From a16d9ed7d56e3d0d3bd2ee1539878f4f3deef895 Mon Sep 17 00:00:00 2001 From: admin Date: Thu, 26 Sep 2024 02:16:49 +0000 Subject: [PATCH] Jenkins install build 1633. --- automated_tool_installation_log.tsv | 1 + requests/gtdbtk_latest.yml | 6 - staging.gvl.org.au/annotation.yml | 118 ++++---- staging.gvl.org.au/assembly.yml | 260 ++++++++-------- staging.gvl.org.au/bacterial_typing.yml | 16 +- staging.gvl.org.au/bb_tools.yml | 10 +- staging.gvl.org.au/bed.yml | 16 +- staging.gvl.org.au/blast.yml | 12 +- staging.gvl.org.au/chemicaltoolbox.yml | 62 ++-- staging.gvl.org.au/chip_seq.yml | 10 +- staging.gvl.org.au/collection_operations.yml | 8 +- staging.gvl.org.au/convert_formats.yml | 42 +-- staging.gvl.org.au/deeptools.yml | 128 ++++---- staging.gvl.org.au/dna_metabarcoding.yml | 10 +- staging.gvl.org.au/emboss.yml | 4 +- staging.gvl.org.au/epigenetics.yml | 4 +- staging.gvl.org.au/fastafastq.yml | 100 +++---- staging.gvl.org.au/fastq_quality_control.yml | 32 +- staging.gvl.org.au/filter_and_sort.yml | 4 +- staging.gvl.org.au/gemini_tools.yml | 20 +- staging.gvl.org.au/genome_editing.yml | 2 +- staging.gvl.org.au/get_data.yml | 34 +-- staging.gvl.org.au/graphdisplay_data.yml | 58 ++-- staging.gvl.org.au/hca_single_cell.yml | 36 +-- staging.gvl.org.au/hicexplorer.yml | 24 +- staging.gvl.org.au/imaging.yml | 62 ++-- staging.gvl.org.au/ivar.yml | 78 ++--- .../join_subtract_and_group.yml | 12 +- staging.gvl.org.au/machine_learning.yml | 38 +-- staging.gvl.org.au/mapping.yml | 58 ++-- staging.gvl.org.au/metabolomics.yml | 32 +- staging.gvl.org.au/metagenomic_analysis.yml | 127 ++++---- staging.gvl.org.au/mothur.yml | 2 +- staging.gvl.org.au/multiple_alignments.yml | 52 ++-- staging.gvl.org.au/nanopore.yml | 42 +-- staging.gvl.org.au/none.yml | 58 ++-- staging.gvl.org.au/phylogenetics.yml | 104 +++---- staging.gvl.org.au/picard.yml | 8 +- staging.gvl.org.au/proteomic_ai.yml | 14 +- staging.gvl.org.au/proteomics.yml | 202 ++++++------- staging.gvl.org.au/rad_seq.yml | 70 ++--- staging.gvl.org.au/rna_seq.yml | 170 +++++------ staging.gvl.org.au/rseqc.yml | 4 +- staging.gvl.org.au/sambam.yml | 76 ++--- staging.gvl.org.au/send_data.yml | 8 +- staging.gvl.org.au/single_cell.yml | 168 +++++------ staging.gvl.org.au/statistics.yml | 26 +- staging.gvl.org.au/text_manipulation.yml | 44 +-- staging.gvl.org.au/variant_calling.yml | 30 +- staging.gvl.org.au/vcfbcf.yml | 282 +++++++++--------- usegalaxy.org.au/annotation.yml | 122 ++++---- usegalaxy.org.au/assembly.yml | 258 ++++++++-------- usegalaxy.org.au/bacterial_typing.yml | 8 +- usegalaxy.org.au/bb_tools.yml | 8 +- usegalaxy.org.au/bed.yml | 14 +- usegalaxy.org.au/blast.yml | 22 +- usegalaxy.org.au/chemicaltoolbox.yml | 60 ++-- usegalaxy.org.au/chip_seq.yml | 12 +- usegalaxy.org.au/collection_operations.yml | 6 +- usegalaxy.org.au/convert_formats.yml | 46 +-- usegalaxy.org.au/deeptools.yml | 124 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 8 +- usegalaxy.org.au/emboss.yml | 2 +- usegalaxy.org.au/epigenetics.yml | 6 +- usegalaxy.org.au/fastafastq.yml | 96 +++--- usegalaxy.org.au/fastq_quality_control.yml | 38 +-- usegalaxy.org.au/filter_and_sort.yml | 2 +- usegalaxy.org.au/gemini_tools.yml | 26 +- usegalaxy.org.au/genome_editing.yml | 2 +- usegalaxy.org.au/get_data.yml | 46 +-- usegalaxy.org.au/graphdisplay_data.yml | 66 ++-- usegalaxy.org.au/hca_single_cell.yml | 18 +- usegalaxy.org.au/hicexplorer.yml | 16 +- usegalaxy.org.au/imaging.yml | 64 ++-- usegalaxy.org.au/ivar.yml | 84 +++--- usegalaxy.org.au/join_subtract_and_group.yml | 6 +- usegalaxy.org.au/machine_learning.yml | 50 ++-- usegalaxy.org.au/mapping.yml | 50 ++-- usegalaxy.org.au/metabolomics.yml | 32 +- usegalaxy.org.au/metagenomic_analysis.yml | 135 ++++----- usegalaxy.org.au/mothur.yml | 6 +- usegalaxy.org.au/multiple_alignments.yml | 54 ++-- usegalaxy.org.au/nanopore.yml | 46 +-- usegalaxy.org.au/none.yml | 58 ++-- usegalaxy.org.au/phylogenetics.yml | 96 +++--- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 14 +- usegalaxy.org.au/proteomics.yml | 204 ++++++------- usegalaxy.org.au/qiime_2.yml | 2 +- usegalaxy.org.au/rad_seq.yml | 76 ++--- usegalaxy.org.au/rna_seq.yml | 160 +++++----- usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 76 ++--- usegalaxy.org.au/send_data.yml | 8 +- usegalaxy.org.au/single_cell.yml | 188 ++++++------ usegalaxy.org.au/statistics.yml | 34 +-- usegalaxy.org.au/text_manipulation.yml | 36 +-- usegalaxy.org.au/variant_calling.yml | 42 +-- usegalaxy.org.au/vcfbcf.yml | 268 ++++++++--------- usegalaxy.org.au/viral_tools.yml | 2 +- 100 files changed, 2795 insertions(+), 2798 deletions(-) delete mode 100644 requests/gtdbtk_latest.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index fad5529f7..5049327da 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7831,3 +7831,4 @@ Update 211 25/09/24 13:48:30 ucsc_fasplit False Installed iuc d3f58a0dc09d d3f58 Update 211 25/09/24 13:49:04 ucsc_fatovcf False Installed iuc 3c19c84fbce2 3c19c84fbce2 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_211/install_log.txt Update 211 25/09/24 13:53:57 ucsc_twobittofa False Installed iuc 3c6f9e8a4c17 3c6f9e8a4c17 1/1 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_211/install_log.txt Update 211 25/09/24 14:01:36 ucsc_wigtobigwig False Installed iuc 98704d357ede 98704d357ede 5/5 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_211/install_log.txt +Install 1633 26/09/24 12:16:29 gtdbtk_classify_wf False Installed iuc 5c7ba3d85a01 latest 1/1 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1633/install_log.txt diff --git a/requests/gtdbtk_latest.yml b/requests/gtdbtk_latest.yml deleted file mode 100644 index 13fb566ad..000000000 --- a/requests/gtdbtk_latest.yml +++ /dev/null @@ -1,6 +0,0 @@ -tools: -- name: gtdbtk_classify_wf - owner: iuc - tool_panel_section_label: Metagenomic Analysis - 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 26bbb7a56..b0f4f6c0e 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - 78c75f134c16 - - 4efdca267d51 - 6e9aea89e388 + - 78c75f134c16 - c2ef298da409 - 3f3e247c053d + - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - 3f438bf5475d - c45c9dd066e2 + - 3f438bf5475d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval @@ -33,22 +33,22 @@ 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: - - f29602ae449e - b5d8e5475247 - - 3e1f6f6d557e - - cd2480f35935 - fe3ca740a485 - - 4f2967b27e67 + - cd2480f35935 - a79ee60b6926 - - 133f36c29579 - 1aae04680c4b + - 3e1f6f6d557e + - 133f36c29579 + - 4f2967b27e67 + - f29602ae449e - 44018dd6b447 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -62,34 +62,34 @@ tools: - name: augustus_training owner: bgruening revisions: - - dc027fa56d55 - - 7be22100e5e1 - 6519ebe25019 + - 7be22100e5e1 + - dc027fa56d55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - ca6d970d931c + - 09855551d713 - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - da5f1924bb2e + - 728dacaf08a9 - d77802fe76f7 - 92eee5f31117 - - 728dacaf08a9 + - da5f1924bb2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -115,16 +115,16 @@ tools: owner: bgruening revisions: - 8e9e228c54c4 - - 1ac12c0cc7a0 - 7ccc6234b54e + - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - 63662ae295d6 - - d9c3016f7283 - 9d1fbff733cf + - d9c3016f7283 + - 63662ae295d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -149,60 +149,60 @@ tools: owner: iuc revisions: - 3bbe70fef6df - - 582fd74dc2a1 - 9f2455341fac - - 14f588312c56 - - 756376aeb1ae - 9c15ca7e764e + - 582fd74dc2a1 + - 756376aeb1ae + - 14f588312c56 - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 30fb23d4c31c - 989f7c061f35 - - 8e1ace8f77c6 - a230ea445788 + - 30fb23d4c31c - 73428a792541 - 0ffe5be70caf - 1691af4a0d17 + - 8e1ace8f77c6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 0418d28136de - - 57c6718cbfcc - - 494f0bb4a993 - 30f08d74024f - - 563a19373357 - - e94187d661df - 5a5ae61da69c + - e94187d661df + - 494f0bb4a993 + - 563a19373357 + - 0418d28136de + - 57c6718cbfcc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 7abc5f6dd595 - f77d7b685bb3 - - 1bc5a03faf2e - - d6c7106b7b2e - - f31125bb85ea - 4b96ced19f75 + - f31125bb85ea - 2bba2ff070d9 + - 7abc5f6dd595 + - 1bc5a03faf2e + - d6c7106b7b2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - b3cf4684e9c7 - - d77fdcca400e - - d3af38b9c7e1 - - 52af33194019 - fed64e676186 + - b3cf4684e9c7 - 520e30695ec3 + - d77fdcca400e - 54961e026fe4 + - 52af33194019 + - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -214,9 +214,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 79261884facd - 2aea122fbd25 - 07d7991bf205 + - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -228,9 +228,9 @@ tools: - name: goseq owner: iuc revisions: + - 602de62d995b - 43798b4caee0 - ef2ad746b589 - - 602de62d995b - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -262,9 +262,9 @@ tools: - name: interproscan owner: bgruening revisions: - - c55643c3d813 - - 98cafcbd2578 - 74810db257cc + - 98cafcbd2578 + - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -289,19 +289,19 @@ tools: - name: maker owner: iuc revisions: - - d46d803ca6cc - 370c210d9541 + - d46d803ca6cc - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - e95d52d295d7 - b815ec682418 - - c8ac28e8ac44 - - 033755194fe9 - 624606f7c996 + - e95d52d295d7 + - 033755194fe9 + - c8ac28e8ac44 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -343,11 +343,11 @@ tools: - name: prokka owner: crs4 revisions: - - 8a22554cdde2 - eaee459f3d69 + - bf68eb663bc3 - a17498c603ec - d643e3b03500 - - bf68eb663bc3 + - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -359,15 +359,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -391,22 +391,22 @@ tools: - name: snpeff owner: iuc revisions: - - 5a29ab10dba6 - cfcf33df7fc0 + - 68693743661e - 8f92c2b26e6d + - 5a29ab10dba6 - 5c7b70713fb5 - - 5b80f544c67f - 9473cd297a76 - - 68693743661e - 268d162b9c49 + - 5b80f544c67f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - 5fab4f81391d - 2b3e65a4252f + - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -431,24 +431,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - 4839e590cb26 - 200c378d85f3 + - 037a11682176 + - 4839e590cb26 - 51dd22484644 - - 809dfc93d593 + - 45083d070fb8 - ba6f87115e13 - - 37213cf56392 + - 809dfc93d593 - d03af1c7002c - - 037a11682176 - e1a9d6fd258d + - 37213cf56392 - ac8250086ac3 - - 45083d070fb8 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index e2df4bf13..9eb09cf2f 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,81 +2,81 @@ tools: - name: abyss owner: iuc revisions: - - 553bfe8bd0b5 - - 7547fcab5d19 - - 8f1b150a2487 - - d6d5ccc2c581 - - a929ce596a34 - - fa5259cc561b - 0e93176640ac - 841084c5fc46 - - 890b794c997d + - fa5259cc561b + - d6d5ccc2c581 - 0124fce4654a + - a929ce596a34 + - 553bfe8bd0b5 + - 890b794c997d + - 7547fcab5d19 + - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 21e491ad532a - ddddce450736 + - 21e491ad532a + - 067592b6b312 - b2860df42e16 - 94fe43e75ddc - b9e31c5c01c7 - - 067592b6b312 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 321347bd0494 - 25ca5d73aedf + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 - a7f16f24e9a1 - 5258e18bbe23 - 22286dab5aa1 - 3371c5bdc17a + - faee8629b460 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 8c2167481e72 - 53dd00a4ab68 + - 8c2167481e72 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 5ecdeca79a0d - - 41030a6c03b7 - - cf13a1e03e5b - - 4048d82f0c88 - - 46ae58b1d792 - 94170eee0ad8 - - e4bd1e99bacf - - 1440ae06552f - - 1e62c28ba91d - - 602fb8e63aa7 + - 2babe6d5c561 - 2dd755c1c6ff + - 602fb8e63aa7 - e824f5d958d0 + - 1440ae06552f + - e4bd1e99bacf - f18f0b887c31 - - 0d243f458b53 + - cf13a1e03e5b - bb935709506a + - 4048d82f0c88 + - 5ecdeca79a0d + - 0d243f458b53 - ea8146ee148f - - 2babe6d5c561 + - 41030a6c03b7 + - 1e62c28ba91d + - 46ae58b1d792 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - c5b7390290b1 - 86f150c8019d - 5732f959936a + - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -88,42 +88,42 @@ tools: - name: flye owner: bgruening revisions: + - 8d4f03b5fe9d - 276f5d8712d5 - - 291923e6f276 - cb8dfd28c16f - - 1f0769f0b56b - - e27815e82dd4 - - 3e4f8642c77e + - 291923e6f276 - 1ce9b1d72ec3 + - 3e4f8642c77e + - 1f0769f0b56b - 3ee0ef312022 - - 8d4f03b5fe9d + - e27815e82dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 460fad600dce - - 3169a38c2656 - - b2f674562a18 - 01210c4e9144 + - b2f674562a18 + - 3169a38c2656 + - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - - 7348b69e5109 - ba88bc5a6446 + - 7348b69e5109 - 8b330a577046 + - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 690c2caa367e - - 3ef480892a9f - 5127a713de83 + - 690c2caa367e - 3fba9c77550a + - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -135,23 +135,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 71740308d412 - - 9ef6920c3089 - - f3c89da3af16 - - 6505bd37670d + - df25d4fb79b7 - 284a1cb82b61 - - 0ee0c3089254 + - 41cea2aa2dce - 2061fb3b81b4 - - 366a11d316a7 - - da9d8bf98802 - - ec9e21e9c71b - - 5f625c63b8bc - 045c7c3d8e59 - - 3f7be05a1597 - - 41cea2aa2dce - - df25d4fb79b7 - 5bec28269d95 + - f3c89da3af16 + - 3f7be05a1597 + - 9ef6920c3089 + - 0ee0c3089254 - 60024a528cbd + - ec9e21e9c71b + - 5f625c63b8bc + - da9d8bf98802 + - 6505bd37670d + - 71740308d412 + - 366a11d316a7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -169,43 +169,43 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - 7518ee87b53d - - de387b2b2803 - a96f3ad4e0d8 + - 14ddfc8ffb93 + - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 09c589057ee8 - - 39edec572bae - - 9d79beb19ac3 - d7edbc9c3a07 - eb7b00ec347d + - 39edec572bae + - 09c589057ee8 - f8113c25bc6b + - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - eadfd71dde37 - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - f369ef5f210b + - f338e9942b27 + - 3ca2d2a9068c - 99ecfdafc64f + - fd128c111ab0 + - f369ef5f210b - e731ea24e48d - 2ecf5a570907 - eb7a370f6588 - - f338e9942b27 - - fd128c111ab0 - 606b09cc9860 - - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -217,10 +217,10 @@ tools: - name: miniasm owner: iuc revisions: - - 8b6d0d85252b + - b799a615995d - a7b889b90140 + - 8b6d0d85252b - 73a3846701e1 - - b799a615995d - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -239,8 +239,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 15200570e926 + - 64a1c751d99b - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -253,46 +253,46 @@ tools: - name: pretext_map owner: iuc revisions: + - 2b16ba799da9 + - 02831bf9e95f + - bbe19ef04a74 - dfb8a4497339 - 8fef980d48b5 - - 79b48f02db49 - - 02831bf9e95f - - 2b16ba799da9 - d256a51a656b - - bbe19ef04a74 + - 79b48f02db49 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - - a315c25dc813 - 76d4cbefff85 + - a315c25dc813 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - 6fcbee531de6 + - 7594365c546b + - 59db8ea8c845 + - 3061c8b029e5 + - ebb0dcdb621a - 72472698a2df + - 875d0f36d66f - 675488238c96 - - ebb0dcdb621a - - 59db8ea8c845 - 342a1d1fed7b - - 875d0f36d66f - - 7594365c546b - - 3061c8b029e5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - aa39b19ca11e + - cd06929b224b - d865b62f501c - 39bed8de8017 - - cd06929b224b - - 78c533842eeb - a199cd7ac344 + - 78c533842eeb + - aa39b19ca11e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -310,11 +310,11 @@ tools: - name: raven owner: iuc revisions: - - 33b7d8481a76 - - 2b2a352488fa - - f11b994b7eb2 - 5c55448d0f33 + - f11b994b7eb2 + - 2b2a352488fa - 3edba9afc9bc + - 33b7d8481a76 - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -328,13 +328,13 @@ tools: - name: rnaspades owner: iuc revisions: - - 378e55aeeb25 - - 53c2bc8c2ae3 - - 28189050e437 - - e122f9101584 - 1d06c8b38e77 - 5fc94b3a4704 - ef69617ecb42 + - 53c2bc8c2ae3 + - e122f9101584 + - 28189050e437 + - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -346,45 +346,45 @@ tools: - name: shovill owner: iuc revisions: - - f698c7604b3b - - 196a599ec43d - - d9f6a00b6db7 - 83ead2be47b2 - - 865119fcb694 - ee17a294d3a3 + - 865119fcb694 + - d9f6a00b6db7 + - 196a599ec43d + - f698c7604b3b - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - 015283de3004 + - 24e471d13fe9 - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 1bb12736175c - - 1fc82fe7ebef - - c33a476f4001 + - 604782a8a53a - 904bf932cf78 + - 1fc82fe7ebef - 051fd2db8a27 + - c33a476f4001 - 7490b213baa9 - - 604782a8a53a + - 1bb12736175c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - fee85957cebe - - d6e617c4e338 - - 808b3a0a6716 - ad8b536d1caa - 655fa188c3cc - - 9678993ca5bd - 34305b013402 + - 9678993ca5bd + - 808b3a0a6716 + - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades @@ -392,58 +392,58 @@ tools: revisions: - e5a3b75a271f - b8002c3f7141 - - 8d4b90bf9caf - 7e27faaad80e + - 21da31ed41a1 - 037f9927c4ff - 6b5a5842531e - - 21da31ed41a1 + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: + - f1532cb33c75 + - 86f66ab58e14 - 2a10645aeadd - 7922870efcca - - 86f66ab58e14 - - f1532cb33c75 - - 328aa71f0f3c - 5b26685e5d3b - 9de69775f512 + - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 340bc17f49cf - - 85fb02c43042 + - e41dcb0e913b + - 6aad515a5270 - 8cc856b935ee + - 85fb02c43042 - 1708851f8804 - - 6aad515a5270 - - e41dcb0e913b + - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - b65a43f70b99 + - 6357b127161e + - d159735a6a9f - b3490b036c5a - 249f6a28c751 - d5fb354f745d - de1260f8a300 - - b65a43f70b99 - - 6357b127161e - - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - b7829778729f - - a90db5dbaaf3 + - 33368fec3b70 - d2d1df21dfb9 + - a90db5dbaaf3 + - dd7ad84f3943 - d5887ace0dd4 + - b7829778729f - 7897763d14ec - - 33368fec3b70 - - dd7ad84f3943 - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -451,8 +451,8 @@ tools: owner: iuc revisions: - 6f4c8ad6ea01 - - ed2425b9fd27 - 189e837009c9 + - ed2425b9fd27 - 8f631679571f - ced385aa976d - 505a9833ab5d @@ -461,57 +461,57 @@ tools: - name: trycycler_consensus owner: iuc revisions: - - 356afed970b4 - - e59bee4565b3 + - 9ded6109434a - d40ed4eb0c0e - f31d376ce725 - 19bdfd1e6fe3 - - 9ded6109434a + - 356afed970b4 + - e59bee4565b3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 80a17897564d - - 6dd935e4984b - - b23249f81bc4 - af40e971a8cc - - ebd801e712bc - 4688ae3b49b5 + - ebd801e712bc + - 6dd935e4984b + - b23249f81bc4 + - 80a17897564d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - 937ea677d437 + - b5e35a2ca4f3 - b64696992ee9 - bb11fefb23a3 - - b5e35a2ca4f3 - 59bd28f6265d - cb1e3db43020 - - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - 6015aa0303f2 - - 05bd7504fdb2 + - 383bb5ad32e2 + - 6bfab4a4a988 - cb4768eeca3b - 2628f6790eda - - 6bfab4a4a988 - - 383bb5ad32e2 + - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - e022dff952df - - e92675014ac9 - - 3e44ef016b45 - - 9e3e80cc4ad4 - 0a3a602cd1e3 - - 8f9f06995f98 - 6e26c9afd301 + - 3e44ef016b45 + - e92675014ac9 + - 8f9f06995f98 + - 9e3e80cc4ad4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet @@ -526,11 +526,11 @@ tools: - name: velvetoptimiser owner: simon-gladman revisions: - - 37d88f41c810 - - 4a53b89fa703 - - 82398ba86ba7 - d81360ea69d8 + - 37d88f41c810 - 0e2b4e3f9ca1 + - 82398ba86ba7 + - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 90c8526a5..ee902b9d3 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: - - 392f100eebcd - - bfd290fe1588 - - 1ae00120dd24 - 4768f7f8e93f + - 1ae00120dd24 + - bfd290fe1588 + - 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: - - 31812e7a1315 - - 1f5641a52664 - - ded48b36f3b7 - 8e8dc9a1e3e5 + - ded48b36f3b7 + - 1f5641a52664 + - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 24a7a95867b0 - - 5c8ff92e38a9 - 17fcac7ddf54 + - 5c8ff92e38a9 + - 24a7a95867b0 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 7c8e97897..28946dda1 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,12 +2,12 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 204a131e47db - - 1c427e24fb79 - - a9c9d768b751 - - d1f62024a08b - - 0840ba83860c - 159b04e36791 + - 0840ba83860c + - d1f62024a08b + - a9c9d768b751 + - 1c427e24fb79 + - 204a131e47db - 7beb76ffbc0f 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 0fcc0c3b7..fd823a883 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: - - a1a923cd89e8 + - a8eabd2838f6 - b28e0cfa7ba1 - - dde39ba9c031 + - 0a5c785ac6db - e19bebe96cd2 - - a8eabd2838f6 - - a68aa6c1204a - - ce3c7f062223 - - 87ee588b3d45 + - 64e2edfe7a2c - 07e8b80f278c + - 87ee588b3d45 + - dde39ba9c031 + - a68aa6c1204a + - a1a923cd89e8 - 589e7e57fd6d - - 64e2edfe7a2c - - 0a5c785ac6db + - ce3c7f062223 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index 5b9fe1563..2c0c66b0b 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,9 +8,9 @@ tools: - name: diamond owner: bgruening revisions: - - f921014aba5a - 54f751e413f4 - 62c9df8382c2 + - f921014aba5a - e8ac2b53f262 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - cbf3f518b668 - - 6f386c5dc4fb - a52d2d93e595 + - acf4e47b734c - 5edc472ec434 + - e25d3acf6e68 - d999e774072a - - acf4e47b734c - 2889433c7ae1 - - e25d3acf6e68 + - 6f386c5dc4fb - 0e3cf9594bb7 + - cbf3f518b668 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus @@ -43,8 +43,8 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 27a0a65b9..2d3c5eb96 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -9,12 +9,12 @@ tools: owner: chemteam revisions: - 6ca543ec1bf8 + - da6bd1975a71 + - 27ee142314a9 - f4230f116196 - 095ad4d096d1 - 710301bc46fa - c8cdde00b105 - - da6bd1975a71 - - 27ee142314a9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -124,74 +124,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - bfb65cb551d8 - - 88076940fa94 - 79cfd9ead848 - - 0fac8e2afc13 - 3b8a9d5ced85 + - 0fac8e2afc13 + - bfb65cb551d8 + - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - f5d979cb4b54 - - 55918daa5651 - - d532b7e5f64b + - eb6564a60136 - 715cd0e87781 + - d532b7e5f64b + - 55918daa5651 - b46d4b4d995c - - eb6564a60136 + - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - fdf2cc80adb5 - f26afd1b7104 + - 5579659312e6 + - fdf2cc80adb5 - d2f955aea23a - 97872d87ba80 - - 5579659312e6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: + - d1d0efda35c0 - bc31d02be922 - 319a28774da9 - - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - - 2c349b027a01 + - 4da9ee404eab - 070e3ecc3fda - cac1886249a2 - - 4da9ee404eab + - 2c349b027a01 + - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - da8753545526 + - d1f803b5943c + - c0c9a5024177 - 73008ef1f487 - 525ca7c8065f - - f197e34c33a9 - 807aa4c9293d + - f197e34c33a9 + - da8753545526 - 2e219a2d9327 - - d1f803b5943c - - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 7568ae18908a - - c4fbab8e03c5 - - 1809414a9454 - - 61094e01eff9 - 27ea4e1a3f95 - 2c8ed1b52bf7 + - 1809414a9454 + - 61094e01eff9 + - 7568ae18908a + - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -203,18 +203,18 @@ tools: - name: md_converter owner: chemteam revisions: - - d7ec25187599 - - ccfbd956a2d3 - 79e8ab8f1e81 - ba83f0923369 + - ccfbd956a2d3 + - d7ec25187599 - 730ef07b90ae 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 @@ -262,10 +262,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - 4242b4d68e9c - - b59c91adeac1 - - 1400d1977e7b - e6011617c748 + - 1400d1977e7b + - b59c91adeac1 + - 4242b4d68e9c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -277,8 +277,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -332,9 +332,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 85fad59f8168 - bf99565cec1f - 9b48456a96fe - - 85fad59f8168 - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 64fbb2044..4e98679b4 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - 163688bb8f73 - - c97a786e8fb5 - f907216064f6 + - c97a786e8fb5 - fa56d93f7980 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,18 +23,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 11cf21ee4242 - 4124781932db + - 11cf21ee4242 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - f5d67c722d67 + - 495a4173006f - 86e2413cf3f8 + - f5d67c722d67 - 640d3af5d833 - 424aefbd7777 - - 495a4173006f tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -54,8 +54,8 @@ tools: owner: devteam revisions: - 4a14714649b4 - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 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 7381b291e..0eac90844 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 - 830961c48e42 - 25136a2b0cfe + - 33151a38533a - 90981f86000f tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - baabc30154cd - 6cbe2f30c2d7 - 0046692724f9 + - baabc30154cd - 2dae863c8f42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 55f72d466..1c33f4b6d 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - abba05ead5d7 - e7449b2c14bf + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: + - f3a19509108a + - ab9350a8ab4d + - 5e1240a87bcb - a3b86937ead6 - 0b3c3ad92827 - - 4a6ee918c13a - - f3a19509108a - - 6ef0b5664c69 - 3b6f97e7094c - - ab9350a8ab4d - - 367b1ed91207 - e3cbd2287f63 - - 5e1240a87bcb + - 4a6ee918c13a + - 367b1ed91207 + - 6ef0b5664c69 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 501c21cce614 + - 72ed72122deb + - 54ccb7e1f49a + - e177a8ea0bf1 - e525f9ffb9ac - - d4d4e9febf5c - - bd46669113b9 + - 091bb5922a82 - 1b5fc03380d4 - - 72ed72122deb - 33c99804a32f - - 091bb5922a82 + - 501c21cce614 + - d4d4e9febf5c - 584008e574b2 - - 54ccb7e1f49a - - e177a8ea0bf1 + - bd46669113b9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,23 +59,23 @@ 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 owner: devteam revisions: - - 186b8d913e6c - - 8979c288aefb - 77b41c89d856 + - 8979c288aefb + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -87,8 +87,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -127,8 +127,8 @@ tools: - name: samtools_bam_to_cram owner: iuc revisions: - - 18dbde5680c0 - b9ea85dfaf45 + - 18dbde5680c0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -141,8 +141,8 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 4e73f50a8..6ac137391 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: - - a1ca9bccc7f2 - - de72ba3ed6f2 - - 268e91e540ee - c929a006727f + - 5f6d123679f4 - 29451af70c52 + - a1ca9bccc7f2 - e821645ef8fc - - 5f6d123679f4 + - 268e91e540ee + - de72ba3ed6f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - 0e49b109abc2 - - 7a7fd0f5f15d - 0e143b4c3987 - 5d11599b8a7d - - bb1e4f63e0e6 - - 2d2cf5c1ea8a + - 7a7fd0f5f15d - 12af64f93288 + - 2d2cf5c1ea8a + - bb1e4f63e0e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - dc059492a995 - - 1d848bc4585f - 81b1e3e1fc6c - - 195e98217334 - 7c1beb6d6eca - c06951d10364 + - 195e98217334 + - 1d848bc4585f + - dc059492a995 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - a67ac707496a - - 07418a30ed01 - - 93eb012d9eed - 3d211717a775 - - 71aa86af6762 - bfff7454b59a + - 93eb012d9eed + - 07418a30ed01 + - 71aa86af6762 - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 29fcfd36e90a - 5be24eba848d - 2bc10a9ca58b - - 29fcfd36e90a - - dd0b7398bb96 - - 26983857c91a - b8858746dc1f + - dd0b7398bb96 - 56d5b797ce84 + - 26983857c91a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - 9384cd033f30 - - 7e6bcd2e5128 - - ee3a1b0f45f1 - - c3e012dfe21f - - 7ef978dc1b8a - 72bfafe3330b - e6d0bff01239 + - c3e012dfe21f + - 7e6bcd2e5128 + - 7ef978dc1b8a + - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fb9cf9c97ec4 + - 167788df3b46 + - d9a637e83828 + - b73e213add0c - 514fa53b5efb - - fd1275e01605 - 9470f29702f8 - - b73e213add0c - - 167788df3b46 + - fd1275e01605 - a60c359ec43c - - d9a637e83828 + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - a02cfa31e9cb - - ca0616bb2cdf + - 2c37ce318bc3 - c34d11ea4ba6 - e479c7ca5570 - - 2c37ce318bc3 - - 86febdcc4283 - 5bffaa8354a1 + - ca0616bb2cdf + - a02cfa31e9cb + - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 1fcb7adc39b8 - - 192ef85c0b0b - - 78f405266706 - - 004aea905d4d - 01fb6a7654e6 + - 004aea905d4d - 69a8621ca2f0 + - 1fcb7adc39b8 + - 192ef85c0b0b - 2d466b530754 + - 78f405266706 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 137c4beed34b - 459cfa861f0b - - d580d6acd1df - - 3c9f0c486cca - - d9ce4897dbb2 + - 137c4beed34b + - db940c262830 - 2f9e4843f480 + - d9ce4897dbb2 + - 3c9f0c486cca + - d580d6acd1df - 9ecba5e225a6 - - db940c262830 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fbe773640707 + - bd7db9e2f2cb - 2c66e43f1c86 - - bad3ca889618 - - f264afa9fa6f + - fbe773640707 - 32e451def88c - fd408d755394 - - bd7db9e2f2cb + - bad3ca889618 + - f264afa9fa6f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 56bce3c82278 - 9368fbc49c8b - - 4e12ea27f788 - - 7fda5607e777 - 231994413f89 + - 56bce3c82278 - 3b9d990a0a0e - 7e361d147872 + - 7fda5607e777 + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - b1779366c8e9 - - e65d16fb2724 - - c03c3384cd81 - 4431f39ede55 - d9114ef1c8a5 - 94ca68515826 + - e65d16fb2724 - ce4ce3316f74 + - b1779366c8e9 + - c03c3384cd81 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 23f7c5f1fdaf - - f8fc4e5aff9d - - 793665fff0f8 - - 2da482e408b8 - 4ed32329e0ed + - 2da482e408b8 - d57251071381 + - f8fc4e5aff9d + - 23f7c5f1fdaf + - 793665fff0f8 - b88ebb3672a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a4dfb122e52b - - c60570fa602f - - e4c7985d4585 + - 512155688d98 - 010e58e9d822 - - a7849312d328 + - e4c7985d4585 - 25d830337d31 + - a7849312d328 - ba6efa77fb79 - - 512155688d98 + - c60570fa602f + - a4dfb122e52b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - aa200e4f3939 - - 00d869ea03a1 - - c899e0ccff8c + - 69264da0ce77 - 38e3f226248b - 443d9a9d6d11 + - 00d869ea03a1 + - c899e0ccff8c + - aa200e4f3939 - 4d678170d29b - - 69264da0ce77 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - - c361b12d207a - 6662b1a8d326 + - aac8444d6681 + - a2d70c4fd406 - 10301d137111 - d806504e96d9 - - a2d70c4fd406 + - 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 c9143b7a7..1f611c25d 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -9,15 +9,15 @@ tools: - name: obi_clean owner: iuc revisions: - - 08d873cdd5f6 - 7d16de45c021 + - 08d873cdd5f6 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -37,22 +37,22 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 91a1ed0b486f + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort owner: iuc revisions: - - b6d9ea2fb41b - 12b9e285ca1c + - b6d9ea2fb41b tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 5f4544915893 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index b265e8fe5..58b655034 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - dba489bfcd62 - - 832c20329690 - 63dd26468588 + - dba489bfcd62 - ce385837c160 + - 832c20329690 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index 007848698..db39a90b0 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - 6da3972210ee + - cf1322aeb137 - d82648ad25a3 - 62f5fab76dfb - 29bdbc353f20 - - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 8748769f8..d30823ca5 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -9,25 +9,25 @@ tools: owner: lparsons revisions: - 48f587c13075 + - e4691e1589d3 + - 5eb7e84243f2 + - c5e2e5902201 + - 8c0175e03cee + - c4b82dce8335 - 135b80fb1ac2 + - 5915ea1ec9b1 + - 49370cb85f0f + - 093678460093 - fe74900d6dc7 - - c5e2e5902201 - - 5eb7e84243f2 - 4e5056fefd88 + - 8665bcc8b847 + - 660cffd8d92a + - 44e2cc14f75b - c053d4cad713 - - e4691e1589d3 - - 8c0175e03cee - - 49370cb85f0f - de6cebe3c043 - - 288f97432497 - b1c926deaa2d - 64172f1c1202 - - 660cffd8d92a - - c4b82dce8335 - - 44e2cc14f75b - - 5915ea1ec9b1 - - 093678460093 - - 8665bcc8b847 + - 288f97432497 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -39,9 +39,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: + - 9db07fd39f85 - f666895cbebd - 8889eb864cef - - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -53,8 +53,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - de2db1bdfbf8 - 7d37cfda8e00 + - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -73,16 +73,16 @@ 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: - - 9457a20156db - - 859422bcb689 - 516b97a23d7e + - 859422bcb689 + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -101,9 +101,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a - f773e98b26cf - f81d4362b6c1 + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -115,10 +115,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 0dbb995c7d35 - - 56022eb50bbd - cd0874854f51 + - 0dbb995c7d35 - 9c620a950d3a + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -130,11 +130,11 @@ tools: - name: fastp owner: iuc revisions: + - d60c3f704da0 - c59d48774d03 - dbf9c561ef29 - - 1d8fe9bc4cb0 - - d60c3f704da0 - 65b93b623c77 + - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -146,8 +146,8 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -160,22 +160,22 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 8611b80a14d6 - 47e5dbc3e790 + - 8611b80a14d6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -188,8 +188,8 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 2ccb8dcabddc - 3e396e702cea + - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -202,9 +202,9 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - - e39cc71d3ed6 - 249c8393f2d4 + - e39cc71d3ed6 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -216,9 +216,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: + - 54053ea6c77e - 045f0e1043f7 - 74db4cffab1f - - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -230,15 +230,15 @@ tools: - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - f0e7deab6518 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -266,8 +266,8 @@ tools: owner: devteam revisions: - 8abdedf55101 - - 4bedca26c133 - 0b7ec11b3c7c + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -308,10 +308,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - f984bb114520 + - 02f8a17a4ebd - 3599f5451ee2 + - f984bb114520 - b29d37ca9e41 - - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -323,10 +323,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 177f0621c266 - e246088b6e34 - - 6027ef51ef91 - 0c2907307ba4 + - 6027ef51ef91 + - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -338,10 +338,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 73194cdd4f57 - 377ac2829eac - - 547e8d00f11c - 61b4cedc8934 + - 547e8d00f11c + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -365,10 +365,10 @@ tools: - name: pear owner: iuc revisions: - - f69501361cec - - 037f0acc7830 - 2f804526f5fd - b4c6f054210a + - f69501361cec + - 037f0acc7830 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -380,15 +380,15 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: - - fdc21382376d - 61eb4cfc7313 + - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats @@ -420,16 +420,16 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - 71f649c23021 - bf04bd405d5b - d3f58a0dc09d + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -441,11 +441,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - e654095ab143 + - 24013bf85a6f - b557acca0b56 - 8250ea3a1501 + - e654095ab143 - a535cf1e5da4 - - 24013bf85a6f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -463,12 +463,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 6a675c3aa610 + - f3759eec3018 - 27ac32a22ad2 + - 6a675c3aa610 + - 9fa7803d1c51 - 828dba98cdb4 - - f3759eec3018 - 7accf7407811 - - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 1a29f8363..329be02c6 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,53 +2,53 @@ tools: - name: fastq_quality_filter owner: devteam revisions: + - 7b4468117008 - e41385662e5e - - ce9cd02d5b88 - 64e9a6afdd0c - - 7b4468117008 + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - f2e8552cf1d0 + - 5ec9f6bceaee + - ff9530579d1f - 2c64fded1286 - - e7b2202befea + - f2e8552cf1d0 - 9da02be9c6cc - - 5ec9f6bceaee + - e7b2202befea - 3d0c7bdf12f5 - - ff9530579d1f - 2b0c9d9fc6ca 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 - 18a51655db17 - b6b54ba71bd8 - - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 59003d0543cd - cc0fd298cc17 - 7306ec78632a + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong @@ -62,23 +62,23 @@ tools: - name: multiqc owner: iuc revisions: - - 3d93dd18d9f8 - f7e2f1eb3a16 + - 75c93c70d094 - b2f1f75d49c4 + - bf675f34b056 + - abfd8a6544d7 - 9a913cdee30e - - 1c2db0054039 - 5e33b465d8d5 - - abfd8a6544d7 + - 3d93dd18d9f8 - f7985e0479b9 - - bf675f34b056 - - 75c93c70d094 + - 1c2db0054039 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - 949f01671246 - 084bbd8ba7b8 - cd7e644cae1d - - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index 54bbfa7ed..ab23c208f 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 @@ -16,7 +16,7 @@ tools: owner: peterjc revisions: - 83a19df00eab - - 141612f8c3e3 - 85ef5f5a0562 + - 141612f8c3e3 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index d06c22de1..e37c65f25 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -24,8 +24,8 @@ tools: - 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 @@ -52,15 +52,15 @@ tools: - name: gemini_dump owner: iuc revisions: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -86,16 +86,16 @@ tools: - name: gemini_load owner: iuc revisions: + - 45296e47d565 - b2c25142267e - cf61daf064fe - - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: + - 840fb4850be3 - 666f60a9331a - da74170c55c7 - - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,29 +137,29 @@ tools: - name: gemini_region owner: iuc revisions: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 9844ff03b..2e186f768 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -23,8 +23,8 @@ tools: - name: mageck_pathway owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index f5f752fa8..8c4c21a16 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,9 +2,9 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - 983bf725dfc2 - b39347891609 - c1b437242fee + - 983bf725dfc2 - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,45 +25,45 @@ tools: - name: sra_tools owner: iuc revisions: - - f8054ea1c365 + - 83c7d564b128 - ba931a59dd59 - - 1ec814014652 - 9a776b080193 - - 83c7d564b128 + - f5ea3ce9b9b0 + - 4317d3cb6cba - e08a7ad4378b - - 7068f48d0ef9 - - 6ea73833cf67 + - 4df8de2d0e48 + - f8054ea1c365 + - 1ec814014652 - 1790dcf3c32d - - 4317d3cb6cba - - 6591f049cf7e - - aad3885b3216 - c441583adae5 - - f5ea3ce9b9b0 - - e407b9da183a + - 8848455c0270 + - 7068f48d0ef9 + - 6ea73833cf67 + - 516a54ddf218 - 734abc7ac21d + - aad3885b3216 - 69ebb7f46e45 - - 516a54ddf218 + - 6591f049cf7e + - e407b9da183a - 653e89d73fc4 - - 4df8de2d0e48 - 5e6237d58b0c - - 8848455c0270 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 21a560af5913 - 34758ab8aaa4 - 75b3b3d0adbf - 9aaa46d45472 - - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - af5eccf83605 - - 468c71dac78a - 054483e27a35 + - af5eccf83605 - bfdc6a7ffd3a + - 468c71dac78a tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index abf715246..6f577929e 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - fd59d783248a + - 290a11559985 + - df7356989ac1 - 4b519282a05b + - 7f13dc906cb9 - c4bde687c846 + - fd59d783248a + - 740057a5126d - ae9994cf526f - - 290a11559985 - - 7f13dc906cb9 - a64dc31ab7f2 - - 740057a5126d - - df7356989ac1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,8 +34,8 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,20 +48,20 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - ca7cb0eaad62 - 3b37b1b1c3a7 + - ca7cb0eaad62 - 53460afd5115 - - '566197475670' - 374e9062d874 + - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - da4c086cff5b - - 10515715c940 - 3d059e9c2fba - 391a4cc45fea + - 10515715c940 - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -80,12 +80,12 @@ tools: - name: ggplot2_point owner: iuc revisions: - - e3a675da7fd0 - - 5fe1dc76176e + - d0fc8b746d57 - 3b12bf9b4b87 - - 1acf88921176 - 299307abd804 - - d0fc8b746d57 + - e3a675da7fd0 + - 1acf88921176 + - 5fe1dc76176e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -103,8 +103,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 97e3b735ed22 - 5d6f8f0bef7c + - 97e3b735ed22 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -117,8 +117,8 @@ tools: - name: histogram owner: devteam revisions: - - cdb9e89e2970 - 6f134426c2b0 + - cdb9e89e2970 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse2 @@ -131,16 +131,16 @@ tools: owner: iuc revisions: - 2bb2e07a7a21 - - 1cfc579079a6 - ca2def38369c - - 4542035c1075 - a6e57ff585c0 + - 1cfc579079a6 + - 667e17248bfe - 112eb40ba6cf + - 6cd09d7b5f37 + - 4542035c1075 - 836d1aa3e89a - - 667e17248bfe - - 17359b808b01 - fd5dbf0f732e - - 6cd09d7b5f37 + - 17359b808b01 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -158,8 +158,8 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - 03c13085aecc + - f1691de443a7 - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -173,16 +173,16 @@ tools: owner: bgruening revisions: - 1c5dcef5ce0f - - 62e3a4e8c54c - f234e2e59d76 - 85da91bbdbfb + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 9958188c6195 - 7b21a9b5922f + - 9958188c6195 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -194,8 +194,8 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 - 6c571966cfb9 + - 7c9417381ad5 - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -208,21 +208,21 @@ tools: - name: pygenometracks owner: iuc revisions: - - 326a3db8d9d1 - - 360df4999907 - 36b848d5f3ec + - 2824d77cd8f8 - 14e7c35f3d00 + - 326a3db8d9d1 + - 360df4999907 + - 4ac4e7083b7e - a1abfa420d9d - - 2824d77cd8f8 - 7dd841a32245 - - 4ac4e7083b7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - 2f557f6abbfb + - 44608d0193ed - 83c573f2e73c - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 81460e333..28d38cd85 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -35,22 +35,22 @@ tools: - name: scanpy_filter_cells owner: ebi-gxa revisions: - - bf1e0bdec1db - 361608369dda + - bf1e0bdec1db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - - 23d838d1569d - cc64914b0cf4 + - 23d838d1569d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: - - 36735850e461 - fc4b3b46dc9d + - 36735850e461 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers @@ -63,8 +63,8 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -77,44 +77,44 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony 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 owner: ebi-gxa revisions: - - 9a2f72d7dbd2 - 94697510d55f + - 9a2f72d7dbd2 - ff6decc0f432 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 3027cb62adbd - 28b1546857b0 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - d4c9061c8fef - 73d43034c860 + - d4c9061c8fef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed @@ -141,43 +141,43 @@ 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: - - 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 owner: ebi-gxa revisions: - - be019b069e31 - 65c3ec07502b + - be019b069e31 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -197,15 +197,15 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: + - 0f98603d0116 - ea91cfd0444e - 767a675b5254 - - 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 - 4cc9362782b4 + - e2d0dc8a50ca 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 7f3ac5cca..cbeb6527e 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,51 +2,51 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: + - 921a2da49a0c - ed2cca6b5de4 - - 29f66c353bcb - a4c13ddcc8ee - - 921a2da49a0c - 9edf8894a22d + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - ec4b948dc6f0 + - 78fb5e286609 - 5746d61f0a91 - - 755df866ad0c + - ec4b948dc6f0 - d404277cc87a - - 78fb5e286609 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 - - 11fa44ee0603 - - 9e357a8b2ec3 - 03dd3c16ae4e - 4d511437b1e5 + - 9e357a8b2ec3 + - 11fa44ee0603 + - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 0ba4f56a3613 - - 41dbf4d162a2 - 3b5b54ed6392 - c3e5e2cf12b7 + - 0ba4f56a3613 + - 41dbf4d162a2 - 77919cc3618e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 - - 7babd8a46fe0 - b63363075c2e + - 7babd8a46fe0 - 12d51d7be66f - 5308ca68ef3d + - 9939786dd9c9 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 425937581..7a300cd99 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: - - 8bccb36e055a + - 699a5e9146b3 + - 3df9f0a4bf34 - 7db4fc31dbee - 81f0cbca04a7 - - 3df9f0a4bf34 + - 8bccb36e055a - 0c777d708acc - - 699a5e9146b3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - 5791a7f65275 - - 2436a8807ad1 - - 5bc8cdc17fd0 - 0a53256b48c6 + - 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 - - 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: - - d51310ab328a - - dba87c4b32d3 - f70b215d155c + - dba87c4b32d3 + - d51310ab328a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 - - 10eed33aa9b2 + - fcadded98e61 - 85edbb7a436b + - f3360fbeda64 - b07f4839ca77 - - fcadded98e61 + - 10eed33aa9b2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -64,16 +64,16 @@ 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: + - 0e4dccaafef5 - e917a2424690 - eb6c08714244 - - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -86,16 +86,16 @@ tools: - name: cp_common owner: bgruening revisions: - - 670975e92458 - e7273daa5ae2 + - 670975e92458 - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - cdf8e3c57dae + - ef4aed1d34c4 - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -118,25 +118,25 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: + - d0178bdcd00e - f8fa0f6718a3 - f24c370e5ea4 - - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - 31d195bedf6d - - ad271f78a87a - 3245681b2f6d + - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - - b6eec6087271 - 87d4d92d7487 + - b6eec6087271 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -150,8 +150,8 @@ tools: - name: cp_mask_image owner: bgruening revisions: - - 3a05117669cf - b178453ea8d1 + - 3a05117669cf - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -166,8 +166,8 @@ tools: - name: cp_measure_image_area_occupied owner: bgruening revisions: - - a32c3f810ade - 20dbb1f7ec7b + - a32c3f810ade - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -175,16 +175,16 @@ tools: owner: bgruening revisions: - b64af54c5c09 - - 8536b1ae0254 - 5499dc6f8ac1 + - 8536b1ae0254 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 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -198,16 +198,16 @@ tools: - name: cp_measure_object_size_shape owner: bgruening revisions: - - 79e10d12d90a - d85f11570109 - acf3aa487283 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 80b200ae516b - 035a58c7f54a + - 80b200ae516b - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -229,8 +229,8 @@ tools: owner: bgruening revisions: - 4ecf93628f97 - - 33f4fa1413fb - 27edbb90ab2b + - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -242,8 +242,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids @@ -255,15 +255,15 @@ tools: - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - - f8b4eada923c - 7b6d9412c7f8 + - f8b4eada923c + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index af4e20790..ae7d15640 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 3a72fede57ce - - e4ee04da1c19 - - 78bbd17d0703 - - 40737febe339 - - d6e72da3ec35 - - e319b5b65879 - a38934e303b9 - - 1069f6db0a0e - 3e4f434a69c6 + - d6e72da3ec35 + - 40737febe339 + - 78bbd17d0703 - f362150bef41 + - e319b5b65879 + - 1069f6db0a0e + - e4ee04da1c19 + - 3a72fede57ce tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - 0135f1d487a0 - - 2b95d5c04908 + - fcbeda41d0ac - 7fe36019c073 - - 72ddd32392cd - - 9537184d421f - - f91cfb73d369 - c88553ec696e - - fcbeda41d0ac - 8f8df367470d + - 2b95d5c04908 + - 9537184d421f + - 72ddd32392cd - 618297d23022 + - f91cfb73d369 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - d7e79eb3bcb3 - - ad0dc9f4c9e2 - fafb3d685fa9 - 2cf4a1cafc16 + - ad0dc9f4c9e2 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 7f1cfa4c0e32 - - ee29337f905c - - a1c2aecd7a0d + - 3d18f8c3c0f6 - ee2beb764a7b - - 9eaadf03e0df - - 28a6f1908fcc + - ee29337f905c - 94df24c6bc00 - - 5dc33613c288 - - 8d36959b000d - - 3d18f8c3c0f6 - - bd2a7d1316b9 - 8c05afb547fa - 43aac8d29685 + - bd2a7d1316b9 + - 9eaadf03e0df + - 5dc33613c288 + - 28a6f1908fcc - 6a1515bb0687 + - a1c2aecd7a0d + - 8d36959b000d + - 7f1cfa4c0e32 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 86a20ae274fc - - a250929be21b - bcaa0d571ce2 - - 5671e1d3d5ee + - e3bb03cf207a + - c092052ed673 + - 9f978da6528a - 5d6ed46cc101 - cb903c9dc33d - - db536ad45f28 + - 5671e1d3d5ee + - 364f4ffec275 + - 86a20ae274fc - d37ede8589b2 - - e3bb03cf207a - - 9f978da6528a + - a250929be21b - 8858fa037a15 - - 364f4ffec275 - - c092052ed673 + - db536ad45f28 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - abbc8041e8ec - - c5c9f02b6167 - - 194e3ceee923 - - 230b05597996 - - ed28dd32141c - 3b6a16d82c1b - - 49236b03e4fd + - 38b91a3190cd - f95f403841ad - - e1a015876aa9 + - 230b05597996 + - c5c9f02b6167 - 12d66d0d05ac - - 38b91a3190cd + - 194e3ceee923 + - e1a015876aa9 - 584beffa972b + - abbc8041e8ec + - 49236b03e4fd + - ed28dd32141c tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index 80ee8a28f..63dc0c5bf 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 - - 17e3b698dd52 - - f198773344e4 - 0f1724dd59d2 + - f198773344e4 + - 17e3b698dd52 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 374cb875d38a + - a513e3fbb4c5 + - ac092723240d - ba0c40780ecf - 22c2a1ac7ae3 - - ac092723240d - - 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 01cd1a68e..e91a459c7 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -10,19 +10,19 @@ tools: - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - 8a794e6d3388 - 4d81e3e2fb63 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - e1317b5502fa - - 