5cb6146337d8 + - a62c4a11a67d + - 480d9e9d156b - d147d6455873 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index dc26ae06d..e354b0963 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,100 +8,100 @@ tools: - name: alevin owner: bgruening revisions: - - e4c01dcece8b - ecb9ea6269ee - - f2000bc73102 + - e4c01dcece8b - e32b215b7c04 - b0fe3e482cb7 + - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - 707023fa62fe - - 7a6655aa6eb2 - c0b037b12765 + - 7a6655aa6eb2 + - 707023fa62fe - e1c3c2f2a834 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 - fb9e030ffae4 - - 55e35e9203cf - - 6f143dfe902a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 6f0d0c784f09 - 038e32885fec - - 39e945f0b2c1 - - ee98d611afc6 - - b9fac48532eb - - 14c576ea6148 - 688357ad5e61 + - 14c576ea6148 + - b9fac48532eb + - 6f0d0c784f09 + - ee98d611afc6 + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 43cb7b5a6fe7 - - d4af736e7b83 - - c4209ea387d4 - 9bd945a03d7b - - 3d748954434b - - b85871dd69f9 - ed4996a16f7f + - c4209ea387d4 + - b85871dd69f9 + - 43cb7b5a6fe7 + - 3d748954434b + - d4af736e7b83 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - fe75d2414dc0 - 890fb06a2893 - - 2e8022f1923c + - fe75d2414dc0 - a4774b7b2e85 + - 2e8022f1923c - 7ebc22f77d86 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 4fff5a293013 - 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: - - aa4a6f0916b4 - c29e7bb492bf - - 344c2af50552 - a90f8efe08b4 + - 344c2af50552 + - aa4a6f0916b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 5b7c81b35b89 + - 050cf43887d3 - b13d3e4c48e1 + - 5b7c81b35b89 - c32347702e12 - - 050cf43887d3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 02fc39c8610d - 239193b96d72 + - 02fc39c8610d - 1d77986f9ddc - ae969fdb8442 tool_panel_section_label: Single-cell @@ -139,11 +139,11 @@ tools: - name: dropletutils owner: iuc revisions: - - a9caad671439 - - cfe1e6c28d95 - 2c1200fba922 - - 8855361fcfc5 - cdf4443d5625 + - a9caad671439 + - 8855361fcfc5 + - cfe1e6c28d95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -174,9 +174,9 @@ tools: owner: bgruening revisions: - fb7068d30ec9 - - c3ffb2c1e314 - - 01c37e54e86e - 952abbc4b1de + - 01c37e54e86e + - c3ffb2c1e314 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest @@ -192,72 +192,72 @@ tools: owner: bgruening revisions: - 23b8d6b8960c + - 1a31e75e979e - 163fd744e235 - cab616fe7e64 - - 1a31e75e979e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - 013e53ccc7ac - - f47ac4a0b337 - '920526260066' + - f47ac4a0b337 - b9ab56aecd18 + - 013e53ccc7ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - 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: + - ff1af7bac1cb - 640e0e45518a - 45a386d18509 - - ff1af7bac1cb - f8320df1866b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - f963c251ac77 - 6f8debcf2ac9 - - c354255ff705 - 9d02f1819e81 + - c354255ff705 + - f963c251ac77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - 37125838e360 - - c4ed35f4f77f - 40fee49bc6c3 - f881c94fb3b3 + - c4ed35f4f77f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - 782bdcb775fb - - 2dccb6bb0add - e8760fc0e29b - e06265d204f6 + - 782bdcb775fb + - 2dccb6bb0add tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - b05f662f9f35 - - 30677e95bc89 - - f0216498a666 - 63c8377c58b3 + - f0216498a666 + - 30677e95bc89 + - b05f662f9f35 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions @@ -265,44 +265,44 @@ tools: revisions: - 3240e8a7c54f - 8a11d70b6cd8 - - c72fa6cb8817 - fe3aa71590d5 + - c72fa6cb8817 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 5dd1aae12f03 - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c - 4f9305d3bb34 + - 5dd1aae12f03 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 87eb9c58cd19 + - 4401ed529d2c - a315574104c6 - 3a6a5381db36 - - 4401ed529d2c + - 87eb9c58cd19 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - a83732c79949 + - c0737631eea1 - 574f295b5ba4 + - a83732c79949 - 2ba6cee8e4db - - c0737631eea1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 937b7b9832d0 - - 62b720dceb56 - ea19190ce5e0 - 30d7390bc918 + - 937b7b9832d0 + - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate @@ -317,18 +317,18 @@ tools: - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - bf9379529c3e - - 0410b6aada45 - ffc33339cd3e + - 0410b6aada45 - 4375e25de06a + - bf9379529c3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 5dfba24d7bdd - - 07dd436ea686 - 4977f65da0ff + - 07dd436ea686 + - 5dfba24d7bdd - 77d8e0fd162a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -336,16 +336,16 @@ tools: owner: bgruening revisions: - 6c5097f6d41e - - f1b3902f8baf - - 972dcccb5bbc - f0b1bd38745a + - 972dcccb5bbc + - f1b3902f8baf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 409396ea5cf0 - 3e5c86c2f80d + - 409396ea5cf0 - 7f7c6ead2d0d - bb8849fca57c tool_panel_section_label: Single-cell @@ -353,99 +353,99 @@ tools: - name: hicexplorer_hicinfo owner: bgruening revisions: - - 7fbd6feba1ca + - e4f8fceab96a - b0f33533181d - 51e40e9b6c3c - - e4f8fceab96a + - 7fbd6feba1ca tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: + - 32173084d53f - 55b013e59018 - c261b6b05ee3 - - 32173084d53f - 908fa330b93b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: + - febfddb0b3e8 - b6b8c8672756 - - 4b194e675916 - b376ef118807 - - febfddb0b3e8 + - 4b194e675916 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - ed900cd4a0a9 - - 1d9799f4b854 - - 1511a8ebe906 - 910c6a1c3a27 + - 1511a8ebe906 + - 1d9799f4b854 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - 6d042c96aceb - - 2aa5b6b65197 + - f34ab9882252 - 5e83c077e31d + - 2aa5b6b65197 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: + - 9b383d429659 - dd9988943f53 - 3f1b286a5c34 - ea5d67ec94ab - - 9b383d429659 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 6326cd29c1c3 - 89cfe7de541b - - 06ced663d24f - 11f39d7f6c64 + - 6326cd29c1c3 + - 06ced663d24f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 - - 337705015ee8 - 1602cc5b673c + - 337705015ee8 + - b4e780e93c91 - beb5b5917d2f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: + - 58de3c7c8e89 + - e285920f8585 - 8d203e74869b - a10fce08c2dc - - e285920f8585 - - 58de3c7c8e89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: - - ea8fb5e899e8 - b13e7a200525 - - 21d859ad4502 - 5cbd7a902a8d + - ea8fb5e899e8 + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 1d6af10874d5 - d74cf4a61d65 - f81750434d70 + - 1d6af10874d5 - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -464,30 +464,30 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - df64cc4dfb4d - - f36828ebdc54 - 1de2276f633f + - df64cc4dfb4d - 27fe5cd1729c + - f36828ebdc54 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 1d201e8378b3 + - cef9fb4ece1c - 11a3385e03b5 + - 1d201e8378b3 - d890828ab02a - - cef9fb4ece1c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - 4b0adaa31c95 - - e98619de2776 - - 59be31ac9dc3 - - eeab712b0b99 - 7784821452ac - db575b4c8b22 + - 59be31ac9dc3 + - e98619de2776 + - eeab712b0b99 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -514,8 +514,8 @@ tools: - 