818f9b69d8a0 - - b6ef6d0cb6b7 - 2af1346e68c9 - f1b9a42d6809 + - 818f9b69d8a0 + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex @@ -30,8 +30,8 @@ tools: revisions: - 1588f9076e32 - c80db5d6fd8c - - 947c2eacccb8 - 8334dc98c48e + - 947c2eacccb8 - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -41,60 +41,60 @@ tools: - 83228baae3c5 - 25b46af53232 - 1552b8cb4a94 - - 29e4122c90de - 9991c4ddde14 + - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 53616c8b0865 - 1a53edc4b438 - - a07ab242b0b5 - - f3dfa4bdf87e - 841a6cc5fc58 + - 53616c8b0865 - 060ca94ac049 + - a07ab242b0b5 + - f3dfa4bdf87e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 - - 40f4447733b2 - - dc4b5fd604a6 - - 927586a18553 - d4808d5b83da + - dc4b5fd604a6 - 91c4e3331208 + - 927586a18553 + - 2fc89dcd41c8 + - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - 301e07345c93 - - c6ae57f774c6 - - 36e8d6d5d01b - e5a5ad882f1f - - 25ab6b4e376e - 7626ea9c2e1b + - 36e8d6d5d01b + - 25ab6b4e376e + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 80852884053f - 02d2be90dedb - - b7c3e9a3b954 - 4ed102b922cb + - b7c3e9a3b954 - 0630258dcf35 - f9639b488779 + - 80852884053f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 61634a87efc7 - - caeb57858702 - 14180f9c831e - 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 9d46c32b0..896e40db7 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: - - 03e9b2fbc005 - - a6d65b0c67af - - 3ba8d4563129 - - 0d4acadabb04 + - f6877ad76b00 - 937aa69e715f + - 749c918495f7 + - 017aba02828d - d5ceb9f3c25b + - 0d4acadabb04 + - 3ba8d4563129 - 17062a0decb7 - - 017aba02828d - - f6877ad76b00 - - 749c918495f7 + - 03e9b2fbc005 + - a6d65b0c67af - cd659e8cc5fa tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 2477830927ec - e188dc7a68e6 - 64f11cf59c6e - - 3fe632431b68 - - 53646aaaafef - dfd8b7f78c37 + - 53646aaaafef + - 2477830927ec + - 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: - - e7f19d6a9af8 + - 60afcc2c1d05 - 3e1ea2facca6 - - 2ff111fac1d7 + - e7f19d6a9af8 - 37b497aa133f - - 60afcc2c1d05 + - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 8c6cd2650d1f - - 037c6e54df11 - - 53c0b7a1a0c3 - 3f4d6399997b - c0c2d0941de8 - - b3eab4b67562 - - f54f5baedfdd - 09b53c1d4ab1 - - be1d967337e4 - 6b1e195506a3 - 5cc34c3f440d - 77b2770508f6 + - f54f5baedfdd - 11a0d50a54e6 + - be1d967337e4 + - 53c0b7a1a0c3 + - 8c6cd2650d1f + - 037c6e54df11 + - b3eab4b67562 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - e403d27e8f24 - - 45795f582ae9 - - 79b885ce78d7 - - 178bdbdb6d24 - - ec9cbd6b9a49 - - 42ce70172b72 - - 1cd2511a396e - 5ef7ec16b04f - - 9ee34ba73ebf - - 13022c3d3076 + - 1cd2511a396e - 00fbfac99d39 + - 13022c3d3076 + - 42ce70172b72 + - 9ee34ba73ebf + - ec9cbd6b9a49 + - 178bdbdb6d24 + - 45795f582ae9 + - e403d27e8f24 - b8f5f6e87f5c + - 79b885ce78d7 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 183386f05..ad430fb97 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 6cd2a9e6ac49 - 90dc951da294 + - 6cd2a9e6ac49 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -93,15 +93,15 @@ tools: - name: matchms_convert owner: recetox revisions: - - c990df6afc24 - b9cc12600553 + - c990df6afc24 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - 00e66c401366 - a177ac3c752c + - 00e66c401366 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -114,8 +114,8 @@ tools: - name: matchms_formatter owner: recetox revisions: - - 1b09315a3f87 - 9e3c83d2afc3 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -128,8 +128,8 @@ tools: - name: matchms_metadata_match owner: recetox revisions: - - 03bc9b7f40f6 - 1d443ed476a1 + - 03bc9b7f40f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -141,8 +141,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 8147d93d372d - 1d74ae228df3 + - 8147d93d372d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -166,8 +166,8 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 9ff95a1a2705 - 7627b40601f6 + - 9ff95a1a2705 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -248,47 +248,47 @@ tools: - 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: - - 79ad928a0dae - 7b42ee54d757 + - 79ad928a0dae - c53a97599181 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - f3a18e020cdd - 149b9cc7499b - 18ec7635bac6 + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - dfebc82ba1f0 - - 134be5abb208 - 481d769e2f7a + - 134be5abb208 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - 51332c2520c7 - - 02c772a49998 - 9064aecc78a7 + - 02c772a49998 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b3413f335327 - b341cfd4baf8 + - b3413f335327 - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -304,16 +304,16 @@ tools: owner: recetox revisions: - 99d118321d5f - - d7f5878a98c3 - 24278c6b6d1c + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - d90187b0f247 - - ffbabefbd2e2 - ea0758b41473 + - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -325,8 +325,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 2c6fa447f6a0 - 6b5dec818827 + - 2c6fa447f6a0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 63fef511b..bc232c210 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,9 +8,9 @@ tools: - name: cat_bins owner: iuc revisions: - - 0094893f5001 - - 0e63d03c8790 - 18676df0cb3a + - 0e63d03c8790 + - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -95,89 +95,89 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: + - 7c2100246a2f - 63f86089423e - - 5b5a7af9fbb4 - 76d3d2b10738 - - 7c2100246a2f + - 5b5a7af9fbb4 - 65db807336bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: + - 96336c6a2bb7 + - 84fd33a60b35 - 00f5005840fa - 18a502a9d287 - - 96336c6a2bb7 - 1c35dadbe76f - - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - addaf9d22850 - - a9f4a217dcd6 - - e8fba04706d3 - f732237754fc + - e8fba04706d3 + - a9f4a217dcd6 + - addaf9d22850 - 34e55239e68b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 04c15826a0b8 - 0776d824d896 - - 5fe3edf19b9c - 75403243703a - 8c202e741d68 + - 04c15826a0b8 + - 5fe3edf19b9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 75c8945b0da2 - - 1c9b3bcd4261 - 8470de786d47 + - 1c9b3bcd4261 - 43c99742158b - e96bbb9e24ea + - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - 35176674168c + - 1d75bd0595e2 - 5c865a382933 - - 84743da21318 - 306a40d4bb8f - - 1d75bd0595e2 + - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 32c9ea835770 - - 8daf4564ccda - 555ccac8a4c5 + - 32c9ea835770 - ac72310b038a + - 8daf4564ccda - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - cae017b76acb - d60df8727f59 - - a58e4a43f49c - - 7b8cb2b02978 + - cae017b76acb - f947b4bb5107 + - 7b8cb2b02978 + - a58e4a43f49c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7136e9ab70db - 1bc3657cd694 - 7f3b59dee073 + - 7136e9ab70db - 073608a50ac3 - 04144473e59e tool_panel_section_label: Metagenomic Analysis @@ -185,10 +185,10 @@ tools: - name: dada2_seqcounts owner: iuc revisions: - - 0a1224c4b781 - 9058d8943303 - 19299bb1c6af - a7817705348e + - 0a1224c4b781 - d943081510da tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -203,10 +203,11 @@ tools: owner: iuc revisions: - 65d52c693b8e - - c4db8c4de66f - - f8f56dd6449f - a68b985913ab + - c4db8c4de66f + - 5c7ba3d85a01 - b907a3c0434f + - f8f56dd6449f - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -243,8 +244,8 @@ tools: owner: iuc revisions: - b084117133af - - d77397f09da1 - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways @@ -289,29 +290,29 @@ tools: owner: iuc revisions: - 79706f10d680 - - e88b731dad59 - - c409a495841f - 31c6d107e7a5 + - c409a495841f + - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 71ea608ddfa3 - - 714d5a28cc5c - - d24841f5c3d2 - 094ad9c068af + - 714d5a28cc5c - 172920f67a84 + - d24841f5c3d2 + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a293a742194f - 12fb63b5f63f - - a4d7148ccee4 + - a293a742194f - d7e9a3c41657 - 4137b492233e + - a4d7148ccee4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -323,11 +324,11 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - e2c71b852aba - - cf87759761eb - - 97f7bb0851e7 - 6fcb8ac37a3e - 64bc7acc22a9 + - cf87759761eb + - e2c71b852aba + - 97f7bb0851e7 - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -346,20 +347,20 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 2d35528d2141 - - 5e5a999ffaa9 - 080ea153677c - 4033827c76b8 - c82508e76ad1 + - 5e5a999ffaa9 + - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 95bf7479d53c - - 2cd76b089570 - 6b7622dda516 + - 2cd76b089570 - fc6c328c292f + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -371,8 +372,8 @@ tools: - name: jellyfish owner: iuc revisions: - - 11658afb8c87 - dcd30574a456 + - 11658afb8c87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single @@ -426,10 +427,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 - - 328c607150ff - 20e2f64aa1fe + - 328c607150ff - cdee7158adf3 + - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -455,8 +456,8 @@ 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 @@ -544,21 +545,21 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 27250f92a01a + - 2cff76cf35c6 + - 7f5d7b0e9884 - e073891b2afc + - 0270541aaf46 - 4fd3b5d8706b - - 7f5d7b0e9884 - 3cc4a60615c0 - - 0270541aaf46 - - 27250f92a01a - - 2cff76cf35c6 - 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 @@ -632,17 +633,17 @@ tools: - name: metaphlan owner: iuc revisions: - - 1a037928504c - - 2131d7dca455 - - ff8f55893e7d - - ef65b083bd0c - - fd69c607b43f - - a92a632c4d9b - - 6dee4abadccb - - b89b0765695d - 289b3807e80c + - fd69c607b43f - a16313517e55 - 1a6cdf55390f + - 2131d7dca455 + - 1a037928504c + - 6dee4abadccb + - b89b0765695d + - a92a632c4d9b + - ef65b083bd0c + - ff8f55893e7d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -667,8 +668,8 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 6034c3f3ecf0 - 2f47a294ef49 + - 6034c3f3ecf0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp @@ -681,8 +682,8 @@ 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 @@ -722,8 +723,8 @@ 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 @@ -784,13 +785,13 @@ tools: - name: staramr owner: nml revisions: - - aeaa20b96ef2 + - 3b22de20bd4b - 2fd4d4c9c5c2 - 4b9a8031ab74 + - aeaa20b96ef2 + - 141afacabcfa - 4d83eccf5f81 - be818ae858e4 - - 141afacabcfa - - 3b22de20bd4b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -820,8 +821,8 @@ tools: - name: vsearch owner: iuc revisions: - - 576963db5f1b - b3c7199d8786 + - 576963db5f1b - 9495df9dd6ef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 8c018af31..334c2c5c3 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 1cc494d53..835a4c720 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: - - 48c13389050d - - cd07731e4434 - - 6ae5a7b5a0a2 - - 9422c5a87ee2 + - 9baa871cb1d1 - 2263989660f5 + - 80f03df2e2ce + - 6ae5a7b5a0a2 + - 9eeb13a92d79 - a74dbfee5a86 + - 48c13389050d - 8b67dd48fec1 - - 098506c54016 - - bdfbaf0c10aa - - 9eeb13a92d79 - - 9baa871cb1d1 - 94b8c6013083 - - 80f03df2e2ce + - cd07731e4434 + - bdfbaf0c10aa + - 098506c54016 + - 9422c5a87ee2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: + - 4a60927aaca5 - f0af8936ed41 - 3ff17bad4006 + - 5abf2c2249aa + - fc2e49f91e52 + - be78f13134e2 + - d7ce0ec78e51 - d390fe1567dc - - 4a60927aaca5 - aaa0d6a8b808 - - c18157c68134 - c44f824c051a - - 5abf2c2249aa - - 2e093badc689 - - be78f13134e2 - - bc3831dd65c1 - - fc2e49f91e52 + - c18157c68134 - f14193ec1f50 - - d7ce0ec78e51 + - 2e093badc689 - '764845535798' + - bc3831dd65c1 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -53,8 +53,8 @@ tools: - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -66,22 +66,22 @@ tools: - name: mafft owner: rnateam revisions: - - bf28a8cff401 - - c5908940967d - f0d493f8f84f + - c5908940967d - 8e649f27aa0d - 15974dd17515 - - a65296ffb4a0 + - bf28a8cff401 - f1a5908ea2cb - 6f28e90db932 + - a65296ffb4a0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - b3acbb3a6af0 - - fbca557a4847 - e8fdceffea4c + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -104,23 +104,23 @@ tools: owner: iuc revisions: - 4fc0cb2ac8ae - - ebe3b0f84de9 - fb43e8887350 + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 7cd7a55a678d - - 636b049e6141 - e18267f90096 + - 636b049e6141 + - 7cd7a55a678d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - cf3c9489c088 - b4124df98b26 + - cf3c9489c088 - 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 a40997ed1..9c7c5e42c 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -16,8 +16,8 @@ tools: - name: dorado owner: galaxy-australia revisions: - - fc5b6491cf78 - 63d8ecfcfab1 + - fc5b6491cf78 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -30,11 +30,11 @@ tools: owner: iuc revisions: - cb34f00cc10f + - 72b5e9dda577 - 0e9e7fcdd543 - - fc8804320156 - 79e9a869f40e - a7228a7ea146 - - 72b5e9dda577 + - fc8804320156 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus @@ -42,8 +42,8 @@ tools: revisions: - db25ec99c3ea - fa11aa8103b2 - - 18505fe2bdb1 - d6cddc06aeae + - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -55,15 +55,15 @@ tools: - name: medaka_variant owner: iuc revisions: - - edf6d4003fad - - eb746fa6f514 - - 0f5f4a208660 - 222669c4afb6 - - cc36773a3681 - ec699520444c + - 2bf63b38ee9b + - cc36773a3681 - 43815fa60f3a + - edf6d4003fad - 19f3b583a9b3 - - 2bf63b38ee9b + - eb746fa6f514 + - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -82,21 +82,21 @@ tools: - name: nanoplot owner: iuc revisions: - - a38bdcec9e4c - a02b8b3f5a0c - - 7b379e98b9a9 + - a38bdcec9e4c - 0f1c34698076 - - edbb6c5028f5 - - 645159bcee2d + - 7b379e98b9a9 - a3c4fe6f49ab + - 645159bcee2d + - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - 3b6f94fc7e1d - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation @@ -110,17 +110,17 @@ tools: - name: nanopolish_polya owner: bgruening revisions: - - 449e9aeded2d - - 4857d5bcce52 - d376944466bf + - 4857d5bcce52 + - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - bec636361cfd - a3afc5f0a96c + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop @@ -134,8 +134,8 @@ tools: - name: poretools_events owner: iuc revisions: - - 1d835c691480 - 28d7819c312f + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -160,8 +160,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 338d15b8d6fb - 336791b5665f + - 338d15b8d6fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -173,8 +173,8 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 4fe6b96aff72 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle @@ -211,8 +211,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - ca22d8497db5 - 64a83664b814 + - ca22d8497db5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index fb405d03e..a9a3b3b92 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -21,8 +21,8 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 71186bb66ca2 - 4e85a3a5dbd1 + - 71186bb66ca2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts @@ -60,9 +60,9 @@ tools: owner: iuc revisions: - baceff842902 - - adfd6bf710bd - d74850cf4e42 - 97b1b5ad1cda + - adfd6bf710bd - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -70,8 +70,8 @@ tools: owner: devteam revisions: - 9dd107db92c2 - - 83da94c0e4a6 - 1586b111d2a3 + - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -83,18 +83,18 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - e4b4837f06f5 + - 2f27f3b86827 - ed1518ce2237 - - 1e34d2e3d285 - edacc4bcd3cb - - 2f27f3b86827 + - e4b4837f06f5 + - 1e34d2e3d285 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 @@ -106,8 +106,8 @@ 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 @@ -135,8 +135,8 @@ tools: - 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 @@ -155,17 +155,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 9a40272f56d0 - 6287d0ee459e + - 9a40272f56d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: + - 172815da3d41 - b4b2b284230a - - 27a6a256cd23 - 5bcf0e24f42c - - 172815da3d41 + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -178,8 +178,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -192,8 +192,8 @@ tools: owner: iuc revisions: - 87febc68b45b - - 19bbd19b74b3 - fea85c467896 + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -206,8 +206,8 @@ 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 @@ -225,36 +225,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 4ba60cb14cb0 - 0cb27ea69dc1 - - 2c61c30a57e7 - 5fe20c915fa6 + - 2c61c30a57e7 - 9c43baa60906 - - 4ba60cb14cb0 - d8dc037e3c13 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - 9d09724f2bf1 - - aec831b54a5b - 0db22932bc39 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 + - 29c738066906 - 6e24e79d3d69 + - df30a2f1db55 - ed7a967cb11b - - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -272,8 +272,8 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 3e4d45aca422 + - ad90c2da4f38 - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -294,16 +294,16 @@ tools: owner: iuc revisions: - c520a52b5174 - - 64deddb6a8ec - d63c1442407f + - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: + - 94a50db37d1a - 9946bc39c834 - 625fd9476402 - - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1053,22 +1053,22 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - d64562a4ebb3 - 544f6d2329ac + - d64562a4ebb3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbcavity owner: bgruening revisions: - - 7e5c2e4bc227 - 744a777e9f90 + - 7e5c2e4bc227 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbdock owner: bgruening revisions: - - c362398df83b - e4b7d1507a75 + - c362398df83b - a22969b08177 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1081,10 +1081,10 @@ tools: - name: salsa owner: iuc revisions: - - f77f7a7f3b83 - - ab5b7f6b7198 - ba7b0f11e470 - 9a22227bb6d0 + - ab5b7f6b7198 + - f77f7a7f3b83 - 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 fb263565e..e5d85cba6 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -26,8 +26,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 26de3a7b1cb9 - - b89cac5156ec - - c78f3d7dd1db - - d033ffc1c161 - - 3f59ebfbfe3d - - 5a7c56a5cc08 + - 81e66674859e + - '841557158611' - 3b8b5bde0bd9 - d7c7ef3353fe + - 107d3ba7024a + - a6619171428e - cce7b18495e4 - - f73435dc282b - 6a457678efcb + - c78f3d7dd1db + - 5a7c56a5cc08 + - 3f59ebfbfe3d + - 26de3a7b1cb9 + - b89cac5156ec - 8834daeb9892 - - 107d3ba7024a - - '841557158611' + - f73435dc282b + - d033ffc1c161 - f04a1264e2a2 - - 81e66674859e - - a6619171428e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 5fcd1ece3a6e - - 02b8758214b0 - - 7a2092844346 - - 659517798cc4 - - e75442c7f4da - - 4755f52427c4 - - 6223845127ea - - 5b777002c2de - - 6a726db04d4b - a185b079b095 - - b0af57c1a968 + - df47d4845b62 + - 5b777002c2de + - 4755f52427c4 - 88c4aa435ded + - 6223845127ea + - e75442c7f4da + - 659517798cc4 + - 5fcd1ece3a6e + - 7a2092844346 - aa8cc71438cf - - df47d4845b62 - 3b96e92e8ec3 + - 02b8758214b0 - 6283babe736e + - b0af57c1a968 + - 6a726db04d4b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - d1c340a5664b - 0878b7fd5260 + - d1c340a5664b + - 111bd54f6bc4 + - 524d31add34a - 70acec670c30 - b8476e82ac20 - - f97743d52b87 - 24d024316465 - - 111bd54f6bc4 - - 524d31add34a + - f97743d52b87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - - 4f6349228462 - 9e10ba792be2 + - 4f6349228462 - feb40665d7cd + - daddf188c13f 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: - - 9d61d3fa046c - 2f1019071464 - - 437e28791761 - - 8ad84c5753ea - - abf6dbe8c9d7 - - 36912871ccdc + - 14ae456b8cc5 + - a2099fb98cdb + - b6abccb1f25b - 5f8727ff21e7 - - 83a69484cb87 - - ca337cce3888 + - 3a43c3982401 - 7bb8726be37c - - a2099fb98cdb - - 14ae456b8cc5 - - 03ed9524dcd1 - - 42a174224817 - - 2fa9d4f1b48f - b7e297c2ede6 - - b6abccb1f25b + - 36912871ccdc - 81804a978fc0 - - 3a43c3982401 + - ca337cce3888 + - abf6dbe8c9d7 + - 03ed9524dcd1 - ca0d8cf80567 + - 83a69484cb87 + - 42a174224817 + - 2fa9d4f1b48f + - 437e28791761 + - 9d61d3fa046c + - 8ad84c5753ea 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: - - b1e68bbe4cef - - 29ff6a849eac - - ea30d3089354 - ba29b5e2a4be - - a4b71be30c3c + - ea30d3089354 + - 29ff6a849eac - 73a469f7dc96 + - b1e68bbe4cef + - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - 15ac71df11a0 - - f1ccc8a6eb05 - - 91887494eb97 - - 809e42326fc2 - - 9b2b122d0415 - dbe2b2204555 + - 9b2b122d0415 - e88a7de55d6e + - 91887494eb97 + - 809e42326fc2 + - f1ccc8a6eb05 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 5faec09b4..c0113ccb5 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: + - 3f254c5ced1d + - a1f0b3f4b781 - f9242e01365a - - f6ced08779c4 - 1aac2a13842a - - a1f0b3f4b781 - - fc288950c3b7 - - 3f254c5ced1d - 881d7645d1bf - 7d34178f2812 + - fc288950c3b7 - b502c227b5e6 + - f6ced08779c4 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 6ae5b4fa0..1d40f7fd6 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,16 +2,16 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - ca90d17ff51b - - d00e15139065 - - c0e71cb2bd1b - - a58f7eb0df2c - eb085b3dbaf8 - - 6ab1a261520a - 5b85006245f3 - - 7fbec959cf2b + - c0e71cb2bd1b + - ca90d17ff51b + - a58f7eb0df2c + - e4a053d67e24 - 2f7702fd0a4c - 3bd420ec162d - - e4a053d67e24 + - 6ab1a261520a + - d00e15139065 + - 7fbec959cf2b 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 b8251d297..a95c307ce 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,94 +2,94 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 277dc652246e - - 4c177985028a - - b18329a8ac14 - 0a18ac48ac53 - - ece627528a78 - f28ad96b76dc - b574b84afc4d + - ece627528a78 + - b18329a8ac14 + - 277dc652246e + - 4c177985028a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - b41107d8fe89 + - 525f201b86c1 - e215f71d7983 - e988563cc6e5 - - bf06d196e23d - a9a28e46d54a - - 525f201b86c1 + - bf06d196e23d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: + - 56da27be956a - bb6397b94018 - 8da3511c9467 - 4fbffddde8cd - - 56da27be956a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - f23d67e28cc8 - 890845926d4b + - a8157342d9a3 - b8c79e70516d - 528fb09022be - - a8157342d9a3 - - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 - - a69865da6f80 - - a95a82eb4d50 - ae304a72db7b - - 80600735685d + - a95a82eb4d50 + - 59e85306eae5 - 25b83cbd596a + - 80600735685d + - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - e0669b1854b1 - - 798da6bdff3d - - 611d80c0e29d - - ed9ed1e6cca2 - 83aac7741200 + - 611d80c0e29d + - 798da6bdff3d + - e0669b1854b1 - f1897eb07081 + - ed9ed1e6cca2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - - d426a9107a6c - 5a35e3a8d013 + - a7fb9b395ddf - 74b61bf5bc4b + - d426a9107a6c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - cc430977c8ff - - 91f0f5922011 - df2187f9013b + - 91f0f5922011 - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - ba92b59cd529 - c5aa9fca18c6 - 1693b2126f30 - - d2483487e077 - 10566783d718 + - d2483487e077 - 043f9c91f686 + - ba92b59cd529 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: + - bf0728e000cd - 9fa3dbf06f17 - - ff8c9e0e8a7b - ae4dc0c041f9 - - bf0728e000cd + - ff8c9e0e8a7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,15 +122,15 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - d0ea7589e95f + - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - 4081e4faa4ab + - 1c5cbf8f79ce - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -144,9 +144,9 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - 0d2e93e01e68 - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 + - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -158,9 +158,9 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: + - 160538a890a6 - d286ff4600dd - e66f552a3c47 - - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -173,23 +173,23 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - e42225f8a659 - - 37d669de2828 - - 1f39c833f65f - - 7f432d87c82c - 97a7f34fcb6a - - 837224ad1694 - - f522c08e900c - 9c52362ae7bb - 2133b0be850a - 4d17fcdeb8ff + - f522c08e900c + - 1f39c833f65f + - 7f432d87c82c + - 37d669de2828 + - 837224ad1694 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,8 +201,8 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - 85b8866f06d7 + - a72ac2c7cc5b - e63db1aa82ee - 0ed07016d668 tool_panel_section_label: Proteomics @@ -210,46 +210,46 @@ tools: - name: metaquantome_expand owner: galaxyp revisions: - - 990b4560ead7 - - 1974224d63c2 - 767c1d761aaf - 352b37c66d97 + - 990b4560ead7 + - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - deaf035bbe9f - 99450519d727 - 35cc7ca0bdc7 + - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c7745841de24 - - e79958768a2c - - c1343e3389ca - 06f6826d380c + - c1343e3389ca + - e79958768a2c + - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: + - d2eac53666f0 + - da986f83631b - b9d453dca8d3 - d46d64e7964d - - da986f83631b - - d2eac53666f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - 8bd7734309f6 - - 1199751329b0 - - 944b43462104 - 9bf325045235 + - 944b43462104 + - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -269,10 +269,10 @@ tools: - name: msstats owner: galaxyp revisions: - - 593839e1f2c3 - - 28434abe6c5c - de7593c29499 + - 28434abe6c5c - 8212e342e482 + - 593839e1f2c3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -285,35 +285,35 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 8960fb791701 + - 01dbaf6a57e0 - 4e77b8f12cd3 + - 8960fb791701 - f4be248c3d47 - - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 25529df60a81 - 370141bc0da3 + - 25529df60a81 - 06cca574e337 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 - - 518b1730cf2a - f7fef900f5b2 - - 6ccbf9a2072c + - 518b1730cf2a + - 9cdf15d3cfc8 - c9eff69a7c62 + - 6ccbf9a2072c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 - 9876bda3ec53 + - ca88bd28f116 - 5e948629bc73 - dff6c756eee5 tool_panel_section_label: Proteomics @@ -321,110 +321,110 @@ tools: - name: openms_fidoadapter owner: galaxyp revisions: - - 658494a2cb00 - 41859bbdc16e - - 890025d6e426 - 1595601708ec + - 890025d6e426 + - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: + - 6634cad7d797 + - 5ad0b5bf1deb - 9b7977080f6d - 2a93a25f0599 - - 5ad0b5bf1deb - - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - fe4e4587d265 - 0bb5056cb775 - 05d5e1ddc985 + - fe4e4587d265 - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - 52ba9695e752 - febd569ad26f - 4af67edd5aef + - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - b2fc8da99bcc - 39e8fde08881 - - 27cba4c5fc42 - 92352a475eed + - 27cba4c5fc42 + - b2fc8da99bcc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - d413dc49d650 - - 0efbc235f314 - 9e26f5c770f8 + - d413dc49d650 - d3546bb9fd8e + - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: + - c28f13cab67a - ca1740533b59 - 8a04ed1c1d1b - 3720e349ba2a - - c28f13cab67a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c427a8628cbe - ca799a7246e7 - - 382cde407f81 - c55dddc5844a + - c427a8628cbe + - 382cde407f81 - a5d785af0ad8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - adca857b4884 - 39caaa778d2e - b5d0905419da + - adca857b4884 - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - f817513840a9 - 1c5f31b8d632 - 8d4db262964c - - 18f93351f8b6 - 34e7afee141d + - 18f93351f8b6 + - f817513840a9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 111c3a00136d - 986e03d3201e - - 5d9f175dff81 - c69f69d7867a + - 5d9f175dff81 + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - 4204882495f2 - - be74a8cd7d66 - 0e52c85f3b15 + - be74a8cd7d66 - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -438,8 +438,8 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - 2b2a7551a857 - c18d8efa4474 + - 2b2a7551a857 - a407b6790342 - f5ec766d80cf tool_panel_section_label: Proteomics @@ -447,17 +447,17 @@ tools: - name: openms_multiplexresolver owner: galaxyp revisions: - - 021fdb80f204 - - 4e66c4e73909 - d0304fb829c0 + - 4e66c4e73909 + - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - bf32e0bcf554 - 8098330f6d91 - ee860980edc6 - - bf32e0bcf554 - 2735db4dd8d9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -465,47 +465,47 @@ tools: owner: galaxyp revisions: - 08488066d588 - - a2a6e9551046 - 0ced5bc9f4dd + - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: + - 8c01da82292c - de7a553552a6 - 2a9ff56cb279 - - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - c1809c05ae8c - e8f64a7dc470 + - c1809c05ae8c - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: + - 9f505cd4428f - 496cf619e311 - f861ec9fbe59 - - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - c99d5004b74f - 0bddef8d144e - d4396637b9f5 + - c99d5004b74f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 4bb198c0bd3e - 89254095cbf6 + - 4bb198c0bd3e - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -521,51 +521,51 @@ tools: owner: galaxyp revisions: - d31426ef20f6 - - 6e8cc5ed2a9b - 18826fb8e5db + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - 4a7b96835140 - - 2aebe58de46e - bc63b4d12779 + - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - 6b01678ec2fc + - 3d8d4ada5405 - decc397c3b7e - 5ae104d0da6e - - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - 539a3a4dcc9e - - e039cc5c7aed - dd173849c3d8 - - 5182338d5e7c - d6aca689dd48 + - e039cc5c7aed + - 5182338d5e7c + - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: + - 8a45fd5a608a - 16026cdb1330 - d426affe977c - - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: + - 43b9ed22e8ce - 9c70a651a53e - dd71e020e2aa - - 43b9ed22e8ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter @@ -579,9 +579,9 @@ tools: - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - ad2ba3a95a02 - f036e8cf1a55 + - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter @@ -596,8 +596,8 @@ tools: - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -609,21 +609,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: + - 7fdd9119cc4f + - 943a34df6047 + - 07ff622ec007 - a72c48001f7c - - 1beff3ddce58 - 3634c90301af - - 943a34df6047 - - 7fdd9119cc4f - 3ec27b4cee7c - da885ca16cb2 - - 07ff622ec007 + - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -683,10 +683,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 1a5690a5eedc + - 12692567c7f9 - 265c35540faa + - 1a5690a5eedc - a371252a2cf6 - - 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 fd55b22b6..7ec241bed 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -3,11 +3,11 @@ tools: owner: iuc revisions: - 2f1d464ebfd2 + - 42201b90e3f4 + - 289b7d6b69a4 - cd5f98911089 - e345aadf914f - - 42201b90e3f4 - 110a346daf36 - - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,11 +19,11 @@ tools: - name: stacks2_cstacks owner: iuc revisions: + - 8501601a118d + - 0345dbaaa79b - 0cd2df8af811 - 42d9087b4789 - fcce77c09289 - - 8501601a118d - - 0345dbaaa79b - c207119ba5f6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - ad5ab22ffe24 - - 89eb29319bf4 - 405a212b32ab + - 89eb29319bf4 - 33486216eec0 - - 421c33b8bf17 + - ad5ab22ffe24 - 04db7fd6b238 + - 421c33b8bf17 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - 7b72fde3d27e - fa51dc5e8386 - - f6e91108b7b1 - - eb784fa07f80 - 1d839ead7ad3 + - 7b72fde3d27e - 7370bb65bad4 + - f6e91108b7b1 + - 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: - - 3d70c2996730 + - 1544278c272e - 8a55d29c8fcf - d30e36c48c93 - - c9b77ced9a78 - a3e86cd9cac7 - - 1544278c272e + - 3d70c2996730 + - c9b77ced9a78 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - 887cf585cafc - - a5969aa9347e + - e2db212d64ad - 7b881f5f5ad5 - - 564c33e5c3e3 - b242deb58952 - - e2db212d64ad + - 887cf585cafc + - 564c33e5c3e3 + - a5969aa9347e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - b4bab607eb05 - - 9a171f9a450b - - 8cff84759bf6 - e897c74a48bb + - 8cff84759bf6 - bd5ff77e2036 + - 9a171f9a450b + - b4bab607eb05 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,11 +120,11 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 33f0793edf93 - - 6dafad990086 + - 887e0991eb24 - 5e10f396979e + - 6dafad990086 + - 33f0793edf93 - 4f65e343ecdf - - 887e0991eb24 - adc7a7610d4f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,11 +137,11 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - c5d7050e4ad7 - 17d39bf0a63a - 4e280b27a831 - c287418eb288 - 97575d01f06b + - c5d7050e4ad7 - 43e3eeb2e0ec tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: + - 09b8edb56d80 - 0b8c84a7fdb5 + - 9586f08634c0 + - d9bf483266a1 - a819ec3b362d - - 09b8edb56d80 - cd034465d4a4 - - d9bf483266a1 - - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - 95351dd0fd3f - 2645575d1bf2 - bf0e43ab0416 - - a9c34a289493 - - 69842dd5aa48 - a4b4bd84f69e + - 69842dd5aa48 + - 95351dd0fd3f + - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -189,11 +189,11 @@ tools: owner: iuc revisions: - 8a35a3bc6752 - - bb0475c884ff - 912f904a6e1e - cfb504394ae1 - - d1fda11e602f + - bb0475c884ff - d033e1ccb386 + - d1fda11e602f 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 - - d504d945a655 - 95286af4139b + - d504d945a655 + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 8bc71f5b3..11e43e94f 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,24 +2,24 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - 2d4e3aff9dc7 - 31f8063eedea + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 32e542c2a773 - 125d20cb23d7 + - 32e542c2a773 - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - 01ccd366690d + - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -68,8 +68,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -82,9 +82,9 @@ tools: - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - - 86285ddd4512 - 6a6717a5f421 + - 86285ddd4512 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -96,8 +96,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -121,10 +121,10 @@ tools: - name: describe_samples owner: iuc revisions: - - e3b16fd7dd08 - - 3b36efd62b3e - 8f0181aacb7a - 0693ccd171c4 + - e3b16fd7dd08 + - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -139,10 +139,10 @@ tools: - 6a3a025714d3 - 24a09ca67621 - 8fe98f7094de + - cd9874cb9019 - 0696db066a5b - d027d1f4984e - 9a882d108833 - - cd9874cb9019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -154,11 +154,11 @@ tools: - name: dexseq owner: iuc revisions: + - df929f257179 + - 62adf13b86ea + - 2872c633f07e - b47c006d90c5 - 9a7c5b6d8f1e - - 2872c633f07e - - 62adf13b86ea - - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -171,17 +171,17 @@ tools: owner: iuc revisions: - ae2aad0a6d50 + - 334ce9b1bac5 - a8305cf0c951 - - df0c8d0a5992 + - f2843df56434 - 0cb907a2a810 - - 555659de7321 - 6e53e565fc6a - - 334ce9b1bac5 - - 070900306913 - - f2843df56434 + - df0c8d0a5992 - 9bdff28ae1b1 - - 5bf899c13979 - 3d89af8a44f0 + - 070900306913 + - 555659de7321 + - 5bf899c13979 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -212,17 +212,17 @@ tools: - name: featurecounts owner: iuc revisions: - - f3a5f075498f - - af814359d244 - - 90d16db017d7 - - a37612abf7f9 - - 38b6d12edc68 - - a56fbe2d6ba7 + - f9d49f5cb597 - 7db9d3ea71c9 + - a56fbe2d6ba7 + - a37612abf7f9 + - 90d16db017d7 + - af814359d244 - ea04b737afa0 - - f9d49f5cb597 - - 6f66ae7c5f7a - e6a2a912677a + - 6f66ae7c5f7a + - 38b6d12edc68 + - f3a5f075498f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -253,8 +253,8 @@ tools: owner: iuc revisions: - f99dd58de04f - - 0f710191a66d - 3c97c841a443 + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -272,13 +272,13 @@ tools: - name: hisat2 owner: iuc revisions: - - d4b55e2beb12 - - 6ab42baa56e9 - - 26371a1df031 + - a86e80d3c09c - 6c19daec423d + - 6ab42baa56e9 - 3fb01a8c902d + - d4b55e2beb12 - f4af63aaf57a - - a86e80d3c09c + - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -296,9 +296,9 @@ tools: - name: htseq_count owner: lparsons revisions: + - 916cb26bd9d3 - 4418229c501e - 67b0b160903a - - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -317,10 +317,10 @@ tools: owner: iuc revisions: - ce5d418183c5 - - 1c75aa5de15e - 87c11c05d238 - - 01247aaf0a10 - 5ae5c312d718 + - 01247aaf0a10 + - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -332,10 +332,10 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 4f9c4e6566e5 - - 40985510cd98 - 10c98fab6c5a - c971db6f0fe5 + - 4f9c4e6566e5 + - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -347,14 +347,14 @@ tools: - name: limma_voom owner: iuc revisions: - - 0921444c832d - - 58c35179ebf0 - - 32511f586472 - - e827f9aae031 - 708348a17fa1 - 97e06a4c7c75 + - e827f9aae031 + - 32511f586472 - d6f5fa4ee473 - 119b069fc845 + - 58c35179ebf0 + - 0921444c832d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -372,8 +372,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -403,8 +403,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - d696cf0a9622 - 72927fc9e9ed + - d696cf0a9622 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -422,21 +422,21 @@ tools: - name: rgrnastar owner: iuc revisions: + - 4074fc1940e2 + - 5ec75f5dae3c + - 980d2a2e1180 + - 79de45b5069b - 4df95e2d7f61 - - e132e7d02a3e + - 4014de1b6daf - 7ed2edc1337f - - c7c55b694974 - - 5ec75f5dae3c + - e132e7d02a3e + - 99b17b74a8cd + - b9e04854e2bb - c772497b2c32 - 0a563fd2f22e - b0f2be869d6d - - 980d2a2e1180 - - 4074fc1940e2 - - b9e04854e2bb - - 4014de1b6daf - - 99b17b74a8cd - 3ea5a2a63fa2 - - 79de45b5069b + - c7c55b694974 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -461,13 +461,13 @@ tools: owner: bgruening revisions: - 53e9709776a0 + - f4d5237a84f6 + - 15cd64d7c58b - cc05793bb896 - - e3d32471da11 + - 49121db48873 - 2c0ca397d302 - - 15cd64d7c58b + - e3d32471da11 - ebab418107f5 - - f4d5237a84f6 - - 49121db48873 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -480,22 +480,22 @@ tools: owner: iuc revisions: - c0fd285eb553 - - 56242ff81c84 - 8c28affc7c48 + - 56242ff81c84 - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - ae618321f34a + - dd4df992d93d - 76d290331481 - 258d696dbd7e - - cef79931dda5 - - 914cfcba0ec8 - 1ebd14235b92 + - 914cfcba0ec8 + - ae618321f34a + - cef79931dda5 - cbf488da3b2c - - dd4df992d93d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -532,9 +532,9 @@ tools: owner: iuc revisions: - d0d4cef4f967 + - ffd1300599a1 - c6334cb383ff - 0db979fead3a - - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -546,10 +546,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - 74217fbfba4d - ba3720d7e68b - d6a479fd4281 + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -561,10 +561,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: + - 478f36effca1 + - c2b82a94493e - 56162e446004 - 2fb4ee002432 - - c2b82a94493e - - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -576,9 +576,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - - 3f4094b6a565 - 9ff3765e7172 + - 3f4094b6a565 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -590,10 +590,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 4687ecf0eb2d - 870ac06dff8e - - 34a018cbee9c - be3f26533209 + - 4687ecf0eb2d + - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -606,10 +606,10 @@ tools: owner: iuc revisions: - 5192f657f305 - - 33406f5a445c - - 05ab8d5e04a2 - c5fbddcac63a + - 05ab8d5e04a2 - 65e7dea767ea + - 33406f5a445c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -621,10 +621,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - e406ac71165d - - 6f0fb35b799c + - 1fdb25a8384d - a35cba31d904 + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -636,10 +636,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 - c2c039e421af - - 37a1129c89d2 - 7c7fbf13aadd + - 37a1129c89d2 + - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -651,10 +651,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 047c22569787 + - eafea3083352 - 24e94d84adc9 + - 047c22569787 - 1d689e4e1caf - - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -666,9 +666,9 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 9871104ea630 - - 3a4ac03d1266 - 04bb8bb7c198 + - 3a4ac03d1266 + - 9871104ea630 - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -693,15 +693,15 @@ tools: - name: trinity owner: iuc revisions: - - d2bc35f3d1c5 - - 9fa24d5aac68 + - d84caa5a98ad - c9cfec002f71 - - cee61b3fcf78 - db1f362cca3e - - 32b86cd8eb50 - 48636f857c4b - 8f1c3df4dd49 - - d84caa5a98ad + - 9fa24d5aac68 + - cee61b3fcf78 + - 32b86cd8eb50 + - d2bc35f3d1c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -713,8 +713,8 @@ tools: - name: trinotate owner: iuc revisions: - - 9e61bc67866f - 2b093007fab9 + - 9e61bc67866f - 4383070d29ed - 6fd16fad465d tool_panel_section_label: RNA-seq diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index 44ba177fb..14ef583f8 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 1a052c827e88 + - 080fd5739bb4 - 27e16a30667a - 473382134e56 - - 080fd5739bb4 + - 1a052c827e88 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 6cd6fd807..60394e76b 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: + - 10184eaa85fc - 88eedb4abea0 - 3c661e57a88f - - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -17,9 +17,9 @@ tools: owner: devteam revisions: - 108db6635177 - - 1dfd95ee241e - 993b19f20c76 - cb20f99fd45b + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -44,8 +44,8 @@ tools: - name: bamtools_split_tag owner: iuc revisions: - - e30af4e78cd3 - e9b9c489aacc + - e30af4e78cd3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -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: + - 30a201c9c310 - 5f8e69cc4c6e - - 19ece8afbaab - e7fd6754d093 - - 30a201c9c310 + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -97,8 +97,8 @@ tools: - name: qualimap_multi_bamqc owner: iuc revisions: - - 17b35d23731f - e38af83df163 + - 17b35d23731f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_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 @@ -150,8 +150,8 @@ tools: owner: devteam revisions: - 56c31114ad4a - - 649a225999a5 - dc6ff68ea5e8 + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -163,9 +163,9 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 46c6639921f1 - 12749212f61b - 9149ad20699a + - 46c6639921f1 - 6856f8a01905 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: + - 06dc50b7b711 - 26b4f9f98aca - - 92ec40abcdcf - 33208952b99d - - 06dc50b7b711 + - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -205,11 +205,11 @@ tools: - name: samtools_fastx owner: iuc revisions: + - b3d99709fe1a - 720217c23995 + - a8d69aee190e - b906586a6596 - 66e23b11feae - - a8d69aee190e - - b3d99709fe1a 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: - - d2df79922531 - e5ece8fa99de + - d2df79922531 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - fefd89ab563c - cc61ade70eb8 - - db17d5321bad - fe34990e5ce7 - 22970df7a40e + - db17d5321bad + - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -246,8 +246,8 @@ tools: revisions: - 88b8c2916784 - 7a6034296ae9 - - 7def34e6cf4d - fa5d3e61e429 + - 7def34e6cf4d - 811fc2d75ad4 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,21 +267,21 @@ tools: - name: samtools_merge owner: iuc revisions: - - 36677f429310 - - 65a38e8c8e2a - 740ce0a18f0d - b40e2d865d52 + - 36677f429310 + - 65a38e8c8e2a - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 583abf29fc8e - - fa7ad9b89f4a - 9da0311ab1dd + - 583abf29fc8e - 329deb17a9f7 - b61f5d6a7f25 + - fa7ad9b89f4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -293,8 +293,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c + - db000c6007a0 - 85e38b31e8b3 - 30388d878f81 - - db000c6007a0 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -342,9 +342,9 @@ tools: owner: devteam revisions: - 6c2c1836728b + - cab3f8d35989 - e613c1ad4c4c - d54a4df48867 - - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,10 +356,10 @@ tools: - name: samtools_split owner: devteam revisions: + - b7f7826ef1cd + - 5d9ae78f34d3 - 135c85f4cfaf - 818030fa6bbf - - 5d9ae78f34d3 - - b7f7826ef1cd - bcedabb53ddf - bd850490c7f1 tool_panel_section_label: SAM/BAM @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - 145f6d74ff5e - - 3a0efe14891f - - 24c5d43cb545 - 5a08c09b9311 + - 24c5d43cb545 - 541082d03bef - 1cc79f49b8d5 + - 145f6d74ff5e + - 3a0efe14891f 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: - - bf328cec6a42 - - 32dc5f781059 - - b01db2684fa5 - - 2dce91e11ca7 + - 6be888be75f9 + - 350bbc5c2ffd - 0dbf49c414ae + - c370440f901e - b72793637686 - - 6be888be75f9 + - 32dc5f781059 + - bf328cec6a42 + - b01db2684fa5 - 5826298f6a73 - - c370440f901e - - 350bbc5c2ffd + - 2dce91e11ca7 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 0bac8ba29..ce128c151 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -3,12 +3,12 @@ tools: owner: iuc revisions: - d147d6455873 - - ea5e944f447d - 6f6537780379 - - 4aab5ae907b6 - - 480d9e9d156b - - 59bb6d34fca6 - 5cb6146337d8 + - 59bb6d34fca6 + - ea5e944f447d + - 480d9e9d156b + - 4aab5ae907b6 - a62c4a11a67d 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 0f55e8d33..9c4917542 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 - - e32b215b7c04 - - c9944a2600f1 - ecb9ea6269ee + - c9944a2600f1 - e4c01dcece8b + - e32b215b7c04 + - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - 707023fa62fe + - c0b037b12765 - e1c3c2f2a834 + - 707023fa62fe - cfaf5a405371 - - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 93dd15e13e6a - - cfc3f5a57dc6 - d330b3082107 + - 00712416fdaa + - 93dd15e13e6a - 55e35e9203cf + - cfc3f5a57dc6 - 32e547223c9e - fb9e030ffae4 - - 00712416fdaa tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -45,13 +45,13 @@ tools: - name: anndata_inspect owner: iuc revisions: + - 6f0d0c784f09 - 038e32885fec + - ee98d611afc6 - 688357ad5e61 + - b9fac48532eb - 39e945f0b2c1 - 0bf7fddf90c7 - - 6f0d0c784f09 - - b9fac48532eb - - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -63,12 +63,12 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 43cb7b5a6fe7 - - ed4996a16f7f - - 3d748954434b - b85871dd69f9 - - 7e8c677a7b71 + - ed4996a16f7f - d4af736e7b83 + - 7e8c677a7b71 + - 3d748954434b + - 43cb7b5a6fe7 - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -81,45 +81,45 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: + - fe75d2414dc0 - a4774b7b2e85 - 2e8022f1923c - - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 4fff5a293013 + - 0e70b2dfe4be - 02b1fe7aed76 - 769d815e4b0d - - 0e70b2dfe4be + - 4fff5a293013 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: + - c29e7bb492bf + - a90f8efe08b4 - aa4a6f0916b4 - 344c2af50552 - - a90f8efe08b4 - - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - b13d3e4c48e1 - - 5b7c81b35b89 - - 050cf43887d3 - c32347702e12 + - 050cf43887d3 + - 5b7c81b35b89 + - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 02fc39c8610d - - 1d77986f9ddc - ae969fdb8442 - 239193b96d72 + - 1d77986f9ddc + - 02fc39c8610d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -155,11 +155,11 @@ tools: - name: dropletutils owner: iuc revisions: - - cdf4443d5625 - - cfe1e6c28d95 - - a9caad671439 - 8855361fcfc5 + - cfe1e6c28d95 - 2c1200fba922 + - a9caad671439 + - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -202,8 +202,8 @@ tools: - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 9d42a6133690 - 57aeaf6b237d + - 9d42a6133690 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata @@ -237,8 +237,8 @@ tools: - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - 9d02f1819e81 - f963c251ac77 + - 9d02f1819e81 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint @@ -258,8 +258,8 @@ tools: - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - b05f662f9f35 - f0216498a666 + - b05f662f9f35 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions @@ -272,15 +272,15 @@ tools: - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - 3a6a5381db36 + - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat @@ -307,8 +307,8 @@ tools: - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - ffc33339cd3e - 0410b6aada45 + - ffc33339cd3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad @@ -321,8 +321,8 @@ tools: - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 972dcccb5bbc - 6c5097f6d41e + - 972dcccb5bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops @@ -335,8 +335,8 @@ tools: - name: hicexplorer_hicinfo owner: bgruening revisions: - - e4f8fceab96a - 51e40e9b6c3c + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad @@ -349,22 +349,22 @@ tools: - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b6b8c8672756 - b376ef118807 + - b6b8c8672756 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1511a8ebe906 - ed900cd4a0a9 + - 1511a8ebe906 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 6d042c96aceb - f34ab9882252 + - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -384,8 +384,8 @@ tools: - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 - 337705015ee8 + - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint @@ -398,8 +398,8 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - ea8fb5e899e8 + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices @@ -431,19 +431,19 @@ tools: - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 1d201e8378b3 - 11a3385e03b5 + - 1d201e8378b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - 59be31ac9dc3 - 4b0adaa31c95 - e98619de2776 - - eeab712b0b99 - - 0f1aaff9b22d - 7784821452ac + - 0f1aaff9b22d + - eeab712b0b99 + - 59be31ac9dc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -456,8 +456,8 @@ tools: owner: bgruening revisions: - 2cfd0db49bbc - - 282819d09a4f - 7ffaa0968da3 + - 282819d09a4f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -489,11 +489,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - a4b734cd253b + - f911a64454fb - c4f39bf4a068 - - 0bff0ee0683a - 7e014059a88d - - f911a64454fb + - a4b734cd253b + - 0bff0ee0683a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -505,9 +505,9 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - d45f092caf24 - 7608d5faee41 - 43c146e25a43 + - d45f092caf24 - b83fbc90161e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -520,9 +520,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: + - 37a47c4fd84d - f3eb2291da05 - 2b0d3e2f402a - - 37a47c4fd84d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -534,9 +534,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: + - 69018f285aa3 - df8e4e54d367 - a6821f856a1e - - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -548,11 +548,11 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 - - e93b008c637a - 44b935f2271b - 2af7c5086a96 + - c92d0f9338c5 - 72979cac22b2 + - e93b008c637a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -576,15 +576,15 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 38db3fef7aad - - 6f83f8fd381f - f9353ee6a0d4 - - edec35114f72 + - b2df381a6004 + - 38db3fef7aad + - 77b91b9bdf52 - 4d8f983cd751 + - edec35114f72 + - 6f83f8fd381f - aaa5da8e73a9 - - b2df381a6004 - 6acb08931836 - - 77b91b9bdf52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -598,12 +598,12 @@ tools: revisions: - 8cb783c81905 - b409c2486353 - - a03ff8633507 - - 72a6bebab2a5 - - d636ce5cde16 - 3c86f71498bc + - a03ff8633507 - a97abb8cd15b + - d636ce5cde16 - 277313130da5 + - 72a6bebab2a5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -615,17 +615,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: + - 18262103fa61 - 6c145a6868cc - 5c3ebe2adc77 - - 5e9171dc8244 - - f54f0f0598ad + - c0a80a16560f - cc0deb593fc8 - - 18262103fa61 - d1cd8c147809 - - 6bd82ed14acd - - 3081ff5c84a3 + - f54f0f0598ad - c5d3684f7c4c - - c0a80a16560f + - 5e9171dc8244 + - 3081ff5c84a3 + - 6bd82ed14acd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -637,15 +637,15 @@ tools: - name: scanpy_normalize owner: iuc revisions: + - 9f354c7c8c92 - a407e7f8bdc1 - - 56c0d4acef02 - - 7b9fafe32c86 - 94c19fb1281c - - ab55fe8030b6 - c9cb76cf8d6c - d844935c906c - - 9f354c7c8c92 - 3bcd5445cd7a + - 7b9fafe32c86 + - ab55fe8030b6 + - 56c0d4acef02 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -657,16 +657,16 @@ tools: - name: scanpy_plot owner: iuc revisions: + - 7647e5cd1b8b - dbbe1ea8ecb1 + - 95777145cb92 - 1072ce66b426 - - 9b0cdb8cf6be - - aa0c474463c2 - f7446fd8d5e7 + - aa0c474463c2 - 6adf98e782f3 - 0185bd174ea0 + - 9b0cdb8cf6be - 6f5349dd5c49 - - 95777145cb92 - - 7647e5cd1b8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -679,14 +679,14 @@ tools: owner: iuc revisions: - 215733a383f2 - - f2f6c703da06 + - 458e8f43a775 - 73ab2ac53d06 - c65fce500915 + - f2f6c703da06 - 9fb627495ec2 - bf2017df9837 - - d18e7a6e5cd4 - - 458e8f43a775 - a39040ae0a38 + - d18e7a6e5cd4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -712,9 +712,9 @@ tools: - name: scater_filter owner: iuc revisions: + - 7a365ec81b52 - 652923ce664f - b7ea9f09c02f - - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -732,9 +732,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 81e5bdff4853 - ef4c80837bc5 - 2e41b35b5bdd + - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -1008,15 +1008,15 @@ tools: - name: snapatac2_plotting owner: iuc revisions: - - 370d45e0d1a8 - fecf9664c885 + - 370d45e0d1a8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy @@ -1028,8 +1028,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 883c33ef3372 - 90e95e9ee190 + - 883c33ef3372 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 2ae3e110c..3a828b9bf 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -34,9 +34,9 @@ tools: revisions: - 746e8e4bf929 - 2f3c6f2dcf39 - - 4c07ddedc198 - 562f3c677828 - 419027d822d6 + - 4c07ddedc198 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,8 +49,8 @@ tools: - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -63,15 +63,15 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 7a15159140d1 - 6c29c7e347e8 + - 7a15159140d1 - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - 9c3e1d3235c8 - aef56d0e7a61 - b1eda492f063 - - 840f29aad145 - 7442b94d6a1e - - 9c3e1d3235c8 - 4c4ec859c31a + - 840f29aad145 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - 9fda0b82f419 + - 07843f917990 + - d0352e8b4c10 - 30d21a6041f6 - 375bbd555f4a - - d0352e8b4c10 - - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - cd02bf168d23 + - 7ae443e6217d + - 8b1b2b91f8d0 - 4cc980df6265 - 2c58b83c9bad - - 8b1b2b91f8d0 - - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - bb9fc9d46ea4 + - 1dd433d2c92c - 7dd3fb35904f + - ad7e0b4291ee - e10e776f2109 + - bb9fc9d46ea4 - 4bbaf77573ef - - 1dd433d2c92c - - 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 b92e74a54..44d680549 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -34,15 +34,15 @@ tools: - name: column_maker owner: devteam revisions: - - aff5135563c6 - - 02026300aa45 - - 6e8d94597139 - 6595517c2dd8 + - aff5135563c6 - 13b6f0007d9e + - 02026300aa45 - 464b9305180e - 626658afe4cb - - 9cd341095afd - be25c075ed54 + - 9cd341095afd + - 6e8d94597139 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 9cc411a62277 - - 90f657745fea - 37cde8134c6a - - 34d29339abab + - 90f657745fea - 557ec8d7087d + - 34d29339abab + - 9cc411a62277 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -115,22 +115,22 @@ tools: - name: query_tabular owner: iuc revisions: - - 83069b38aa85 - - 623f3eb7aa48 - - 33d61c89fb8d - - 3a6b78c39dca - - 2e8f945f7285 - cf4397560712 - 1ea4e668bf73 + - 3a6b78c39dca + - 83069b38aa85 + - 2e8f945f7285 - cf34c344508d + - 623f3eb7aa48 + - 33d61c89fb8d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - ae8c4b2488e7 - 399da6b5ec21 - 503bcd6ebe4b - - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -142,10 +142,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - bce29ec10b78 - b722161a845a - - f768f6183386 - c4d18aa4ec4a + - f768f6183386 + - bce29ec10b78 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -158,15 +158,15 @@ tools: - name: text_processing owner: bgruening revisions: - - 9ff72e942410 - - ddf54b12c295 - - fbf99087e067 - - 86755160afbf + - a6f147a050a2 + - 12615d397df7 - d698c222f354 + - 86755160afbf + - ddf54b12c295 + - 9ff72e942410 - f46f0e4f75c4 - - 12615d397df7 - - a6f147a050a2 - - 74a8bef53a00 + - fbf99087e067 - 0a8c6b61f0f4 + - 74a8bef53a00 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 d63dba4b7..163b9a59e 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -34,9 +34,9 @@ tools: - name: freebayes owner: devteam revisions: - - 57def2d7c093 - - a5937157062f - ef2c525bd8cd + - a5937157062f + - 57def2d7c093 - 04fa42777df9 - 156b60c1530f tool_panel_section_label: Variant Calling @@ -44,30 +44,30 @@ tools: - name: lofreq_alnqual owner: iuc revisions: - - 09d6e4693887 + - 435b157bed6d - e61c9ac190ad + - 09d6e4693887 - 791f73caa0c8 - - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: + - 4805fe3d8fda + - 3b4b2121842f - e1461b5c52a0 - 65432c3abf6c - - 03627f24605f - - 3b4b2121842f - - 4805fe3d8fda - dfadc322b065 + - 03627f24605f - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 7dfca164d2e3 - - 9cb929f21cfa - 701d134358ad + - 9cb929f21cfa + - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual @@ -102,11 +102,11 @@ tools: - name: snippy owner: iuc revisions: - - c9a8ef2aa380 + - 9bccc8404a3c + - 5bbf9eada9c2 - fa016f1eea1a + - c9a8ef2aa380 - d220115f882b - - 5bbf9eada9c2 - - 9bccc8404a3c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -150,8 +150,8 @@ tools: revisions: - e7aff4a85df5 - ee4a90760848 - - 3b1e7c170b10 - 32f14a2723ec + - 3b1e7c170b10 - 40f0591deda0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -159,10 +159,10 @@ tools: owner: iuc revisions: - 42818629ec4c + - 02d81b994ef5 - 4934c0ac6197 - - 9793bc5d741b - adc0645b945c - - 02d81b994ef5 + - 9793bc5d741b 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 16def6285..234c66dab 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -4,12 +4,12 @@ tools: revisions: - 8a2e296c07ef - 95815a0bb307 - - b7ea370b8f5d - - 2c372041ed8c + - ebe5fc018e72 - e075b1be5abb - - 265fe0f9ea64 + - 2c372041ed8c - 6a88248893c4 - - ebe5fc018e72 + - 265fe0f9ea64 + - b7ea370b8f5d 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: - - 544cb432072b - - c37b684e7f4e - 22637b1a55bf - - b03984136ce4 + - 544cb432072b + - 21687e35f066 - 1001172b5089 + - b03984136ce4 - 0fba2c15b40d - - 21687e35f066 + - 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: + - 3a7084316a6e + - 0238f68ad641 + - 01d6b7d6365e - 8ca3647c90fd + - 143796b504eb - 8408bffd5616 - ccb83bf54de0 - 8627b2b383b4 - - 0238f68ad641 - - 143796b504eb - - 01d6b7d6365e - bf1f4994f104 - - 3a7084316a6e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,14 +59,14 @@ tools: - name: bcftools_concat owner: iuc revisions: + - 6b6c992d3a14 - d144af39073a - - 62ca6da715bf - - f430a1ec7ee4 - 9b5abbf50d23 - - 03e0645395d2 - - 6b6c992d3a14 - abd489215f73 + - 62ca6da715bf + - 03e0645395d2 - 81426b3cf18b + - f430a1ec7ee4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -79,13 +79,13 @@ tools: owner: iuc revisions: - 8aa352093d73 + - e522022137f6 + - 2363ef414c9b - 95c6f3f4c77f - d37e313a41be + - 1829900b5dcd - 1171446da5db - - 2363ef414c9b - - e522022137f6 - d3081540d175 - - 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 - 348cd212dbad + - 1137ce8efc1e + - b14ff40958cb + - d58d2e8c7a57 + - 012656fd329f - 09f37afb3621 - 9b29129fb491 - 92c0aff8b53e - - b14ff40958cb - - 1137ce8efc1e - - 012656fd329f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,12 +116,12 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - cfd81f17580b - - de68c11034f6 - - ecc9192912b8 - 55c0e906c14c - - 1f2183a23823 + - de68c11034f6 - 7291189e98b4 + - 1f2183a23823 + - ecc9192912b8 + - cfd81f17580b - 367ba501b6eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -135,12 +135,12 @@ tools: owner: iuc revisions: - 039ea3f1dea9 - - 7cbf3c66d4ad - - e6f4badbe6f3 - 6c790a091c7c + - 7cbf3c66d4ad - d237eaef451f - - ae68ceb4cca3 - 64a8f7dae3ad + - ae68ceb4cca3 + - e6f4badbe6f3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -152,14 +152,14 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 46fcafba49ec - - 963a3635b2e1 - 5d6653c989cb - - 33bd9301568c + - 277719af4dd7 - e7452697afd9 + - 963a3635b2e1 - 6ea7170a016d - cdb7b4927742 - - 277719af4dd7 + - 46fcafba49ec + - 33bd9301568c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,13 +171,13 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - b7f0f59baa7e - - a1213a0b7b66 - - a29a2f40b665 - - 501bfb078342 - 5a321fab1fe4 - - 7b4454382d39 - 91c1e57d5c7f + - 7b4454382d39 + - a29a2f40b665 + - 501bfb078342 + - b7f0f59baa7e + - a1213a0b7b66 - 26d97cdd5410 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: + - d7d1663559e9 - 97d19c008d15 - - 81e4014fa809 - - 768d04526638 - - 709dd8291b83 - - c803c34361e0 + - 5f27e814a119 - 39bca000353d - 15da1ddcfeff - - d7d1663559e9 - - 5f27e814a119 + - 709dd8291b83 + - c803c34361e0 + - 768d04526638 + - 81e4014fa809 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -210,12 +210,12 @@ tools: - name: bcftools_merge owner: iuc revisions: - - 2215287d5cc9 - 5b006286a458 - - 86296490704e + - 2215287d5cc9 + - 85ee7e6c4204 - b1eba148b35b - 7ba36babba2d - - 85ee7e6c4204 + - 86296490704e - b84fda8ebef0 - b931e65638b8 tool_panel_section_label: VCF/BCF @@ -229,16 +229,16 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 4e1d23e5c691 + - 5660b21a0dbd + - 37757ffb4c5f + - ce9396ddcb2b + - 31ea13dfe5e6 - cf06b44624c7 + - 56556e1267de - 9c711df3258d - - f506df85c652 - - ce9396ddcb2b + - 4e1d23e5c691 - 0a5dcc9a8ec2 - - 37757ffb4c5f - - 56556e1267de - - 31ea13dfe5e6 - - 5660b21a0dbd + - f506df85c652 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -250,13 +250,13 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 1ca7418e46ee - - 021693fdadaa - - 6deb4d549bc9 - - 48291658fdf6 - 19905c025d2a - 271965b55437 - a404f786a94c + - 1ca7418e46ee + - 021693fdadaa + - 48291658fdf6 + - 6deb4d549bc9 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: - - dadbd61dc4cf - - 69d8b7567281 - - c450406f722b - - f7879f1e77f9 - 71c78e0eea52 - - 5ad5d4243987 + - f7879f1e77f9 - 3f6fadf8b8ff + - c450406f722b + - 69d8b7567281 + - dadbd61dc4cf - 97e8145d7e30 + - 5ad5d4243987 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: - - 283911fe7e1a - - cc7f9a4e186b + - 79f7a1acc2cd + - 6cf13a657cf6 - 2514e684f8a3 + - 52f9e4a660e3 + - cc7f9a4e186b - 0fe007201caf - d31a2e310a52 - - 52f9e4a660e3 - - 6cf13a657cf6 - - 79f7a1acc2cd + - 283911fe7e1a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 026a989b7cee - - 80e6e399ccd0 - - a12844ca467a - - 0a62420cb9cd - - 75ddd081f608 - 1411bef27a75 - 6963a6841d22 + - a12844ca467a + - 75ddd081f608 + - 0a62420cb9cd - 230e424bde67 + - 80e6e399ccd0 + - 026a989b7cee tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,13 +325,13 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - b10d1510fa84 + - ba20340426fe - 5acfca5a76af - 5808f77b2bb6 + - b10d1510fa84 - 444e6a756c35 - - ba20340426fe - - 450a265f92e8 - bca7ce81688f + - 450a265f92e8 - e493702b19eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -344,14 +344,14 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - 4d236c696844 - - 12152af85697 - - 68fec03a63b7 - - d52b8947b269 + - 157ffcdd3fa7 - c43399f161f4 + - 12152af85697 + - 4d236c696844 - dd72ff87cfd0 + - 68fec03a63b7 - f2482aa4862e - - 157ffcdd3fa7 + - d52b8947b269 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: - - 75becf493cd3 - - 6f8e223f78f3 - - 29ba253e2e05 - - cbe39e530cbf - - 8f2fc0ab30fb - 0e5d11004815 + - 6f8e223f78f3 - 8dbce095986c + - 8f2fc0ab30fb + - cbe39e530cbf + - 29ba253e2e05 + - 75becf493cd3 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: - - a8630d4fbaf8 - - 88bb477f45f7 - - f544f71adb73 - - a367a15c6de5 - - 3ff5654b4e7d - 9708e3086f32 - e0a856def0b0 + - 88bb477f45f7 + - a367a15c6de5 - 8f5962c43868 + - 3ff5654b4e7d + - f544f71adb73 + - a8630d4fbaf8 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: - - 96d0145c041a - - 5c9729d54721 - - 34dc0bbc7e93 - - 8b260d252ff4 - 4ed46189d6c6 + - 5c9729d54721 + - 96d0145c041a - 6ce175385dd9 + - 34dc0bbc7e93 - 03e30f06f15f - 31c096c6b156 + - 8b260d252ff4 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: + - a730269af659 - a1aad8b559c6 - - 11af7fce71cf + - 2c4941386820 - 40daf124be88 - 46eb13bc2c73 - - 681bdf1e22ff + - 11af7fce71cf - 09f5e45a8212 - - a730269af659 - - 2c4941386820 + - 681bdf1e22ff 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: - - 882b2e649602 - - 0594ea1417c8 - 743cd1472aeb + - 882b2e649602 - 6cbb9c47795c - - 8cb121b6a1d2 - - 3897eaadfbff + - f272b8ba0983 - 12038f59c0f4 - b74b8cbfc1f1 - - f272b8ba0983 + - 8cb121b6a1d2 + - 0594ea1417c8 + - 3897eaadfbff 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: - - eccb508bb678 - 238f78e38a8b - - adee7e8b746f - 18cf9de1cf73 - - cced6715f926 - dba06328556a + - adee7e8b746f + - cced6715f926 - a9826db86d9a + - eccb508bb678 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: - - e0ad88dec40d - - 3ce32adc55b2 - fdec14f69010 - e53501abf992 + - c9935c9e8a24 + - 31a1b89eab9b - 9f36041495a3 + - 3ce32adc55b2 - f64e7ca2efd2 - - 31a1b89eab9b - - c9935c9e8a24 + - e0ad88dec40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - b7be725976b6 - fd3539749127 - - d68c43202172 - 79489d5685dd - - 3b7b1fe7b937 + - d68c43202172 + - b7be725976b6 - d43eb39b989e - - 2331ddcbd5aa - 4db0695a6fc7 + - 3b7b1fe7b937 + - 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: - - 1ccf0e7fb4f6 + - 78cd8b69da4c + - b0d39ef600a7 - 6a636d58dfc2 + - 5296d26b0373 - 58091e1be01b - - b0d39ef600a7 + - 1ccf0e7fb4f6 - 1a989b4110da - - 78cd8b69da4c - - 5296d26b0373 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: - - '388983871932' - - bf8325a07ce7 - - b641062a2587 - 591cc8518033 - e8af591435d1 + - b641062a2587 + - bf8325a07ce7 + - '388983871932' + - baa8823f8073 - 4d3ce9dc1525 - b17394940c7a - - baa8823f8073 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: + - 1a2ef636f48e - 59fa8742285e - 3ca3de4e5291 - - 38d75661c235 - - e6b5cbbf449b - c2ab91a0d506 - - 1a2ef636f48e - 3a233c8eb814 - d1f8f55f564d + - 38d75661c235 + - e6b5cbbf449b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -570,29 +570,29 @@ tools: - name: vcf2tsv owner: devteam revisions: - - e92b3c0f9224 - 285060661b45 + - e92b3c0f9224 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives owner: devteam revisions: - - a8a4f94aa321 - 57a16b310fe8 + - a8a4f94aa321 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -612,8 +612,8 @@ tools: - name: vcfbreakcreatemulti owner: devteam revisions: - - 9fd5d91eb91b - 690b1d846263 + - 9fd5d91eb91b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck @@ -633,23 +633,23 @@ tools: - name: vcfcommonsamples owner: devteam revisions: - - f1852ecef841 - 254f285dbaaa + - f1852ecef841 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - fa24bf0598f4 - 6b935ab36d7b - eae7c08ebb6f + - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -676,15 +676,15 @@ 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 @@ -704,22 +704,22 @@ tools: - name: vcfrandomsample owner: devteam revisions: - - 6257ee3b50d3 - 12b570dd0bc5 + - 6257ee3b50d3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples owner: devteam revisions: - - 2ba3b87f904f - 958b6484a7f1 + - 2ba3b87f904f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort owner: devteam revisions: - - 5b7120c66efc - dd44c3f416c3 + - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate @@ -749,7 +749,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 6f6bf10618d7 - 166c4f50525f + - 6f6bf10618d7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 973dfc8b4..d1730f348 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 4efdca267d51 - 78c75f134c16 + - 6e9aea89e388 + - 4efdca267d51 - 3f3e247c053d - c2ef298da409 - - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -19,77 +19,77 @@ 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 owner: iuc revisions: - - 1fdc517743e6 - c4ac24510b55 + - 1fdc517743e6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - a79ee60b6926 - fe3ca740a485 - - b5d8e5475247 + - f29602ae449e - 4f2967b27e67 - 3e1f6f6d557e - - 1aae04680c4b + - b5d8e5475247 - 44018dd6b447 - - 133f36c29579 + - a79ee60b6926 - cd2480f35935 - - f29602ae449e + - 1aae04680c4b + - 133f36c29579 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - - dc027fa56d55 - 6519ebe25019 + - dc027fa56d55 - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - ca6d970d931c - 28433faa6e42 - 09855551d713 + - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: + - 92eee5f31117 - d77802fe76f7 - da5f1924bb2e - 728dacaf08a9 - - 92eee5f31117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: + - 8fd427007e93 - 7355bbf5e05f - fe48aa4ccd5e - - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -101,8 +101,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -115,16 +115,16 @@ tools: owner: bgruening revisions: - 1ac12c0cc7a0 - - 8e9e228c54c4 - 7ccc6234b54e + - 8e9e228c54c4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: + - 63662ae295d6 - d9c3016f7283 - 9d1fbff733cf - - 63662ae295d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -148,61 +148,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 9c15ca7e764e + - 14f588312c56 - 9f2455341fac + - b6b5cd37f2a2 + - 3bbe70fef6df - 582fd74dc2a1 - 756376aeb1ae - - 14f588312c56 - - 3bbe70fef6df - - b6b5cd37f2a2 - - 9c15ca7e764e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - a230ea445788 + - 0ffe5be70caf - 30fb23d4c31c - - 8e1ace8f77c6 - - 73428a792541 - 989f7c061f35 - - 0ffe5be70caf + - 8e1ace8f77c6 - 1691af4a0d17 + - a230ea445788 + - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - e94187d661df - 30f08d74024f - - 5a5ae61da69c - - 563a19373357 - - 494f0bb4a993 - 0418d28136de - 57c6718cbfcc + - 494f0bb4a993 + - e94187d661df + - 563a19373357 + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - f31125bb85ea - - f77d7b685bb3 - - 2bba2ff070d9 - - 1bc5a03faf2e + - d6c7106b7b2e - 7abc5f6dd595 - 4b96ced19f75 - - d6c7106b7b2e + - 1bc5a03faf2e + - f77d7b685bb3 + - 2bba2ff070d9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - 54961e026fe4 + - 52af33194019 - 520e30695ec3 - - b3cf4684e9c7 - fed64e676186 - - 54961e026fe4 - d3af38b9c7e1 + - b3cf4684e9c7 - d77fdcca400e - - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -214,9 +214,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 07d7991bf205 - - 79261884facd - 2aea122fbd25 + - 79261884facd + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -229,8 +229,8 @@ tools: owner: iuc revisions: - 602de62d995b - - ef2ad746b589 - 8b3e3657034e + - ef2ad746b589 - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -255,8 +255,8 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan @@ -289,19 +289,19 @@ tools: - name: maker owner: iuc revisions: + - 3c1a01127868 - 370c210d9541 - d46d803ca6cc - - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - b815ec682418 + - 033755194fe9 - e95d52d295d7 - - c8ac28e8ac44 - 624606f7c996 - - 033755194fe9 + - b815ec682418 + - c8ac28e8ac44 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -349,10 +349,10 @@ tools: - name: prokka owner: crs4 revisions: - - d643e3b03500 - - 8a22554cdde2 - bf68eb663bc3 - a17498c603ec + - d643e3b03500 + - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -364,8 +364,8 @@ tools: - name: repeat_masker owner: bgruening revisions: - - 3f987772e283 - ba6d2c32f797 + - 3f987772e283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler @@ -396,21 +396,21 @@ tools: - name: snpeff owner: iuc revisions: - - 5b80f544c67f + - 5c7b70713fb5 + - 9473cd297a76 - 5a29ab10dba6 - 8f92c2b26e6d - - cfcf33df7fc0 - - 9473cd297a76 - 268d162b9c49 + - 5b80f544c67f + - cfcf33df7fc0 - 68693743661e - - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - 2b3e65a4252f + - 5fab4f81391d - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -430,24 +430,24 @@ tools: - name: tbprofiler owner: iuc revisions: + - 809dfc93d593 + - ac8250086ac3 + - 51dd22484644 + - 200c378d85f3 - 37213cf56392 - - d03af1c7002c - e1a9d6fd258d - - 4839e590cb26 - - 45083d070fb8 - - 809dfc93d593 - ba6f87115e13 - - 200c378d85f3 + - d03af1c7002c + - 45083d070fb8 + - 4839e590cb26 - 037a11682176 - - ac8250086ac3 - - 51dd22484644 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 63c83e3af..9dfad5e7d 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,27 +2,27 @@ tools: - name: abyss owner: iuc revisions: - - fa5259cc561b - - 0124fce4654a - 890b794c997d - 841084c5fc46 - - a929ce596a34 + - 0124fce4654a - 553bfe8bd0b5 - - 7547fcab5d19 - - 8f1b150a2487 - d6d5ccc2c581 + - fa5259cc561b + - a929ce596a34 + - 7547fcab5d19 - 0e93176640ac + - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - ddddce450736 - b2860df42e16 - 21e491ad532a - - 94fe43e75ddc - b9e31c5c01c7 - - ddddce450736 - 067592b6b312 + - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -35,11 +35,11 @@ tools: - name: bionano_scaffold owner: bgruening revisions: + - 3371c5bdc17a + - 22286dab5aa1 + - a7f16f24e9a1 - 5258e18bbe23 - faee8629b460 - - a7f16f24e9a1 - - 22286dab5aa1 - - 3371c5bdc17a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -52,30 +52,30 @@ tools: - name: busco owner: iuc revisions: - - 4048d82f0c88 + - bb935709506a + - 46ae58b1d792 + - 1e62c28ba91d - ea8146ee148f + - 0d243f458b53 + - cf13a1e03e5b + - 602fb8e63aa7 + - e824f5d958d0 + - 2dd755c1c6ff - 41030a6c03b7 - 1440ae06552f + - 94170eee0ad8 - e4bd1e99bacf - - 2babe6d5c561 - - e824f5d958d0 - - 1e62c28ba91d - 5ecdeca79a0d - - 94170eee0ad8 - - bb935709506a - - 0d243f458b53 - - 46ae58b1d792 - - 602fb8e63aa7 - - 2dd755c1c6ff - - cf13a1e03e5b + - 4048d82f0c88 + - 2babe6d5c561 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 86f150c8019d - 5732f959936a - c5b7390290b1 - - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -87,42 +87,42 @@ tools: - name: flye owner: bgruening revisions: - - 1f0769f0b56b - - 8d4f03b5fe9d - - cb8dfd28c16f - - 291923e6f276 + - 3ee0ef312022 - e27815e82dd4 - 3e4f8642c77e + - 291923e6f276 + - 1f0769f0b56b - 276f5d8712d5 - 1ce9b1d72ec3 - - 3ee0ef312022 + - cb8dfd28c16f + - 8d4f03b5fe9d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 460fad600dce + - 3169a38c2656 - 01210c4e9144 + - 460fad600dce - b2f674562a18 - - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - - 7348b69e5109 - - ba88bc5a6446 - 8b330a577046 + - ba88bc5a6446 + - 7348b69e5109 + - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 3fba9c77550a + - 5127a713de83 - 3ef480892a9f - 690c2caa367e - - 5127a713de83 + - 3fba9c77550a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -134,23 +134,23 @@ tools: - name: hifiasm owner: bgruening revisions: + - 71740308d412 + - 6505bd37670d + - 60024a528cbd - da9d8bf98802 - - 5f625c63b8bc - - 366a11d316a7 - - 41cea2aa2dce - 2061fb3b81b4 - - 9ef6920c3089 - - 6505bd37670d - - df25d4fb79b7 - - 3f7be05a1597 + - ec9e21e9c71b - 5bec28269d95 - - 0ee0c3089254 - f3c89da3af16 + - 41cea2aa2dce + - 5f625c63b8bc + - df25d4fb79b7 - 284a1cb82b61 - 045c7c3d8e59 - - ec9e21e9c71b - - 60024a528cbd - - 71740308d412 + - 0ee0c3089254 + - 9ef6920c3089 + - 3f7be05a1597 + - 366a11d316a7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -174,43 +174,43 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - - 14ddfc8ffb93 - - 7518ee87b53d - de387b2b2803 + - 7518ee87b53d + - 14ddfc8ffb93 + - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 39edec572bae - - d7edbc9c3a07 - - f8113c25bc6b - - 9d79beb19ac3 - eb7b00ec347d - 09c589057ee8 + - f8113c25bc6b + - 9d79beb19ac3 + - d7edbc9c3a07 + - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: + - 51c2360aa807 - eadfd71dde37 - 29dabd8db6f2 - - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - 2ecf5a570907 + - 3ca2d2a9068c - e731ea24e48d - eb7a370f6588 - - fd128c111ab0 + - f369ef5f210b - 99ecfdafc64f - f338e9942b27 - - f369ef5f210b - - 3ca2d2a9068c - - 2ecf5a570907 - 606b09cc9860 + - fd128c111ab0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -222,11 +222,11 @@ tools: - name: miniasm owner: iuc revisions: + - 73a3846701e1 - a7b889b90140 + - 8dee0218ac7d - b799a615995d - - 73a3846701e1 - 8b6d0d85252b - - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -244,8 +244,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 15200570e926 + - 64a1c751d99b - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -258,45 +258,45 @@ tools: - name: pretext_map owner: iuc revisions: - - 2b16ba799da9 - bbe19ef04a74 - - d256a51a656b - 79b48f02db49 - - dfb8a4497339 - - 8fef980d48b5 + - d256a51a656b - 02831bf9e95f + - 8fef980d48b5 + - 2b16ba799da9 + - dfb8a4497339 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - e9bd16ba5ebd - - 76d4cbefff85 - a315c25dc813 + - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 875d0f36d66f - - 59db8ea8c845 - 7594365c546b + - ebb0dcdb621a - 3061c8b029e5 - - 342a1d1fed7b - - 675488238c96 - 6fcbee531de6 + - 875d0f36d66f + - 59db8ea8c845 - 72472698a2df - - ebb0dcdb621a + - 342a1d1fed7b + - 675488238c96 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - aa39b19ca11e - - a199cd7ac344 + - d865b62f501c - cd06929b224b - 78c533842eeb - - d865b62f501c + - a199cd7ac344 + - aa39b19ca11e - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -309,29 +309,29 @@ tools: - name: raven owner: iuc revisions: - - f8564b2d7f63 - - 5c55448d0f33 - 2b2a352488fa - - 33b7d8481a76 - - 3edba9afc9bc - f11b994b7eb2 + - f8564b2d7f63 + - 3edba9afc9bc + - 33b7d8481a76 + - 5c55448d0f33 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: - - 53c2bc8c2ae3 - e122f9101584 - 378e55aeeb25 - - 28189050e437 - 5fc94b3a4704 + - 28189050e437 + - 53c2bc8c2ae3 - ef69617ecb42 - 1d06c8b38e77 tool_panel_section_label: Assembly @@ -345,138 +345,138 @@ tools: - name: shovill owner: iuc revisions: - - 196a599ec43d + - 83ead2be47b2 - ad80238462c1 - f698c7604b3b - - d9f6a00b6db7 - 865119fcb694 + - 196a599ec43d - ee17a294d3a3 - - 83ead2be47b2 + - d9f6a00b6db7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - - 5e0825476fb7 - 015283de3004 + - 5e0825476fb7 + - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 7490b213baa9 + - 051fd2db8a27 - c33a476f4001 + - 1fc82fe7ebef - 1bb12736175c + - 7490b213baa9 - 604782a8a53a - - 1fc82fe7ebef - 904bf932cf78 - - 051fd2db8a27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - d6e617c4e338 - - 808b3a0a6716 - - 34305b013402 - fee85957cebe - - 9678993ca5bd - - 655fa188c3cc - ad8b536d1caa + - 34305b013402 + - 655fa188c3cc + - 808b3a0a6716 + - d6e617c4e338 + - 9678993ca5bd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 21da31ed41a1 - 7e27faaad80e - - 6b5a5842531e - 037f9927c4ff + - 21da31ed41a1 + - b8002c3f7141 - 8d4b90bf9caf - e5a3b75a271f - - b8002c3f7141 + - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - f1532cb33c75 - - 9de69775f512 - 7922870efcca - - 2a10645aeadd - 5b26685e5d3b + - f1532cb33c75 + - 9de69775f512 - 328aa71f0f3c + - 2a10645aeadd - 86f66ab58e14 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 8cc856b935ee - 1708851f8804 - 340bc17f49cf - 85fb02c43042 - - 6aad515a5270 - e41dcb0e913b + - 8cc856b935ee + - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - 6357b127161e + - d159735a6a9f + - de1260f8a300 - d5fb354f745d - b65a43f70b99 - - 6357b127161e - 249f6a28c751 - b3490b036c5a - - de1260f8a300 - - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d5887ace0dd4 + - dd7ad84f3943 - d2d1df21dfb9 - - 33368fec3b70 + - d5887ace0dd4 - b7829778729f + - 33368fec3b70 - 9006e5836729 - 7897763d14ec - a90db5dbaaf3 - - dd7ad84f3943 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 505a9833ab5d - 8f631679571f + - 505a9833ab5d + - ed2425b9fd27 + - ced385aa976d - 6f4c8ad6ea01 - 189e837009c9 - - ced385aa976d - - ed2425b9fd27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - - 9ded6109434a - 19bdfd1e6fe3 - - 356afed970b4 - e59bee4565b3 + - 356afed970b4 + - d40ed4eb0c0e + - 9ded6109434a - f31d376ce725 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - af40e971a8cc - - 80a17897564d + - b23249f81bc4 + - ebd801e712bc - 6dd935e4984b + - 80a17897564d + - af40e971a8cc - 4688ae3b49b5 - - ebd801e712bc - - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa @@ -484,50 +484,50 @@ tools: revisions: - b64696992ee9 - bb11fefb23a3 + - 937ea677d437 - 59bd28f6265d - - b5e35a2ca4f3 - cb1e3db43020 - - 937ea677d437 + - b5e35a2ca4f3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 383bb5ad32e2 + - 6bfab4a4a988 - 6015aa0303f2 - - 05bd7504fdb2 - cb4768eeca3b + - 383bb5ad32e2 - 2628f6790eda - - 6bfab4a4a988 + - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 0a3a602cd1e3 - - e92675014ac9 - 6e26c9afd301 - - e022dff952df - - 8f9f06995f98 - 9e3e80cc4ad4 + - 8f9f06995f98 + - e022dff952df + - 0a3a602cd1e3 - 3e44ef016b45 + - e92675014ac9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 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 - 4a53b89fa703 - 37d88f41c810 + - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index 5b7fba629..97fd9483c 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: - - bfd290fe1588 - - 1ae00120dd24 - 392f100eebcd + - bfd290fe1588 - 4768f7f8e93f + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - 31812e7a1315 - 1f5641a52664 - ded48b36f3b7 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - 24a7a95867b0 + - 5c8ff92e38a9 - 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 8f5e5414c..c9f823a16 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,13 +2,13 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 0840ba83860c - 204a131e47db - - 7beb76ffbc0f - - d1f62024a08b + - 0840ba83860c - 159b04e36791 - - a9c9d768b751 - 1c427e24fb79 + - a9c9d768b751 + - d1f62024a08b + - 7beb76ffbc0f 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 50f3691db..ff5f2322d 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: + - 0a5c785ac6db - a68aa6c1204a - - a8eabd2838f6 - 589e7e57fd6d - - 0a5c785ac6db - - dde39ba9c031 - - b28e0cfa7ba1 - - ce3c7f062223 - a1a923cd89e8 - - 87ee588b3d45 - - 64e2edfe7a2c + - a8eabd2838f6 - e19bebe96cd2 + - b28e0cfa7ba1 - 07e8b80f278c + - 64e2edfe7a2c + - ce3c7f062223 + - dde39ba9c031 + - 87ee588b3d45 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 0c886f6bb..11398d3aa 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,30 +8,30 @@ tools: - name: diamond owner: bgruening revisions: - - 62c9df8382c2 - - e8ac2b53f262 - - 54f751e413f4 - f921014aba5a + - 54f751e413f4 + - e8ac2b53f262 + - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - acf4e47b734c - - 2889433c7ae1 - - d999e774072a - - 5edc472ec434 - - e25d3acf6e68 - - 6f386c5dc4fb - - a52d2d93e595 - 0e3cf9594bb7 - cbf3f518b668 + - 6f386c5dc4fb + - a52d2d93e595 + - 5edc472ec434 + - 2889433c7ae1 + - e25d3acf6e68 + - d999e774072a + - acf4e47b734c tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 440cce4fc..4044b9026 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: + - 27ee142314a9 + - da6bd1975a71 - 6ca543ec1bf8 - - 710301bc46fa - c8cdde00b105 - - da6bd1975a71 - 095ad4d096d1 - f4230f116196 - - 27ee142314a9 + - 710301bc46fa tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_rxn_maker @@ -105,8 +105,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -124,30 +124,30 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 79cfd9ead848 - - 3b8a9d5ced85 - - 88076940fa94 - bfb65cb551d8 - 0fac8e2afc13 + - 88076940fa94 + - 3b8a9d5ced85 + - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - f5d979cb4b54 + - eb6564a60136 - 715cd0e87781 - - 55918daa5651 - b46d4b4d995c - - eb6564a60136 + - 55918daa5651 - d532b7e5f64b - - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - d2f955aea23a - - dae135dfd519 - f26afd1b7104 + - dae135dfd519 - fdf2cc80adb5 - 5579659312e6 tool_panel_section_label: ChemicalToolBox @@ -155,42 +155,42 @@ tools: - name: gmx_merge_topology_files owner: chemteam revisions: + - 319a28774da9 - bc31d02be922 - d1d0efda35c0 - - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 070e3ecc3fda - - cac1886249a2 - - ed736e6eee39 - 2c349b027a01 + - 070e3ecc3fda - 4da9ee404eab + - ed736e6eee39 + - cac1886249a2 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - da8753545526 + - d1f803b5943c + - c0c9a5024177 - 807aa4c9293d - f197e34c33a9 - - 2e219a2d9327 - 73008ef1f487 + - da8753545526 - 525ca7c8065f - - c0c9a5024177 - - d1f803b5943c + - 2e219a2d9327 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 61094e01eff9 - - 2c8ed1b52bf7 - - c4fbab8e03c5 - 7568ae18908a - 1809414a9454 + - c4fbab8e03c5 + - 2c8ed1b52bf7 + - 61094e01eff9 - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -204,17 +204,17 @@ tools: owner: chemteam revisions: - 730ef07b90ae - - d7ec25187599 + - ccfbd956a2d3 - 79e8ab8f1e81 + - d7ec25187599 - ba83f0923369 - - ccfbd956a2d3 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 @@ -262,10 +262,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - 4242b4d68e9c - - b59c91adeac1 - e2c36f62e22f + - b59c91adeac1 - e6011617c748 + - 4242b4d68e9c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -277,8 +277,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -345,8 +345,8 @@ tools: owner: bgruening revisions: - d4c67ced6abc - - 9b48456a96fe - 85fad59f8168 + - 9b48456a96fe - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 41e3aa1a7..d79953368 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -3,9 +3,9 @@ tools: owner: bgruening revisions: - f907216064f6 - - 2605cbdaa7d8 - fa56d93f7980 - 163688bb8f73 + - 2605cbdaa7d8 - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,25 +18,25 @@ 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 - - 424aefbd7777 + - 495a4173006f - f5d67c722d67 - 640d3af5d833 - - 495a4173006f + - 424aefbd7777 + - 86e2413cf3f8 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index dd460a53f..4a78f624d 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -11,8 +11,8 @@ tools: revisions: - 90981f86000f - 33151a38533a - - 830961c48e42 - 25136a2b0cfe + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: + - 2dae863c8f42 - 0046692724f9 - baabc30154cd - - 2dae863c8f42 - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index e74f6824c..9640852f9 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - e7449b2c14bf - abba05ead5d7 + - e7449b2c14bf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 6ef0b5664c69 - f3a19509108a + - 0b3c3ad92827 + - 6ef0b5664c69 + - ab9350a8ab4d + - 5e1240a87bcb - e3cbd2287f63 - - 367b1ed91207 - 3b6f97e7094c + - 367b1ed91207 - 4a6ee918c13a - - 0b3c3ad92827 - a3b86937ead6 - - ab9350a8ab4d - - 5e1240a87bcb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 1b5fc03380d4 - bd46669113b9 - - 72ed72122deb + - d4d4e9febf5c - 584008e574b2 - - 091bb5922a82 - - 54ccb7e1f49a - 501c21cce614 - - e177a8ea0bf1 - - e525f9ffb9ac - - d4d4e9febf5c + - 1b5fc03380d4 - 33c99804a32f + - 72ed72122deb + - e525f9ffb9ac + - 091bb5922a82 + - e177a8ea0bf1 + - 54ccb7e1f49a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -58,8 +58,8 @@ 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 @@ -73,15 +73,15 @@ tools: - name: fastq_to_tabular owner: devteam revisions: - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa owner: iuc revisions: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -94,8 +94,8 @@ tools: owner: devteam revisions: - 3e436657dcd0 - - 4dea02886337 - 154d00cbbf2d + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -113,8 +113,8 @@ 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 @@ -140,11 +140,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 92ac8e086317 - - b9b385097f13 - - 63769c4217a7 - 19e45916daf9 - 26c6706bfb07 + - b9b385097f13 + - 92ac8e086317 + - 63769c4217a7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -156,15 +156,15 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - 8067dfa00ed2 - 3c6f9e8a4c17 + - 8067dfa00ed2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - a2f83a375bf2 - 98704d357ede + - a2f83a375bf2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 5e9695b42..1b20e81e2 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,205 +2,205 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 5f6d123679f4 - - 29451af70c52 + - 268e91e540ee - a1ca9bccc7f2 - - c929a006727f - e821645ef8fc + - c929a006727f - de72ba3ed6f2 - - 268e91e540ee + - 5f6d123679f4 + - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: + - 0e143b4c3987 - 7a7fd0f5f15d + - bb1e4f63e0e6 - 12af64f93288 - - 2d2cf5c1ea8a - 5d11599b8a7d + - 2d2cf5c1ea8a - 0e49b109abc2 - - bb1e4f63e0e6 - - 0e143b4c3987 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 1d848bc4585f - - 7c1beb6d6eca - - c06951d10364 - - dc059492a995 - 195e98217334 + - dc059492a995 + - 7c1beb6d6eca - 81b1e3e1fc6c + - c06951d10364 + - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - a67ac707496a - - 07418a30ed01 - - 93eb012d9eed - bfff7454b59a - - 3d211717a775 - 71aa86af6762 + - 93eb012d9eed - 26e7304d6737 + - 07418a30ed01 + - 3d211717a775 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 2bc10a9ca58b + - 5be24eba848d - b8858746dc1f - 26983857c91a - 29fcfd36e90a - - 2bc10a9ca58b - dd0b7398bb96 - 56d5b797ce84 - - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - 72bfafe3330b - - 9384cd033f30 - - 7e6bcd2e5128 - e6d0bff01239 + - 7e6bcd2e5128 - 7ef978dc1b8a - - c3e012dfe21f - ee3a1b0f45f1 + - c3e012dfe21f + - 9384cd033f30 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fd1275e01605 - - d9a637e83828 - a60c359ec43c - - 9470f29702f8 - - b73e213add0c - 514fa53b5efb - - 167788df3b46 + - b73e213add0c - fb9cf9c97ec4 + - fd1275e01605 + - 167788df3b46 + - d9a637e83828 + - 9470f29702f8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - a02cfa31e9cb - - 5bffaa8354a1 + - 2c37ce318bc3 - c34d11ea4ba6 + - 5bffaa8354a1 - e479c7ca5570 - 86febdcc4283 - - 2c37ce318bc3 + - a02cfa31e9cb - ca0616bb2cdf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 69a8621ca2f0 - 192ef85c0b0b + - 004aea905d4d - 1fcb7adc39b8 - 78f405266706 - - 004aea905d4d - 01fb6a7654e6 - 2d466b530754 + - 69a8621ca2f0 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 9ecba5e225a6 - - 137c4beed34b - - d580d6acd1df - - 459cfa861f0b - 2f9e4843f480 + - 459cfa861f0b + - db940c262830 + - 137c4beed34b - d9ce4897dbb2 - 3c9f0c486cca - - db940c262830 + - 9ecba5e225a6 + - d580d6acd1df tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - bad3ca889618 - - bd7db9e2f2cb - 2c66e43f1c86 - - f264afa9fa6f + - fd408d755394 - 32e451def88c + - bad3ca889618 - fbe773640707 - - fd408d755394 + - bd7db9e2f2cb + - f264afa9fa6f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 231994413f89 - 7fda5607e777 - - 7e361d147872 - - 3b9d990a0a0e + - 56bce3c82278 - 4e12ea27f788 + - 3b9d990a0a0e + - 7e361d147872 - 9368fbc49c8b - - 56bce3c82278 - - 231994413f89 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - c03c3384cd81 + - 4431f39ede55 - b1779366c8e9 - ce4ce3316f74 - - d9114ef1c8a5 - - e65d16fb2724 - - 4431f39ede55 - 94ca68515826 + - c03c3384cd81 + - e65d16fb2724 + - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - d57251071381 - 793665fff0f8 + - 4ed32329e0ed - 2da482e408b8 + - b88ebb3672a1 - 23f7c5f1fdaf - - d57251071381 - - 4ed32329e0ed - f8fc4e5aff9d - - b88ebb3672a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a7849312d328 + - e4c7985d4585 - 010e58e9d822 - - 25d830337d31 + - ba6efa77fb79 - a4dfb122e52b - - e4c7985d4585 - - c60570fa602f - 512155688d98 - - ba6efa77fb79 + - a7849312d328 + - 25d830337d31 + - c60570fa602f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 443d9a9d6d11 - - 00d869ea03a1 + - c899e0ccff8c - 38e3f226248b - - 4d678170d29b + - 00d869ea03a1 - 69264da0ce77 + - 4d678170d29b + - 443d9a9d6d11 - aa200e4f3939 - - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a - - 6662b1a8d326 - - 10301d137111 + - aac8444d6681 - d806504e96d9 + - 10301d137111 - 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 40eadf37d..b8c51caac 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -2,8 +2,8 @@ tools: - name: obi_annotate owner: iuc revisions: - - d50dc96e3ce9 - 3021b9f5809f + - d50dc96e3ce9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean @@ -16,15 +16,15 @@ tools: - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - 02bab5ff7c37 - e9e49cf06b42 + - 02bab5ff7c37 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -58,8 +58,8 @@ tools: - name: obi_tab owner: iuc revisions: - - 4cf47c504672 - 3299c7d5268f + - 4cf47c504672 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 90da8fd01..68ea85a08 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - 832c20329690 - ce385837c160 - 63dd26468588 - dba489bfcd62 - - 832c20329690 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 01b09e704..90b0bdb1f 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 6da3972210ee - - cf1322aeb137 - 62f5fab76dfb - d82648ad25a3 - 29bdbc353f20 + - 6da3972210ee + - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index bf91616b3..66bcf5d3b 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -9,32 +9,32 @@ tools: owner: lparsons revisions: - b1c926deaa2d - - c053d4cad713 - - 288f97432497 - - 4e5056fefd88 - - 5915ea1ec9b1 + - 48f587c13075 + - e4691e1589d3 + - 660cffd8d92a + - 093678460093 - 8c0175e03cee - - fe74900d6dc7 - - c5e2e5902201 - - 49370cb85f0f - de6cebe3c043 - - 660cffd8d92a + - 5915ea1ec9b1 + - 4e5056fefd88 + - 135b80fb1ac2 - 5eb7e84243f2 + - fe74900d6dc7 + - 288f97432497 + - c053d4cad713 - 64172f1c1202 - - 135b80fb1ac2 - - 48f587c13075 - - c4b82dce8335 - - 8665bcc8b847 - - 093678460093 + - 49370cb85f0f - 44e2cc14f75b - - e4691e1589d3 + - 8665bcc8b847 + - c5e2e5902201 + - c4b82dce8335 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - - 9db07fd39f85 - 8889eb864cef + - 9db07fd39f85 - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -68,8 +68,8 @@ tools: - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - f546e7278f04 - 2904d46167da + - f546e7278f04 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -84,19 +84,19 @@ tools: owner: iuc revisions: - 56022eb50bbd + - cd0874854f51 - 9c620a950d3a - 0dbb995c7d35 - - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: + - 1d8fe9bc4cb0 - c59d48774d03 + - 65b93b623c77 - d60c3f704da0 - - 1d8fe9bc4cb0 - dbf9c561ef29 - - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -137,15 +137,15 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - - 2ccb8dcabddc - 3e396e702cea + - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -158,24 +158,24 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 249c8393f2d4 - e39cc71d3ed6 - 35e38452bb3f + - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - 045f0e1043f7 - - 74db4cffab1f - 54053ea6c77e + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - f0e7deab6518 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -194,62 +194,62 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: + - d5e9e83cd3d8 - 529bccd5e4a1 - - 567d5b3c52b1 - 09070cacefd8 - - d5e9e83cd3d8 + - 567d5b3c52b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 4bedca26c133 + - 8abdedf55101 - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: + - 736b8f6ee456 - bdf1ce174e39 - - 90858c306551 - cb1e251cac37 - - 736b8f6ee456 + - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: + - 07497255281e - 7ce1891db6f5 - 421f0af4ee95 - - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - 02f8a17a4ebd - f984bb114520 - - 3599f5451ee2 - b29d37ca9e41 + - 02f8a17a4ebd + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - 6027ef51ef91 + - 177f0621c266 - 0c2907307ba4 - e246088b6e34 - - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 377ac2829eac - - 73194cdd4f57 - 61b4cedc8934 + - 377ac2829eac - 547e8d00f11c + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -261,10 +261,10 @@ tools: - name: pear owner: iuc revisions: - - 037f0acc7830 - - b4c6f054210a - 2f804526f5fd - f69501361cec + - b4c6f054210a + - 037f0acc7830 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -277,8 +277,8 @@ tools: - name: seqkit_sort owner: iuc revisions: - - 61eb4cfc7313 - fdc21382376d + - 61eb4cfc7313 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats @@ -291,33 +291,33 @@ tools: - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - 71f649c23021 - - d3f58a0dc09d - bf04bd405d5b + - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f - - e654095ab143 - 8250ea3a1501 - - a535cf1e5da4 - b557acca0b56 + - a535cf1e5da4 + - 24013bf85a6f + - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -329,12 +329,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 27ac32a22ad2 - - 828dba98cdb4 - f3759eec3018 - - 6a675c3aa610 - - 7accf7407811 + - 828dba98cdb4 - 9fa7803d1c51 + - 7accf7407811 + - 6a675c3aa610 + - 27ac32a22ad2 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 b9034d34f..19bf4877b 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 7b4468117008 - 64e9a6afdd0c - - e41385662e5e + - 7b4468117008 - ce9cd02d5b88 + - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,30 +18,30 @@ tools: - name: fastqc owner: devteam revisions: - - e7b2202befea - - 9da02be9c6cc + - f2e8552cf1d0 + - 2c64fded1286 - ff9530579d1f - - 3d0c7bdf12f5 - 5ec9f6bceaee - - 2c64fded1286 + - 3d0c7bdf12f5 - 2b0c9d9fc6ca - - f2e8552cf1d0 + - 9da02be9c6cc + - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - c1a33f603da2 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - 18a51655db17 - - ad116ae3f4d9 - b6b54ba71bd8 + - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics @@ -55,31 +55,31 @@ tools: - 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: - - b2f1f75d49c4 - - bf675f34b056 - - 75c93c70d094 - - 9a913cdee30e - - c1a4b5f3b432 + - 3d93dd18d9f8 - f7e2f1eb3a16 + - c1a4b5f3b432 - 1c2db0054039 - - 3d93dd18d9f8 + - bf675f34b056 + - 9a913cdee30e + - 75c93c70d094 - abfd8a6544d7 - 5e33b465d8d5 + - b2f1f75d49c4 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 949f01671246 - - cd7e644cae1d - 084bbd8ba7b8 + - cd7e644cae1d + - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 1fac53c95..2d183e1d1 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -17,7 +17,7 @@ tools: owner: peterjc revisions: - 83a19df00eab - - 141612f8c3e3 - 85ef5f5a0562 + - 141612f8c3e3 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 13dd6c25e..b476ff2a6 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,23 +9,23 @@ tools: - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - 0c8f7322f8fc - f2f3bc622a16 - 8f53b238a360 + - 0c8f7322f8fc 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 @@ -38,15 +38,15 @@ tools: - 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 @@ -87,44 +87,44 @@ tools: owner: iuc revisions: - b2c25142267e - - cf61daf064fe - 45296e47d565 + - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways owner: iuc revisions: - - 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 - 840fb4850be3 + - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -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 1445c9d17..dd5bc64db 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.