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 @@ -533,9 +533,9 @@ tools: - name: raceid_clustering owner: iuc revisions: + - a4b734cd253b - 49776718ae90 - 7e014059a88d - - a4b734cd253b - f911a64454fb - c4f39bf4a068 tool_panel_section_label: Single-cell @@ -543,36 +543,36 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - 8b917923f7d4 - - 7608d5faee41 - d45f092caf24 - 43c146e25a43 + - 8b917923f7d4 + - 7608d5faee41 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: + - 37a47c4fd84d - 2b0d3e2f402a - c7ddb719554d - - 37a47c4fd84d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - 6e90c8adf84f + - 69018f285aa3 - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - 44b935f2271b - - 72979cac22b2 - e93b008c637a - - c92d0f9338c5 + - 44b935f2271b - 2bfd55b87af3 + - c92d0f9338c5 + - 72979cac22b2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -590,30 +590,30 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - cb43c5d3acd3 - - 6f83f8fd381f + - b2df381a6004 - aaa5da8e73a9 - 8983e7a04ba7 - - 77b91b9bdf52 - - f9353ee6a0d4 - - b2df381a6004 - - 6acb08931836 - 4d8f983cd751 + - f9353ee6a0d4 + - cb43c5d3acd3 - 38db3fef7aad + - 6f83f8fd381f + - 77b91b9bdf52 + - 6acb08931836 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 64388be6d510 - - 8cb783c81905 - - d636ce5cde16 - - 277313130da5 + - a03ff8633507 + - a97abb8cd15b - b409c2486353 - 3c86f71498bc - - a97abb8cd15b - - a03ff8633507 + - 8cb783c81905 - 72a6bebab2a5 + - d636ce5cde16 + - 277313130da5 + - 64388be6d510 - fc0321c000a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -622,79 +622,79 @@ tools: revisions: - 18262103fa61 - d86cb2ce311b - - c5d3684f7c4c - - 5c3ebe2adc77 - - 3081ff5c84a3 - - 5e9171dc8244 - - 6bd82ed14acd - f54f0f0598ad - 6c145a6868cc + - 6bd82ed14acd - 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: - - a407e7f8bdc1 - 7b9fafe32c86 - 94c19fb1281c - - 146ae5d70b47 - - c9cb76cf8d6c - - 9f354c7c8c92 - 4bda4412b8c2 - ab55fe8030b6 - - 3bcd5445cd7a + - 146ae5d70b47 - d844935c906c - 56c0d4acef02 + - a407e7f8bdc1 + - 3bcd5445cd7a + - c9cb76cf8d6c + - 9f354c7c8c92 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 6f5349dd5c49 - 62acdd96d4a0 - - 7647e5cd1b8b - - 40812a65a78b - - 9b0cdb8cf6be - - aa0c474463c2 - 1072ce66b426 + - aa0c474463c2 + - dbbe1ea8ecb1 + - 6f5349dd5c49 - 95777145cb92 - - f7446fd8d5e7 + - 9b0cdb8cf6be - 0185bd174ea0 + - f7446fd8d5e7 + - 7647e5cd1b8b + - 40812a65a78b - 6adf98e782f3 - - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 215733a383f2 - - d18e7a6e5cd4 - - f2f6c703da06 - c65fce500915 - - 73ab2ac53d06 - - a39040ae0a38 - - 458e8f43a775 - - 9fb627495ec2 - fe8f16c594ec - bf2017df9837 + - 215733a383f2 - c5541bfb8feb + - f2f6c703da06 + - 458e8f43a775 + - a39040ae0a38 + - 73ab2ac53d06 + - d18e7a6e5cd4 + - 9fb627495ec2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: + - 8f333f90d8d6 - b834074a9aff - fd808de478b1 - - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: - - 652923ce664f - 7a365ec81b52 - b7ea9f09c02f + - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -707,8 +707,8 @@ tools: owner: iuc revisions: - 81e5bdff4853 - - ef4c80837bc5 - 2e41b35b5bdd + - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_exprs_freq @@ -720,9 +720,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: + - 46fc6751d746 - c99ba278dfa9 - 9e5c0bb18d08 - - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -944,15 +944,15 @@ tools: - name: sinto_barcode owner: iuc revisions: - - fb61eb03e313 - d1b34ac42b8f + - fb61eb03e313 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: sinto_fragments