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 diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 89516e4f4..f76241d26 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 - - e9df53a75f3c - 983bf725dfc2 + - c1b437242fee - b39347891609 + - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,54 +17,54 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 1c58de56d587 - 28587613264f + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 1790dcf3c32d - - 6ea73833cf67 + - e407b9da183a + - 5e6237d58b0c + - 4317d3cb6cba + - 653e89d73fc4 + - 516a54ddf218 + - ba931a59dd59 - 734abc7ac21d + - 6ea73833cf67 + - f5ea3ce9b9b0 + - 1ec814014652 + - 9a776b080193 + - e08a7ad4378b - aad3885b3216 + - 8848455c0270 + - f8054ea1c365 - 7068f48d0ef9 - - e08a7ad4378b - - 5e6237d58b0c + - 4df8de2d0e48 - 69ebb7f46e45 - - 1ec814014652 - 6591f049cf7e - - 83c7d564b128 - - f5ea3ce9b9b0 - - 4df8de2d0e48 - - e407b9da183a - - 4317d3cb6cba + - 1790dcf3c32d - c441583adae5 - - 653e89d73fc4 - - 8848455c0270 - - 9a776b080193 - - f8054ea1c365 - - 516a54ddf218 - - ba931a59dd59 + - 83c7d564b128 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 21a560af5913 - - 75b3b3d0adbf - - 9aaa46d45472 - 34758ab8aaa4 + - 9aaa46d45472 + - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: + - 95fb5712344f - bfdc6a7ffd3a - - 054483e27a35 - 468c71dac78a - - 95fb5712344f - af5eccf83605 + - 054483e27a35 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 01930ebc6..dbaef156c 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: - - ae9994cf526f - - df7356989ac1 + - 4b519282a05b + - 7f13dc906cb9 - c4bde687c846 - - a64dc31ab7f2 - fd59d783248a - 740057a5126d - - 7f13dc906cb9 - - 4b519282a05b - 290a11559985 + - ae9994cf526f + - a64dc31ab7f2 + - df7356989ac1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,9 +28,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: + - 867ab348287d - f95284aa2946 - 7cf5b1d072b5 - - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,21 +42,21 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - ca7cb0eaad62 - '566197475670' - - 374e9062d874 - 3b37b1b1c3a7 + - 374e9062d874 - 53460afd5115 + - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 10515715c940 - d3a9e32672ec - da4c086cff5b - - 391a4cc45fea - 3d059e9c2fba + - 391a4cc45fea + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -74,12 +74,12 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 3b12bf9b4b87 - - 1acf88921176 - 299307abd804 - e3a675da7fd0 - - 5fe1dc76176e - d0fc8b746d57 + - 3b12bf9b4b87 + - 1acf88921176 + - 5fe1dc76176e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -97,15 +97,15 @@ 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 @@ -123,17 +123,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 17359b808b01 + - 2bb2e07a7a21 + - fd5dbf0f732e + - a6e57ff585c0 - 836d1aa3e89a - 1cfc579079a6 - - 4542035c1075 - - fd5dbf0f732e - - 112eb40ba6cf - - 2bb2e07a7a21 + - 6cd09d7b5f37 - 667e17248bfe - ca2def38369c - - 6cd09d7b5f37 - - a6e57ff585c0 + - 112eb40ba6cf + - 4542035c1075 + - 17359b808b01 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -151,9 +151,9 @@ tools: - name: pathview owner: iuc revisions: + - 03c13085aecc - f1691de443a7 - fe154a7af404 - - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -165,8 +165,8 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - f234e2e59d76 - 85da91bbdbfb + - f234e2e59d76 - 62e3a4e8c54c - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data @@ -187,9 +187,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 - - 44c66e8d21e6 - 6c571966cfb9 + - 44c66e8d21e6 + - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -201,23 +201,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 2824d77cd8f8 - - a1abfa420d9d + - 36b848d5f3ec - 360df4999907 - - 14e7c35f3d00 + - 2824d77cd8f8 - 4ac4e7083b7e - - 36b848d5f3ec - - 326a3db8d9d1 - 7dd841a32245 + - a1abfa420d9d + - 326a3db8d9d1 + - 14e7c35f3d00 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 83c573f2e73c - 2f557f6abbfb - - 73b8cb5bddcd + - 83c573f2e73c - 44608d0193ed + - 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 752c4504b..499230d31 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -21,15 +21,15 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells @@ -63,8 +63,8 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -91,9 +91,9 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: + - 9a2f72d7dbd2 - 94697510d55f - ff6decc0f432 - - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -113,15 +113,15 @@ tools: - 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: - - 1be0fc4d8654 - 7d5c97823f8b + - 1be0fc4d8654 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet @@ -162,8 +162,8 @@ tools: - 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 @@ -183,8 +183,8 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: - - 4428dba93375 - 0cf90e01d9f8 + - 4428dba93375 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne @@ -205,7 +205,7 @@ tools: - name: scanpy_scale_data owner: ebi-gxa revisions: - - 4cc9362782b4 - e2d0dc8a50ca + - 4cc9362782b4 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 42d22e7b7..cdd227d0f 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,11 +2,11 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: + - 29f66c353bcb - 921a2da49a0c - 9edf8894a22d - a4c13ddcc8ee - ed2cca6b5de4 - - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads @@ -22,31 +22,31 @@ tools: - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 4d511437b1e5 + - 03dd3c16ae4e - 11fa44ee0603 - 9e357a8b2ec3 - - 4d511437b1e5 - 977dc15add20 - - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - c3e5e2cf12b7 - - 3b5b54ed6392 - - 0ba4f56a3613 - 77919cc3618e - 41dbf4d162a2 + - 3b5b54ed6392 + - c3e5e2cf12b7 + - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 - 7babd8a46fe0 - - 5308ca68ef3d - 12d51d7be66f - b63363075c2e + - 9939786dd9c9 + - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index 2db2ed622..7a973ba4e 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,19 +2,19 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 8bccb36e055a - - 3df9f0a4bf34 - 0c777d708acc + - 699a5e9146b3 - 7db4fc31dbee + - 3df9f0a4bf34 + - 8bccb36e055a - 81f0cbca04a7 - - 699a5e9146b3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 2436a8807ad1 - 5791a7f65275 + - 2436a8807ad1 - 0a53256b48c6 - 5bc8cdc17fd0 tool_panel_section_label: Imaging @@ -22,24 +22,24 @@ tools: - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - e576b73a2e2f - - 6ad1d3cfdea1 - 9d47aabda459 + - 6ad1d3cfdea1 + - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: + - 70316d792fc9 - b1c2c210813c - 77f7159d775a - - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - f70b215d155c + - dba87c4b32d3 - d51310ab328a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -52,8 +52,8 @@ tools: - name: bfconvert owner: imgteam revisions: - - b07f4839ca77 - f3360fbeda64 + - b07f4839ca77 - fcadded98e61 - 85edbb7a436b - 10eed33aa9b2 @@ -62,38 +62,38 @@ tools: - name: binary2labelimage owner: imgteam revisions: - - 984358e43242 - 6e65fd971e13 + - 984358e43242 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - b58447a2eed2 - - 5bf8eb50b280 - 664232d2a3f7 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - e917a2424690 + - 0e4dccaafef5 - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - bad171ed1e96 - e8f822eeb9fd + - bad171ed1e96 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - 6070780813d9 - 670975e92458 + - 6070780813d9 - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -101,24 +101,24 @@ tools: owner: bgruening revisions: - cdf8e3c57dae - - ef4aed1d34c4 - df3ad3ba5c6f + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - 2484086dee41 - - 6a7da2e5f696 - 5d28ac336861 + - 6a7da2e5f696 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 + - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet @@ -133,32 +133,32 @@ tools: owner: bgruening revisions: - ad271f78a87a - - 31d195bedf6d - 3245681b2f6d + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - 87d4d92d7487 + - 993faa34333b - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - 6100a22bf4f2 - c09dcda1143f - ff1a86a87364 + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - 3a05117669cf - - b178453ea8d1 - 667a513e67e4 + - b178453ea8d1 + - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity @@ -172,25 +172,25 @@ tools: - 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: - - 5499dc6f8ac1 - 8536b1ae0254 - b64af54c5c09 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - e972e07c7845 - 6f4715b8540a + - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -204,40 +204,40 @@ tools: - name: cp_measure_object_size_shape owner: bgruening revisions: - - acf3aa487283 - - d85f11570109 - 79e10d12d90a + - d85f11570109 + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - b76841ee5560 - 80b200ae516b - 035a58c7f54a - - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines owner: bgruening revisions: - - 91560258e972 - b44b081bcf37 + - 91560258e972 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - 8083a87d2fdf - 3a3033222f61 + - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - 27edbb90ab2b - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -262,8 +262,8 @@ tools: - name: image_info owner: imgteam revisions: - - f8b4eada923c - 236ec78b2e53 + - f8b4eada923c - 7b6d9412c7f8 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 8cc394e63..6cb095ce1 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - d6e72da3ec35 - - e319b5b65879 - - 40737febe339 - - 1069f6db0a0e - - 3e4f434a69c6 - a38934e303b9 - - e4ee04da1c19 + - d6e72da3ec35 - f362150bef41 - 3a72fede57ce + - 40737febe339 + - 1069f6db0a0e - 78bbd17d0703 + - e4ee04da1c19 + - e319b5b65879 + - 3e4f434a69c6 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 0135f1d487a0 - f91cfb73d369 - - 8f8df367470d - - 618297d23022 - - fcbeda41d0ac - - 2b95d5c04908 - - 7fe36019c073 - - c88553ec696e - 72ddd32392cd + - 0135f1d487a0 + - c88553ec696e + - fcbeda41d0ac - 9537184d421f + - 7fe36019c073 + - 2b95d5c04908 + - 618297d23022 + - 8f8df367470d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 - d7e79eb3bcb3 - - 2cf4a1cafc16 + - ad0dc9f4c9e2 - fafb3d685fa9 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - ee29337f905c - - 5dc33613c288 - - 6a1515bb0687 - - 43aac8d29685 - - 7f1cfa4c0e32 - - 3d18f8c3c0f6 - - 9eaadf03e0df + - 94df24c6bc00 + - a1c2aecd7a0d - bd2a7d1316b9 + - 6a1515bb0687 - 8c05afb547fa - 28a6f1908fcc - - 94df24c6bc00 - - 8d36959b000d - ee2beb764a7b - - a1c2aecd7a0d + - 8d36959b000d + - 43aac8d29685 + - ee29337f905c + - 5dc33613c288 + - 3d18f8c3c0f6 + - 7f1cfa4c0e32 + - 9eaadf03e0df tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5d6ed46cc101 - - 9f978da6528a - - e3bb03cf207a - - d37ede8589b2 - - c092052ed673 - 8858fa037a15 - - bcaa0d571ce2 + - db536ad45f28 - cb903c9dc33d - - 86a20ae274fc + - d37ede8589b2 + - e3bb03cf207a + - bcaa0d571ce2 + - c092052ed673 + - 5d6ed46cc101 - 5671e1d3d5ee + - 9f978da6528a + - 86a20ae274fc - a250929be21b - 364f4ffec275 - - db536ad45f28 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - f95f403841ad - - ed28dd32141c - - 3b6a16d82c1b - - 38b91a3190cd - - 194e3ceee923 + - 230b05597996 - 49236b03e4fd - - c5c9f02b6167 + - abbc8041e8ec + - 584beffa972b + - 194e3ceee923 - 12d66d0d05ac + - c5c9f02b6167 - e1a015876aa9 - - 230b05597996 - - 584beffa972b - - abbc8041e8ec + - f95f403841ad + - 3b6a16d82c1b + - 38b91a3190cd + - ed28dd32141c 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 69c2769f5..82664802d 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -3,17 +3,17 @@ tools: owner: iuc revisions: - 17e3b698dd52 - - 0f1724dd59d2 - b8a457820315 + - 0f1724dd59d2 - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ba0c40780ecf - - ac092723240d - a513e3fbb4c5 + - ac092723240d + - ba0c40780ecf - 22c2a1ac7ae3 - 374cb875d38a tool_panel_section_label: Join, Subtract and Group diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 4a56904e1..108e05164 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,99 +2,99 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - - 772e0e89fc68 - 522137aaa9c4 + - 772e0e89fc68 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: + - f22a9297440f - 4d81e3e2fb63 - 8a794e6d3388 - - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - 818f9b69d8a0 - - 2af1346e68c9 - - b6ef6d0cb6b7 - - f1b9a42d6809 - e1317b5502fa + - f1b9a42d6809 + - b6ef6d0cb6b7 + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 8334dc98c48e - - c80db5d6fd8c - 1588f9076e32 - 05143043ca13 + - 8334dc98c48e - 947c2eacccb8 + - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 29e4122c90de - - 25b46af53232 - - 1552b8cb4a94 - 83228baae3c5 - 9991c4ddde14 + - 25b46af53232 + - 29e4122c90de + - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 1a53edc4b438 - - a07ab242b0b5 + - 53616c8b0865 - f3dfa4bdf87e + - 1a53edc4b438 - 060ca94ac049 - 841a6cc5fc58 - - 53616c8b0865 + - a07ab242b0b5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 - 927586a18553 - - 40f4447733b2 - - 91c4e3331208 - dc4b5fd604a6 + - 2fc89dcd41c8 + - 40f4447733b2 - d4808d5b83da + - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 301e07345c93 - 7626ea9c2e1b - - e5a5ad882f1f + - 25ab6b4e376e - c6ae57f774c6 - 36e8d6d5d01b - - 25ab6b4e376e + - 301e07345c93 + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 02d2be90dedb - - 0630258dcf35 - f9639b488779 - 4ed102b922cb - - b7c3e9a3b954 - 80852884053f + - b7c3e9a3b954 + - 02d2be90dedb + - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 61634a87efc7 + - 14180f9c831e - ec69cbe34b73 - caeb57858702 - - 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 5f32c5ae7..002d1a4e9 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - 749c918495f7 + - 0d4acadabb04 + - d5ceb9f3c25b + - 03e9b2fbc005 - f6877ad76b00 + - 749c918495f7 + - a6d65b0c67af + - 017aba02828d - 17062a0decb7 - 3ba8d4563129 - - 0d4acadabb04 - 937aa69e715f - cd659e8cc5fa - - 03e9b2fbc005 - - 017aba02828d - - d5ceb9f3c25b - - a6d65b0c67af 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 + - 53646aaaafef + - dfd8b7f78c37 - e188dc7a68e6 - 3fe632431b68 - 2477830927ec - - dfd8b7f78c37 - - 64f11cf59c6e - - 53646aaaafef tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - e7f19d6a9af8 - 37b497aa133f - - 60afcc2c1d05 - 3e1ea2facca6 + - e7f19d6a9af8 + - 60afcc2c1d05 - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - be1d967337e4 - - 6b1e195506a3 + - 3f4d6399997b + - 53c0b7a1a0c3 - 037c6e54df11 - - 8c6cd2650d1f - - f54f5baedfdd - 11a0d50a54e6 - - c0c2d0941de8 - - b3eab4b67562 - - 53c0b7a1a0c3 + - be1d967337e4 - 77b2770508f6 - - 3f4d6399997b + - b3eab4b67562 - 5cc34c3f440d + - f54f5baedfdd + - 8c6cd2650d1f + - 6b1e195506a3 - 09b53c1d4ab1 + - c0c2d0941de8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - b8f5f6e87f5c - - 9ee34ba73ebf - - 00fbfac99d39 + - 1cd2511a396e - 45795f582ae9 - 79b885ce78d7 - ec9cbd6b9a49 - - 178bdbdb6d24 - - 5ef7ec16b04f + - 00fbfac99d39 - e403d27e8f24 + - 5ef7ec16b04f - 13022c3d3076 - - 1cd2511a396e + - 9ee34ba73ebf - 42ce70172b72 + - 178bdbdb6d24 + - b8f5f6e87f5c 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 6c6200b47..aed0d6a8b 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 90dc951da294 - 6cd2a9e6ac49 + - 90dc951da294 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -82,8 +82,8 @@ tools: - name: matchms_filtering owner: recetox revisions: - - 00e66c401366 - a177ac3c752c + - 00e66c401366 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -103,15 +103,15 @@ tools: - name: matchms_metadata_export owner: recetox revisions: - - f04610d25411 - b576ed720711 + - f04610d25411 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: - - 1d443ed476a1 - 03bc9b7f40f6 + - 1d443ed476a1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -148,8 +148,8 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 9ff95a1a2705 - 7627b40601f6 + - 9ff95a1a2705 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -217,8 +217,8 @@ 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 @@ -231,17 +231,17 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: + - 79ad928a0dae - c53a97599181 - 7b42ee54d757 - - 79ad928a0dae tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: + - f3a18e020cdd - 18ec7635bac6 - 149b9cc7499b - - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template @@ -255,8 +255,8 @@ tools: - name: recetox_aplcms_correct_time owner: recetox revisions: - - 51332c2520c7 - 9064aecc78a7 + - 51332c2520c7 - 02c772a49998 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -264,32 +264,32 @@ tools: owner: recetox revisions: - b341cfd4baf8 - - e7305ba0dd38 - b3413f335327 + - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - cf061712a184 - 17a48d0a80f4 - 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 - - 24278c6b6d1c - 99d118321d5f + - 24278c6b6d1c + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - d90187b0f247 - - ffbabefbd2e2 - ea0758b41473 + - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -301,8 +301,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 2c6fa447f6a0 - 6b5dec818827 + - 2c6fa447f6a0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -320,8 +320,8 @@ tools: - name: rmassbank owner: recetox revisions: - - 0b28816c1c2c - 5a6bb93ec656 + - 0b28816c1c2c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 04e22f5b5..936faa0fa 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -9,9 +9,9 @@ tools: - name: cat_bins owner: iuc revisions: + - 18676df0cb3a - 0e63d03c8790 - 0094893f5001 - - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -90,71 +90,71 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: + - 76d3d2b10738 - 5b5a7af9fbb4 - - 7c2100246a2f - 65db807336bc - - 76d3d2b10738 + - 7c2100246a2f - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 84fd33a60b35 - 00f5005840fa - - 18a502a9d287 - - 1c35dadbe76f - 96336c6a2bb7 + - 1c35dadbe76f + - 18a502a9d287 + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - a9f4a217dcd6 - - addaf9d22850 - e8fba04706d3 + - addaf9d22850 - f732237754fc - 34e55239e68b + - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 8c202e741d68 - 0776d824d896 - - 75403243703a - - 04c15826a0b8 - 5fe3edf19b9c - - 8c202e741d68 + - 04c15826a0b8 + - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 43c99742158b - - 1c9b3bcd4261 - 8470de786d47 + - 43c99742158b - 75c8945b0da2 - e96bbb9e24ea + - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 1d75bd0595e2 - - 84743da21318 - 5c865a382933 - - 306a40d4bb8f - 35176674168c + - 306a40d4bb8f + - 1d75bd0595e2 + - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - 78faebd0879c - - 555ccac8a4c5 - - ac72310b038a - - 8daf4564ccda - 32c9ea835770 + - 8daf4564ccda + - ac72310b038a + - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile @@ -170,21 +170,21 @@ tools: - name: dada2_removebimeradenovo owner: iuc revisions: + - 04144473e59e - 7136e9ab70db + - 1bc3657cd694 - 7f3b59dee073 - 073608a50ac3 - - 04144473e59e - - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - a7817705348e - - d943081510da + - 0a1224c4b781 - 19299bb1c6af - 9058d8943303 - - 0a1224c4b781 + - d943081510da tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -198,18 +198,19 @@ tools: owner: iuc revisions: - 65d52c693b8e + - f8f56dd6449f - b907a3c0434f + - 5c7ba3d85a01 - a68b985913ab - dbf1798c0dcc - - f8f56dd6449f - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level @@ -229,9 +230,9 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - bd7a9c6efb10 - e66ab198ec15 - 6aad8ca3918b - - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table @@ -245,9 +246,9 @@ tools: - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - - cad93abecac9 - 7f208f1eb64f + - cad93abecac9 + - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -285,28 +286,28 @@ tools: revisions: - e88b731dad59 - 31c6d107e7a5 - - 79706f10d680 - c409a495841f + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - d24841f5c3d2 - - 172920f67a84 - - 094ad9c068af - 714d5a28cc5c - 71ea608ddfa3 + - 172920f67a84 + - 094ad9c068af + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - a293a742194f + - 12fb63b5f63f + - d7e9a3c41657 - 4137b492233e - a4d7148ccee4 - - d7e9a3c41657 - - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -318,12 +319,12 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 6fcb8ac37a3e - - cf87759761eb + - e2c71b852aba - 64bc7acc22a9 - - 75bedfb2078b + - cf87759761eb - 97f7bb0851e7 - - e2c71b852aba + - 75bedfb2078b + - 6fcb8ac37a3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -341,27 +342,27 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: + - 5e5a999ffaa9 + - c82508e76ad1 - 2d35528d2141 - 080ea153677c - - c82508e76ad1 - 4033827c76b8 - - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 95bf7479d53c - - fc6c328c292f - 6b7622dda516 + - fc6c328c292f - 2cd76b089570 + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish owner: iuc revisions: - - dcd30574a456 - 11658afb8c87 + - dcd30574a456 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single @@ -415,10 +416,10 @@ tools: - name: kraken2 owner: iuc revisions: - - cdee7158adf3 - - 20e2f64aa1fe - 4a9da2b6c2e3 - 328c607150ff + - cdee7158adf3 + - 20e2f64aa1fe tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -444,8 +445,8 @@ 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 @@ -464,8 +465,8 @@ tools: - name: kraken owner: devteam revisions: - - 8ba2174315aa - 766d5f63b0f4 + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -496,8 +497,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -534,21 +535,21 @@ tools: owner: iuc revisions: - 7f5d7b0e9884 - - 4fd3b5d8706b - 0270541aaf46 + - 27250f92a01a - 327d9f4cc95f + - e073891b2afc - 2cff76cf35c6 + - 4fd3b5d8706b - 3cc4a60615c0 - - 27250f92a01a - - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - eb50e7eca3dc - 708abf08a626 - 76bc4efa1aeb - - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -614,24 +615,24 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - ff8f55893e7d - - b89b0765695d - - 1a6cdf55390f - - 1a037928504c - ef65b083bd0c - - fd69c607b43f - - 289b3807e80c - - a16313517e55 - a92a632c4d9b - 2131d7dca455 + - 1a6cdf55390f - 6dee4abadccb + - ff8f55893e7d + - a16313517e55 + - b89b0765695d + - fd69c607b43f + - 1a037928504c + - 289b3807e80c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -662,8 +663,8 @@ 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 @@ -676,8 +677,8 @@ tools: - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 709adbfcf308 - 415cb5d91168 + - 709adbfcf308 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline @@ -717,8 +718,8 @@ 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 @@ -767,12 +768,12 @@ tools: - name: staramr owner: nml revisions: + - 4b9a8031ab74 + - 3b22de20bd4b - 4d83eccf5f81 - - be818ae858e4 - - 141afacabcfa - aeaa20b96ef2 - - 3b22de20bd4b - - 4b9a8031ab74 + - 141afacabcfa + - be818ae858e4 - 2fd4d4c9c5c2 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 bc3ed5768..d64c813ba 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - 7238968f58f7 - ab12df91b47f + - 7238968f58f7 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 48c0eed0c..2b4ad038d 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 94b8c6013083 - - 9eeb13a92d79 + - 6ae5a7b5a0a2 - a74dbfee5a86 - - 098506c54016 + - 8b67dd48fec1 - cd07731e4434 - - 6ae5a7b5a0a2 - - bdfbaf0c10aa - - 9422c5a87ee2 - 80f03df2e2ce + - 9422c5a87ee2 + - 9eeb13a92d79 + - 94b8c6013083 - 48c13389050d - - 2263989660f5 - - 8b67dd48fec1 + - bdfbaf0c10aa - 9baa871cb1d1 + - 2263989660f5 + - 098506c54016 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 2e093badc689 + - '764845535798' + - f14193ec1f50 + - d390fe1567dc + - 5abf2c2249aa - c18157c68134 - - be78f13134e2 + - c44f824c051a - d7ce0ec78e51 - - bc3831dd65c1 - - f14193ec1f50 - aaa0d6a8b808 - - d390fe1567dc - - 4a60927aaca5 - f0af8936ed41 - - '764845535798' - - fc2e49f91e52 - - c44f824c051a - - 5abf2c2249aa + - 4a60927aaca5 + - bc3831dd65c1 + - 2e093badc689 - 3ff17bad4006 + - be78f13134e2 + - fc2e49f91e52 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,15 +46,15 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -66,30 +66,30 @@ tools: - name: mafft owner: rnateam revisions: - - 15974dd17515 - - c5908940967d + - 6f28e90db932 - a65296ffb4a0 - - f0d493f8f84f - bf28a8cff401 + - f0d493f8f84f - 8e649f27aa0d - f1a5908ea2cb - - 6f28e90db932 + - 15974dd17515 + - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - b3acbb3a6af0 - - fbca557a4847 - e8fdceffea4c + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 5561a1193611 - 60698466facd - c9685bc0407c + - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer @@ -119,8 +119,8 @@ tools: - name: mummer_show_coords owner: iuc revisions: + - b4124df98b26 - 959c1f8dae95 - cf3c9489c088 - - b4124df98b26 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index fafddb243..a45fa1f83 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -9,36 +9,36 @@ tools: owner: galaxy-australia revisions: - 18a8d140ec6f - - 7c47b3c9e493 - 28928576e1ea + - 7c47b3c9e493 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado owner: galaxy-australia revisions: - 63d8ecfcfab1 - - fc5b6491cf78 - 99c9427219d3 + - fc5b6491cf78 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - 79e9a869f40e - 72b5e9dda577 - - cb34f00cc10f - 0e9e7fcdd543 - - a7228a7ea146 + - cb34f00cc10f - fc8804320156 + - 79e9a869f40e + - a7228a7ea146 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - db25ec99c3ea - - d6cddc06aeae - fa11aa8103b2 + - d6cddc06aeae - 18505fe2bdb1 + - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -50,22 +50,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - 43815fa60f3a - - 19f3b583a9b3 - edf6d4003fad - - cc36773a3681 - - 2bf63b38ee9b - - 0f5f4a208660 - - eb746fa6f514 - ec699520444c + - 43815fa60f3a + - eb746fa6f514 + - 0f5f4a208660 + - 2bf63b38ee9b - 222669c4afb6 + - 19f3b583a9b3 + - 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 @@ -78,36 +78,36 @@ tools: owner: iuc revisions: - 0f1c34698076 + - a02b8b3f5a0c - 7b379e98b9a9 + - a38bdcec9e4c - 645159bcee2d - - a3c4fe6f49ab - - a02b8b3f5a0c - edbb6c5028f5 - - a38bdcec9e4c + - a3c4fe6f49ab tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 3b6f94fc7e1d - - d219b6d8158a - 85a394edc247 + - d219b6d8158a + - 3b6f94fc7e1d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - - a8d4be409446 - be95355fef8d + - a8d4be409446 + - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 449e9aeded2d - d376944466bf - 4857d5bcce52 + - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants @@ -206,8 +206,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - ca22d8497db5 - 64a83664b814 + - ca22d8497db5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 89adf52a5..fabc45b75 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -27,18 +27,18 @@ tools: - name: data_manager_bakta owner: iuc revisions: + - baceff842902 - adfd6bf710bd - - 3e73c97f025d - - 97b1b5ad1cda - d74850cf4e42 - - baceff842902 + - 97b1b5ad1cda + - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - 83da94c0e4a6 + - 1586b111d2a3 - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -51,19 +51,19 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - ed1518ce2237 - 2f27f3b86827 - - e4b4837f06f5 - - 13851aefa67a - 19b6a2f0dbe2 + - 13851aefa67a + - e4b4837f06f5 - 1e34d2e3d285 - - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -82,9 +82,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 48a42ca61006 - 5711fc06a63e - 38ccd4589990 - - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -131,10 +131,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 - 52b6a4d98009 - - 172815da3d41 - b4b2b284230a + - 27a6a256cd23 + - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -146,8 +146,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -159,16 +159,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: + - 87febc68b45b - fea85c467896 - 19bbd19b74b3 - - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -195,34 +195,34 @@ tools: revisions: - 0cb27ea69dc1 - 9c43baa60906 - - 5fe20c915fa6 - - d8dc037e3c13 - 2c61c30a57e7 + - 5fe20c915fa6 - 4ba60cb14cb0 + - d8dc037e3c13 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - 14785f8a3725 - d9339bb8127e + - 14785f8a3725 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - 9d09724f2bf1 - - 0db22932bc39 - aec831b54a5b + - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - - 29c738066906 - ed7a967cb11b + - 29c738066906 - 6e24e79d3d69 + - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -241,15 +241,15 @@ tools: owner: devteam revisions: - ad90c2da4f38 - - 1865e693d8b2 - 3e4d45aca422 + - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -261,17 +261,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - - 64deddb6a8ec - d63c1442407f + - 64deddb6a8ec + - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: + - 9946bc39c834 - 625fd9476402 - 94a50db37d1a - - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -325,8 +325,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 @@ -795,11 +795,11 @@ tools: - name: salsa owner: iuc revisions: - - ba7b0f11e470 - - 58a870ef434c + - f77f7a7f3b83 - 9a22227bb6d0 + - ba7b0f11e470 - ab5b7f6b7198 - - f77f7a7f3b83 + - 58a870ef434c 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 6d545e2bf..58201a360 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,57 +33,57 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 26de3a7b1cb9 - - 3b8b5bde0bd9 - - 8834daeb9892 - 5a7c56a5cc08 - - b89cac5156ec - 6a457678efcb - - a6619171428e - - c78f3d7dd1db - - 3f59ebfbfe3d - d7c7ef3353fe - - 107d3ba7024a - - f73435dc282b - - 81e66674859e + - b89cac5156ec + - c78f3d7dd1db - cce7b18495e4 - - '841557158611' - d033ffc1c161 + - '841557158611' + - f73435dc282b + - 107d3ba7024a + - a6619171428e + - 3b8b5bde0bd9 + - 81e66674859e + - 26de3a7b1cb9 + - 3f59ebfbfe3d + - 8834daeb9892 - f04a1264e2a2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: + - 7a2092844346 + - aa8cc71438cf + - 88c4aa435ded + - 659517798cc4 - 6a726db04d4b - - b0af57c1a968 - - 6223845127ea - - 4755f52427c4 - - 02b8758214b0 - df47d4845b62 - - aa8cc71438cf + - 6283babe736e - e75442c7f4da + - 02b8758214b0 + - 3b96e92e8ec3 - 5b777002c2de - - 5fcd1ece3a6e - - 6283babe736e - - 7a2092844346 + - 6223845127ea + - b0af57c1a968 + - 4755f52427c4 - a185b079b095 - - 3b96e92e8ec3 - - 659517798cc4 - - 88c4aa435ded + - 5fcd1ece3a6e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 24d024316465 - - 111bd54f6bc4 + - c1d53e95327f - 0878b7fd5260 - - d1c340a5664b - - 70acec670c30 - b8476e82ac20 + - 111bd54f6bc4 + - 70acec670c30 + - d1c340a5664b + - 24d024316465 - f97743d52b87 - - c1d53e95327f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade @@ -104,26 +104,26 @@ tools: - name: pangolin owner: iuc revisions: - - 2fa9d4f1b48f - - 9d61d3fa046c - - 81804a978fc0 - - 8ad84c5753ea - - ca337cce3888 - - b7e297c2ede6 - - b6abccb1f25b - - 83a69484cb87 - 3a43c3982401 - - 5f8727ff21e7 + - a2099fb98cdb + - 9d61d3fa046c - 36912871ccdc - - 14ae456b8cc5 - - 42a174224817 + - ca337cce3888 - 2f1019071464 - 437e28791761 - - ca0d8cf80567 + - abf6dbe8c9d7 + - 42a174224817 + - 81804a978fc0 + - 83a69484cb87 + - 8ad84c5753ea - 03ed9524dcd1 + - 2fa9d4f1b48f + - 5f8727ff21e7 + - ca0d8cf80567 - 7bb8726be37c - - a2099fb98cdb - - abf6dbe8c9d7 + - b6abccb1f25b + - 14ae456b8cc5 + - b7e297c2ede6 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - 29ff6a849eac - - a4b71be30c3c - ea30d3089354 - - b1e68bbe4cef - - 73a469f7dc96 - ba29b5e2a4be + - 73a469f7dc96 + - b1e68bbe4cef + - 29ff6a849eac + - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - f1ccc8a6eb05 - e88a7de55d6e + - 809e42326fc2 - 15ac71df11a0 - - 9b2b122d0415 - dbe2b2204555 - 91887494eb97 - - 809e42326fc2 + - 9b2b122d0415 + - f1ccc8a6eb05 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index cd94c886f..d535b96d3 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - fc288950c3b7 + - f6ced08779c4 - b502c227b5e6 - - 7d34178f2812 - 3f254c5ced1d - - a1f0b3f4b781 - - f6ced08779c4 - - 881d7645d1bf + - fc288950c3b7 - f9242e01365a + - 7d34178f2812 + - 881d7645d1bf + - a1f0b3f4b781 - 1aac2a13842a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index 8bb530cd5..b4bf974b1 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,16 +2,16 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - a58f7eb0df2c - - 2f7702fd0a4c - - ca90d17ff51b - - c0e71cb2bd1b - eb085b3dbaf8 - 5b85006245f3 - - 6ab1a261520a - - e4a053d67e24 - - d00e15139065 - 7fbec959cf2b + - 2f7702fd0a4c + - d00e15139065 - 3bd420ec162d + - 6ab1a261520a + - ca90d17ff51b + - c0e71cb2bd1b + - a58f7eb0df2c + - e4a053d67e24 tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomics.yml b/usegalaxy.org.au/proteomics.yml index 5a76f05ea..7b823a91e 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,22 +2,22 @@ tools: - name: cardinal_classification owner: galaxyp revisions: + - 277dc652246e - 0a18ac48ac53 - - f28ad96b76dc - - b18329a8ac14 - 4c177985028a - - b574b84afc4d - - 277dc652246e - ece627528a78 + - b18329a8ac14 + - b574b84afc4d + - f28ad96b76dc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - 525f201b86c1 - a9a28e46d54a - - bf06d196e23d - e215f71d7983 + - 525f201b86c1 + - bf06d196e23d - e988563cc6e5 - b41107d8fe89 tool_panel_section_label: Proteomics @@ -25,17 +25,17 @@ tools: - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - 56da27be956a - - 8da3511c9467 - bb6397b94018 + - 8da3511c9467 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - a8157342d9a3 + - 528fb09022be - 890845926d4b - f23d67e28cc8 - b8c79e70516d @@ -44,52 +44,52 @@ tools: - name: cardinal_mz_images owner: galaxyp revisions: + - ae304a72db7b + - a69865da6f80 - 25b83cbd596a + - a95a82eb4d50 - 59e85306eae5 - 80600735685d - - a69865da6f80 - - ae304a72db7b - - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - e0669b1854b1 - - 611d80c0e29d + - ed9ed1e6cca2 + - 83aac7741200 - f1897eb07081 - 798da6bdff3d - - 83aac7741200 - - ed9ed1e6cca2 + - 611d80c0e29d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - - 74b61bf5bc4b - d426a9107a6c - 5a35e3a8d013 + - a7fb9b395ddf + - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - cc430977c8ff - 91f0f5922011 - 82f6c2f4332d - - cc430977c8ff - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: + - 1693b2126f30 + - c5aa9fca18c6 - 043f9c91f686 - d2483487e077 - - 10566783d718 - ba92b59cd529 - - c5aa9fca18c6 - - 1693b2126f30 + - 10566783d718 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -109,8 +109,8 @@ tools: revisions: - bf0728e000cd - ae4dc0c041f9 - - 9fa3dbf06f17 - ff8c9e0e8a7b + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -123,16 +123,16 @@ tools: owner: galaxyp revisions: - d263296cd73e - - eac99effe86f - d0ea7589e95f + - eac99effe86f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: + - 1c5cbf8f79ce - 4081e4faa4ab - 0fa397f4f40b - - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -159,16 +159,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - d286ff4600dd + - e66f552a3c47 - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -181,16 +181,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - e42225f8a659 - - 9c52362ae7bb - - 2133b0be850a - - 837224ad1694 - - 37d669de2828 - 7f432d87c82c - - 4d17fcdeb8ff + - 37d669de2828 + - 837224ad1694 - 1f39c833f65f - - f522c08e900c + - 4d17fcdeb8ff - 97a7f34fcb6a + - f522c08e900c + - 9c52362ae7bb + - e42225f8a659 + - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,62 +202,62 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - - 0ed07016d668 - - 85b8866f06d7 - e63db1aa82ee + - 85b8866f06d7 + - 0ed07016d668 + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: + - 352b37c66d97 - 990b4560ead7 - 767c1d761aaf - 1974224d63c2 - - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - 4f359549383c - - 35cc7ca0bdc7 - 99450519d727 + - 35cc7ca0bdc7 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - e79958768a2c - - c7745841de24 - 06f6826d380c + - e79958768a2c - c1343e3389ca + - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: + - d2eac53666f0 + - da986f83631b - b9d453dca8d3 - d46d64e7964d - - da986f83631b - - d2eac53666f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 8bd7734309f6 + - 944b43462104 - 1199751329b0 - 9bf325045235 - - 944b43462104 + - 8bd7734309f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - 8295d959ca28 - e0104a9f20f0 + - 8295d959ca28 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert @@ -272,69 +272,69 @@ tools: revisions: - 593839e1f2c3 - 8212e342e482 - - de7593c29499 - 28434abe6c5c + - de7593c29499 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - a5e394b36d87 - bd1535813cfe + - a5e394b36d87 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - 4e77b8f12cd3 - - f4be248c3d47 - 8960fb791701 - 01dbaf6a57e0 + - f4be248c3d47 + - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - 25529df60a81 - 06cca574e337 + - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: + - 518b1730cf2a - f7fef900f5b2 + - 6ccbf9a2072c - c9eff69a7c62 - - 518b1730cf2a - 9cdf15d3cfc8 - - 6ccbf9a2072c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: + - 5e948629bc73 - dff6c756eee5 - ca88bd28f116 - 9876bda3ec53 - - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - 41859bbdc16e - - 658494a2cb00 - - 1595601708ec - 890025d6e426 + - 1595601708ec + - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: + - 9b7977080f6d - 2a93a25f0599 - 6634cad7d797 - 5ad0b5bf1deb - - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter @@ -349,64 +349,64 @@ tools: - name: openms_fileinfo owner: galaxyp revisions: - - 52ba9695e752 - - febd569ad26f - 4af67edd5aef - 5ad830edc021 + - febd569ad26f + - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: + - 27cba4c5fc42 + - 39e8fde08881 - b2fc8da99bcc - 92352a475eed - - 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 - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - ca1740533b59 - - 3720e349ba2a - c28f13cab67a + - 8a04ed1c1d1b + - 3720e349ba2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: + - 382cde407f81 + - c55dddc5844a + - ca799a7246e7 - c427a8628cbe - a5d785af0ad8 - - ca799a7246e7 - - c55dddc5844a - - 382cde407f81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - adca857b4884 - 39caaa778d2e - - b5d0905419da - 8ddb7bab1138 + - adca857b4884 + - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - 18f93351f8b6 - - 34e7afee141d - f817513840a9 + - 34e7afee141d - 1c5f31b8d632 - 8d4db262964c tool_panel_section_label: Proteomics @@ -414,124 +414,124 @@ tools: - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 986e03d3201e - - 111c3a00136d - 5d9f175dff81 + - 986e03d3201e - c69f69d7867a + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - be74a8cd7d66 - 4204882495f2 - 0e52c85f3b15 + - be74a8cd7d66 - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - a407b6790342 - - 2b2a7551a857 - c18d8efa4474 + - a407b6790342 - f5ec766d80cf + - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: + - 4e66c4e73909 - 021fdb80f204 - d0304fb829c0 - - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - bf32e0bcf554 - - ee860980edc6 - 2735db4dd8d9 + - ee860980edc6 - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - 0ced5bc9f4dd - - 08488066d588 - a2a6e9551046 + - 08488066d588 + - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - de7a553552a6 - 8c01da82292c - 2a9ff56cb279 + - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: + - 1bf940c18d93 - c1809c05ae8c - e8f64a7dc470 - - 1bf940c18d93 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 owner: galaxyp revisions: + - 0bddef8d144e - d4396637b9f5 - c99d5004b74f - - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 8b814eafce2c - 89254095cbf6 + - 8b814eafce2c - 4bb198c0bd3e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - f82b320ceb90 + - 05ec9fb05ed1 - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 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 - 2aebe58de46e + - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 3d8d4ada5405 - 5ae104d0da6e + - 3d8d4ada5405 - decc397c3b7e - 6b01678ec2fc tool_panel_section_label: Proteomics @@ -540,34 +540,34 @@ tools: owner: galaxyp revisions: - 5182338d5e7c + - 539a3a4dcc9e - d6aca689dd48 - dd173849c3d8 - - 539a3a4dcc9e - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 8a45fd5a608a - 16026cdb1330 - d426affe977c + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - 9c70a651a53e - - dd71e020e2aa - 43b9ed22e8ce + - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - 1b03536aa3c9 - d063e2fe4ba4 - 9020199dba0a - - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator @@ -581,17 +581,17 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - 7f6a1f27553e - - 5c2a97a234d6 - c8b225c69a7f + - fb52e95a370c + - 5c2a97a234d6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -610,14 +610,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 943a34df6047 - - 1beff3ddce58 - 3ec27b4cee7c - - 07ff622ec007 - - 7fdd9119cc4f - 3634c90301af - - da885ca16cb2 + - 943a34df6047 - a72c48001f7c + - 07ff622ec007 + - da885ca16cb2 + - 1beff3ddce58 + - 7fdd9119cc4f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -677,8 +677,8 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - a371252a2cf6 - 12692567c7f9 + - a371252a2cf6 - 1a5690a5eedc - 265c35540faa tool_panel_section_label: Proteomics diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index bf015d3f9..52697721b 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 10447a4b0cc3 - 18c6b2b6740f + - 10447a4b0cc3 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 6936b6394..9f255044a 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,120 +2,120 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 289b7d6b69a4 - e345aadf914f - - 110a346daf36 - 42201b90e3f4 - 2f1d464ebfd2 - cd5f98911089 - - 289b7d6b69a4 + - 110a346daf36 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: + - 8501601a118d - 0345dbaaa79b - fcce77c09289 - 42d9087b4789 - 0cd2df8af811 - c207119ba5f6 - - 8501601a118d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - ad5ab22ffe24 - - 33486216eec0 - - 405a212b32ab - 421c33b8bf17 - - 04db7fd6b238 + - 405a212b32ab + - 33486216eec0 - 89eb29319bf4 + - 04db7fd6b238 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - 7b72fde3d27e - - 1d839ead7ad3 - - eb784fa07f80 + - f6e91108b7b1 - fa51dc5e8386 + - 1d839ead7ad3 - 7370bb65bad4 - - f6e91108b7b1 + - 7b72fde3d27e + - eb784fa07f80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - 8a55d29c8fcf - - a3e86cd9cac7 - 3d70c2996730 - - c9b77ced9a78 - - 1544278c272e - d30e36c48c93 + - 1544278c272e + - 8a55d29c8fcf + - c9b77ced9a78 + - a3e86cd9cac7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - 564c33e5c3e3 - - b242deb58952 - - e2db212d64ad + - a5969aa9347e - 887cf585cafc - 7b881f5f5ad5 - - a5969aa9347e + - e2db212d64ad + - 564c33e5c3e3 + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - 8cff84759bf6 - - 9a171f9a450b - b4bab607eb05 - - e897c74a48bb - bd5ff77e2036 + - e897c74a48bb + - 8cff84759bf6 + - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - 33f0793edf93 - - 887e0991eb24 + - 5e10f396979e - 4f65e343ecdf - - 6dafad990086 + - 887e0991eb24 - adc7a7610d4f - - 5e10f396979e + - 6dafad990086 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - c5d7050e4ad7 - - c287418eb288 - 97575d01f06b - - 4e280b27a831 - - 43e3eeb2e0ec + - c287418eb288 - 17d39bf0a63a + - 43e3eeb2e0ec + - 4e280b27a831 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - cd034465d4a4 - - 9586f08634c0 - 0b8c84a7fdb5 - - a819ec3b362d - - 09b8edb56d80 - d9bf483266a1 + - 09b8edb56d80 + - a819ec3b362d + - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 2645575d1bf2 + - a4b4bd84f69e - 95351dd0fd3f - - 69842dd5aa48 - a9c34a289493 - - a4b4bd84f69e + - 69842dd5aa48 + - 2645575d1bf2 - bf0e43ab0416 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -123,11 +123,11 @@ tools: owner: iuc revisions: - d033e1ccb386 + - cfb504394ae1 - bb0475c884ff + - d1fda11e602f - 912f904a6e1e - 8a35a3bc6752 - - d1fda11e602f - - cfb504394ae1 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: - - 95286af4139b - - d504d945a655 - d1fad35bdb4a + - d504d945a655 + - 95286af4139b 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 112b39548..221f039aa 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,24 +2,24 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 31f8063eedea - cf01dd6c6b1f - 2d4e3aff9dc7 + - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - 32e542c2a773 + - 125d20cb23d7 - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -31,8 +31,8 @@ tools: - name: blockclust owner: rnateam revisions: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: chira_collapse @@ -80,8 +80,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -94,16 +94,16 @@ tools: - name: cuffmerge owner: devteam revisions: - - 86285ddd4512 - - 6a6717a5f421 - cf747d1bd79a + - 6a6717a5f421 + - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 9a854107dbb2 - 6cbfede05833 + - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -138,45 +138,45 @@ tools: revisions: - cd9874cb9019 - 9a882d108833 - - 6a3a025714d3 - - 8fe98f7094de - - 0696db066a5b - 24a09ca67621 - d027d1f4984e + - 6a3a025714d3 + - 0696db066a5b + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - 2872c633f07e - - b47c006d90c5 + - 62adf13b86ea - 9a7c5b6d8f1e + - b47c006d90c5 - df929f257179 - - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 070900306913 - - a8305cf0c951 + - df0c8d0a5992 + - 555659de7321 + - 5bf899c13979 - 6e53e565fc6a - 334ce9b1bac5 + - a8305cf0c951 - ae2aad0a6d50 - - 555659de7321 + - f2843df56434 - 9bdff28ae1b1 - 3d89af8a44f0 - - df0c8d0a5992 - - 5bf899c13979 - - f2843df56434 - 0cb907a2a810 + - 070900306913 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: express @@ -188,17 +188,17 @@ tools: - name: featurecounts owner: iuc revisions: - - 90d16db017d7 - - 6f66ae7c5f7a - - a56fbe2d6ba7 - a37612abf7f9 - - af814359d244 - f9d49f5cb597 - - e6a2a912677a - 38b6d12edc68 - - f3a5f075498f - - 7db9d3ea71c9 + - e6a2a912677a + - a56fbe2d6ba7 - ea04b737afa0 + - 90d16db017d7 + - 7db9d3ea71c9 + - f3a5f075498f + - 6f66ae7c5f7a + - af814359d244 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -222,9 +222,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - - 3c97c841a443 - f99dd58de04f + - 3c97c841a443 + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -236,13 +236,13 @@ tools: - name: hisat2 owner: iuc revisions: + - 6c19daec423d - d4b55e2beb12 - - 26371a1df031 + - 6ab42baa56e9 - f4af63aaf57a + - 26371a1df031 - a86e80d3c09c - 3fb01a8c902d - - 6c19daec423d - - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -262,33 +262,33 @@ tools: - name: kallisto_pseudo owner: iuc revisions: + - 5ae5c312d718 - 01247aaf0a10 + - 87c11c05d238 - ce5d418183c5 - - 5ae5c312d718 - 1c75aa5de15e - - 87c11c05d238 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 - 4f9c4e6566e5 - 40985510cd98 + - c971db6f0fe5 - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 708348a17fa1 - - e827f9aae031 - 119b069fc845 - 97e06a4c7c75 + - e827f9aae031 + - 708348a17fa1 + - 32511f586472 + - d6f5fa4ee473 - 58c35179ebf0 - 0921444c832d - - d6f5fa4ee473 - - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -300,8 +300,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -325,8 +325,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - d696cf0a9622 - 72927fc9e9ed + - d696cf0a9622 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -344,21 +344,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 4df95e2d7f61 - - 3ea5a2a63fa2 - - b0f2be869d6d + - 4014de1b6daf - 79de45b5069b - 7ed2edc1337f - - e132e7d02a3e + - 5ec75f5dae3c - c7c55b694974 - - b9e04854e2bb - - 4074fc1940e2 + - e132e7d02a3e - 0a563fd2f22e - 980d2a2e1180 - 99b17b74a8cd - - 5ec75f5dae3c + - b0f2be869d6d + - 4df95e2d7f61 + - 4074fc1940e2 + - b9e04854e2bb - c772497b2c32 - - 4014de1b6daf + - 3ea5a2a63fa2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -370,35 +370,35 @@ tools: - name: salmon owner: bgruening revisions: + - e3d32471da11 + - 2c0ca397d302 - f4d5237a84f6 - - ebab418107f5 - 53e9709776a0 - - e3d32471da11 - - 15cd64d7c58b - 49121db48873 + - ebab418107f5 - cc05793bb896 - - 2c0ca397d302 + - 15cd64d7c58b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: + - c0fd285eb553 + - 56242ff81c84 - 8c28affc7c48 - fab6ff46e019 - - 56242ff81c84 - - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 914cfcba0ec8 - - dd4df992d93d + - 258d696dbd7e - cbf488da3b2c - cef79931dda5 - - ae618321f34a + - dd4df992d93d - 1ebd14235b92 - - 258d696dbd7e + - ae618321f34a + - 914cfcba0ec8 - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -429,45 +429,45 @@ tools: - name: transdecoder owner: iuc revisions: - - ffd1300599a1 - - d0d4cef4f967 - c6334cb383ff + - ffd1300599a1 - 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: + - 74217fbfba4d - d6a479fd4281 - bcc5f03f1900 - ba3720d7e68b - - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - c2b82a94493e - 56162e446004 - - 2fb4ee002432 + - c2b82a94493e - 478f36effca1 + - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - fab23c3b5258 - - 9ff3765e7172 - 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 - 34a018cbee9c - 870ac06dff8e - 4687ecf0eb2d - - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -475,44 +475,44 @@ tools: revisions: - 33406f5a445c - 5192f657f305 - - 05ab8d5e04a2 - - c5fbddcac63a - 65e7dea767ea + - c5fbddcac63a + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: + - 6f0fb35b799c - a35cba31d904 - - 1fdb25a8384d - e406ac71165d - - 6f0fb35b799c + - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: + - 964b7efe2639 + - 37a1129c89d2 - 7c7fbf13aadd - c2c039e421af - - 37a1129c89d2 - - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - eafea3083352 + - 047c22569787 - 24e94d84adc9 + - eafea3083352 - 1d689e4e1caf - - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 9871104ea630 - 3a4ac03d1266 - 1812dbc5bb7b + - 9871104ea630 - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -531,15 +531,15 @@ tools: - name: trinity owner: iuc revisions: + - c9cfec002f71 + - db1f362cca3e + - d2bc35f3d1c5 - cee61b3fcf78 - 9fa24d5aac68 - - d2bc35f3d1c5 + - d84caa5a98ad - 48636f857c4b - - c9cfec002f71 - - 8f1c3df4dd49 - - db1f362cca3e - 32b86cd8eb50 - - d84caa5a98ad + - 8f1c3df4dd49 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 69cd3678d..44ba177fb 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: + - 1a052c827e88 - 27e16a30667a - 473382134e56 - 080fd5739bb4 - - 1a052c827e88 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index 6f3db1fa4..e8fd02ab3 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,16 +2,16 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 3c661e57a88f - - 88eedb4abea0 - 10184eaa85fc + - 88eedb4abea0 + - 