owner: iuc revisions: - - 29e6bfb2cf49 - 6f66f523a9b7 + - 29e6bfb2cf49 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 572a02e3b..74d7386c2 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 - - 746e8e4bf929 - 562f3c677828 + - 746e8e4bf929 - 4c07ddedc198 + - 419027d822d6 - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - cb1c59d69557 - 7a15159140d1 - 6c29c7e347e8 + - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 840f29aad145 - - aef56d0e7a61 - - 4c4ec859c31a - - 9c3e1d3235c8 - b1eda492f063 - 7442b94d6a1e + - 4c4ec859c31a + - aef56d0e7a61 + - 840f29aad145 + - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 9fda0b82f419 - - 30d21a6041f6 - 07843f917990 + - 9fda0b82f419 - 375bbd555f4a - d0352e8b4c10 + - 30d21a6041f6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - 8b1b2b91f8d0 - 2c58b83c9bad - 7ae443e6217d - - 8b1b2b91f8d0 - - 4cc980df6265 - cd02bf168d23 + - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - bb9fc9d46ea4 - - 7dd3fb35904f - 1dd433d2c92c + - e10e776f2109 + - 7dd3fb35904f + - bb9fc9d46ea4 - 4bbaf77573ef - ad7e0b4291ee - - e10e776f2109 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 5847aaa81..cee56526f 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -34,14 +34,14 @@ tools: - name: column_maker owner: devteam revisions: - - 02026300aa45 + - 6e8d94597139 - 13b6f0007d9e + - 464b9305180e + - aff5135563c6 - 6595517c2dd8 + - 02026300aa45 - 9cd341095afd - - 464b9305180e - be25c075ed54 - - 6e8d94597139 - - aff5135563c6 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -79,10 +79,10 @@ tools: owner: iuc revisions: - 557ec8d7087d - - 9cc411a62277 - - 90f657745fea - 34d29339abab - 37cde8134c6a + - 90f657745fea + - 9cc411a62277 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -113,22 +113,22 @@ tools: - name: query_tabular owner: iuc revisions: - - cf34c344508d - - 1ea4e668bf73 - - 3a6b78c39dca + - 623f3eb7aa48 - cf4397560712 - - 2e8f945f7285 - - 83069b38aa85 + - 1ea4e668bf73 - 33d61c89fb8d - - 623f3eb7aa48 + - 83069b38aa85 + - 2e8f945f7285 + - cf34c344508d + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - ae8c4b2488e7 - 503bcd6ebe4b - 399da6b5ec21 + - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -140,10 +140,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - c4d18aa4ec4a - bce29ec10b78 - b722161a845a - f768f6183386 + - c4d18aa4ec4a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -156,14 +156,14 @@ tools: - name: text_processing owner: bgruening revisions: - - 86755160afbf - - 12615d397df7 - - 9ff72e942410 - - a6f147a050a2 - - 74a8bef53a00 - - f46f0e4f75c4 - ddf54b12c295 - fbf99087e067 + - 12615d397df7 + - 86755160afbf + - 74a8bef53a00 - d698c222f354 + - a6f147a050a2 + - 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 23951855b..46e6a3328 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -14,9 +14,9 @@ tools: - name: breseq owner: iuc revisions: - - 85c57cc9b558 - - 82fb5e3bb93e - 0d18a3ba2d1c + - 82fb5e3bb93e + - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -28,67 +28,67 @@ tools: - name: cutesv owner: iuc revisions: - - c0f8fe52948e - - cb441f258c37 - 23d7e75d850e + - cb441f258c37 + - c0f8fe52948e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: - - 57def2d7c093 - - ef2c525bd8cd - 156b60c1530f - - 3e954e7125bf - - 04fa42777df9 - a5937157062f + - 04fa42777df9 + - ef2c525bd8cd + - 3e954e7125bf + - 57def2d7c093 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 09d6e4693887 - 791f73caa0c8 - e61c9ac190ad - 435b157bed6d - - 09d6e4693887 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - e1461b5c52a0 + - 3b4b2121842f - 03627f24605f + - e1461b5c52a0 + - dfadc322b065 - 65432c3abf6c - - 074d44697036 - - 3b4b2121842f - b11e8e9c23bf - - dfadc322b065 - 4805fe3d8fda + - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 9cb929f21cfa - 7dfca164d2e3 - 701d134358ad - - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: + - c27549b9aa1f + - 426d707dfc47 - f4473557ffc7 - 971e07ca4456 - - 426d707dfc47 - - c27549b9aa1f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: + - cdaab621d454 - dbd9f2db9ed8 - aa35ee7f3ab2 - - cdaab621d454 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -146,21 +146,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 32f14a2723ec - - 40f0591deda0 - 3b1e7c170b10 - e7aff4a85df5 + - 32f14a2723ec + - 40f0591deda0 - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - adc0645b945c - - 42818629ec4c - - 4934c0ac6197 - 02d81b994ef5 - 9793bc5d741b + - 42818629ec4c + - 4934c0ac6197 + - adc0645b945c 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 721c7e057..cb844afb0 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ b/usegalaxy.org.au/vcfbcf.yml @@ -2,233 +2,233 @@ tools: - name: bcftools_annotate owner: iuc revisions: + - b7ea370b8f5d - 2c372041ed8c - - 95815a0bb307 - - 265fe0f9ea64 - 6a88248893c4 - 8a2e296c07ef - - e075b1be5abb + - 95815a0bb307 - ebe5fc018e72 - - b7ea370b8f5d + - e075b1be5abb + - 265fe0f9ea64 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call owner: iuc revisions: - - 0fba2c15b40d - - b03984136ce4 - - 1001172b5089 - - 544cb432072b - - 22637b1a55bf - c37b684e7f4e + - b03984136ce4 - 07396b423218 - 21687e35f066 + - 22637b1a55bf + - 1001172b5089 + - 0fba2c15b40d + - 544cb432072b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv owner: iuc revisions: - - 8ca3647c90fd - - bf1f4994f104 - - 3a7084316a6e - - 143796b504eb - - 0238f68ad641 - 01d6b7d6365e - 8408bffd5616 - 8627b2b383b4 + - bf1f4994f104 + - 0238f68ad641 + - 143796b504eb - ccb83bf54de0 + - 3a7084316a6e + - 8ca3647c90fd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat owner: iuc revisions: + - d144af39073a + - 9b5abbf50d23 + - f430a1ec7ee4 - 6b6c992d3a14 - 03e0645395d2 - - f430a1ec7ee4 - abd489215f73 - - 81426b3cf18b - 05f317e50e61 - - d144af39073a - - 9b5abbf50d23 + - 81426b3cf18b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus owner: iuc revisions: - - 1171446da5db - - d37e313a41be + - 95c6f3f4c77f + - e522022137f6 + - d3081540d175 - 2363ef414c9b - 8aa352093d73 + - d37e313a41be - 1829900b5dcd - - e522022137f6 - - d3081540d175 - - 95c6f3f4c77f + - 1171446da5db tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf owner: iuc revisions: - - 92c0aff8b53e - - d58d2e8c7a57 - - 09f37afb3621 - 348cd212dbad - - 9b29129fb491 - - 012656fd329f - 1137ce8efc1e + - 92c0aff8b53e - b14ff40958cb + - 9b29129fb491 + - 012656fd329f + - 09f37afb3621 + - d58d2e8c7a57 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf owner: iuc revisions: - - de68c11034f6 - - 7291189e98b4 - cfd81f17580b - - 1f2183a23823 + - 7291189e98b4 + - de68c11034f6 + - 367ba501b6eb - 55c0e906c14c + - 1f2183a23823 - ecc9192912b8 - - 367ba501b6eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq owner: iuc revisions: - - 64a8f7dae3ad - - e6f4badbe6f3 - 7cbf3c66d4ad + - e6f4badbe6f3 + - ae68ceb4cca3 + - 64a8f7dae3ad - d237eaef451f - 6c790a091c7c - 039ea3f1dea9 - - ae68ceb4cca3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter owner: iuc revisions: - - 6ea7170a016d + - 963a3635b2e1 - 33bd9301568c - - 277719af4dd7 - 5d6653c989cb - e7452697afd9 - - 963a3635b2e1 - 46fcafba49ec + - 277719af4dd7 + - 6ea7170a016d - cdb7b4927742 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck owner: iuc revisions: - - 26d97cdd5410 + - 91c1e57d5c7f - b7f0f59baa7e - - 7b4454382d39 - - a1213a0b7b66 - 501bfb078342 - - 91c1e57d5c7f - - a29a2f40b665 + - 26d97cdd5410 - 5a321fab1fe4 + - a29a2f40b665 + - 7b4454382d39 + - a1213a0b7b66 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec owner: iuc revisions: - - 81e4014fa809 - - c803c34361e0 - - 39bca000353d - 709dd8291b83 - - 768d04526638 - - 97d19c008d15 - - 5f27e814a119 - d7d1663559e9 + - 5f27e814a119 + - 97d19c008d15 + - 39bca000353d + - 81e4014fa809 - 15da1ddcfeff + - 768d04526638 + - c803c34361e0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge owner: iuc revisions: - - 5b006286a458 - - 85ee7e6c4204 - 2215287d5cc9 - - b1eba148b35b - - b84fda8ebef0 - 7ba36babba2d + - 5b006286a458 - b931e65638b8 + - b1eba148b35b - 86296490704e + - 85ee7e6c4204 + - b84fda8ebef0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup owner: iuc revisions: - cf06b44624c7 - - 9c711df3258d - 5660b21a0dbd - - 56556e1267de + - 0a5dcc9a8ec2 - 31ea13dfe5e6 - 37757ffb4c5f - - f506df85c652 - - 0a5dcc9a8ec2 + - 56556e1267de + - 9c711df3258d - ce9396ddcb2b + - f506df85c652 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm owner: iuc revisions: - - 48291658fdf6 - - a404f786a94c - - 021693fdadaa - 1ca7418e46ee - - 271965b55437 - 6deb4d549bc9 + - a404f786a94c + - 48291658fdf6 + - 271965b55437 + - 021693fdadaa - 19905c025d2a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts owner: iuc revisions: - - dadbd61dc4cf + - 97e8145d7e30 + - 5ad5d4243987 + - 3f6fadf8b8ff - 71c78e0eea52 + - f7879f1e77f9 + - dadbd61dc4cf - 69d8b7567281 - - 3f6fadf8b8ff - - 5ad5d4243987 - c450406f722b - - 97e8145d7e30 - - f7879f1e77f9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage owner: iuc revisions: + - 0fe007201caf + - 283911fe7e1a - 79f7a1acc2cd - - 52f9e4a660e3 - 2514e684f8a3 - - cc7f9a4e186b - - 0fe007201caf - 6cf13a657cf6 + - 52f9e4a660e3 + - cc7f9a4e186b - d31a2e310a52 - - 283911fe7e1a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 1411bef27a75 + - 026a989b7cee + - 6963a6841d22 - 80e6e399ccd0 - 230e424bde67 - 0a62420cb9cd - - 75ddd081f608 + - 1411bef27a75 - a12844ca467a - - 6963a6841d22 - - 026a989b7cee + - 75ddd081f608 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags owner: iuc revisions: - - 5acfca5a76af - - 5808f77b2bb6 - - bca7ce81688f - - b10d1510fa84 - ba20340426fe + - b10d1510fa84 + - 5808f77b2bb6 - e493702b19eb + - 5acfca5a76af + - bca7ce81688f - 450a265f92e8 - 444e6a756c35 tool_panel_section_label: VCF/BCF @@ -236,158 +236,158 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - c43399f161f4 + - d52b8947b269 + - dd72ff87cfd0 - 68fec03a63b7 - 157ffcdd3fa7 - f2482aa4862e - - dd72ff87cfd0 - - d52b8947b269 - 12152af85697 - 4d236c696844 + - c43399f161f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info owner: iuc revisions: + - 75becf493cd3 - cbe39e530cbf - bc5332d47b1c - 29ba253e2e05 + - 0e5d11004815 + - 6f8e223f78f3 - 8dbce095986c - - 75becf493cd3 - 8f2fc0ab30fb - - 6f8e223f78f3 - - 0e5d11004815 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian owner: iuc revisions: - - a8630d4fbaf8 - - e0a856def0b0 - - 3ff5654b4e7d - a367a15c6de5 - f544f71adb73 - - 9708e3086f32 - 88bb477f45f7 + - 9708e3086f32 - 8f5962c43868 + - a8630d4fbaf8 + - 3ff5654b4e7d + - e0a856def0b0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref owner: iuc revisions: + - 34dc0bbc7e93 + - 8b260d252ff4 + - 6ce175385dd9 + - 4ed46189d6c6 - 03e30f06f15f - 96d0145c041a - - 4ed46189d6c6 - 5c9729d54721 - - 34dc0bbc7e93 - - 8b260d252ff4 - 31c096c6b156 - - 6ce175385dd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt owner: iuc revisions: - - 2c4941386820 - - 11af7fce71cf - - a730269af659 - - 46eb13bc2c73 - - 09f5e45a8212 + - a1aad8b559c6 - 681bdf1e22ff + - 09f5e45a8212 - 40daf124be88 - - a1aad8b559c6 + - a730269af659 + - 46eb13bc2c73 + - 11af7fce71cf + - 2c4941386820 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 882b2e649602 - - b74b8cbfc1f1 - f272b8ba0983 - - 3897eaadfbff - - 0594ea1417c8 - - 8cb121b6a1d2 + - b74b8cbfc1f1 - 6cbb9c47795c + - 3897eaadfbff + - 882b2e649602 - 12038f59c0f4 - 743cd1472aeb + - 0594ea1417c8 + - 8cb121b6a1d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples owner: iuc revisions: - - a9826db86d9a - - 2c80b0d6bde0 - - dba06328556a - 238f78e38a8b - cced6715f926 - adee7e8b746f + - 2c80b0d6bde0 - 18cf9de1cf73 - eccb508bb678 + - dba06328556a + - a9826db86d9a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query owner: iuc revisions: - - fdec14f69010 - - f64e7ca2efd2 - - c9935c9e8a24 - 31a1b89eab9b - - e0ad88dec40d + - fdec14f69010 - e53501abf992 - - 9f36041495a3 + - e0ad88dec40d + - c9935c9e8a24 + - f64e7ca2efd2 - 3ce32adc55b2 + - 9f36041495a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader owner: iuc revisions: - - d43eb39b989e + - b7be725976b6 + - d68c43202172 - 79489d5685dd - fd3539749127 - - d68c43202172 - - b7be725976b6 - 3b7b1fe7b937 - - 2331ddcbd5aa - 4db0695a6fc7 + - 2331ddcbd5aa + - d43eb39b989e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh owner: iuc revisions: - - 58091e1be01b - - 6a636d58dfc2 - - 78cd8b69da4c - - 5296d26b0373 - 1ccf0e7fb4f6 - 1a989b4110da - - fa65af07ce7d + - 78cd8b69da4c + - 6a636d58dfc2 - b0d39ef600a7 + - fa65af07ce7d + - 5296d26b0373 + - 58091e1be01b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats owner: iuc revisions: - - b17394940c7a - - e8af591435d1 + - 4d3ce9dc1525 + - bf8325a07ce7 - baa8823f8073 - - 591cc8518033 - '388983871932' + - 591cc8518033 + - b17394940c7a - b641062a2587 - - bf8325a07ce7 - - 4d3ce9dc1525 + - e8af591435d1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view owner: iuc revisions: - - d1f8f55f564d - - 3a233c8eb814 - - e6b5cbbf449b - c2ab91a0d506 - - 3ca3de4e5291 + - 3a233c8eb814 - 38d75661c235 - - 1a2ef636f48e + - 3ca3de4e5291 + - e6b5cbbf449b - 59fa8742285e + - d1f8f55f564d + - 1a2ef636f48e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2tsv @@ -407,15 +407,15 @@ 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 @@ -428,8 +428,8 @@ tools: - name: vcfbedintersect owner: devteam revisions: - - aea8e90ad788 - 9edfe5145ba8 + - aea8e90ad788 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -442,44 +442,44 @@ tools: - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine 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: - - 254f285dbaaa - f1852ecef841 + - 254f285dbaaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - 6b935ab36d7b - 4bdc111b2470 - eae7c08ebb6f + - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -499,15 +499,15 @@ tools: - name: vcfgenotypes owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom owner: devteam revisions: - - b07ef36cf7e6 - 8254e0fe7358 + - b07ef36cf7e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign @@ -520,8 +520,8 @@ 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 @@ -554,7 +554,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 166c4f50525f - 6f6bf10618d7 + - 166c4f50525f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu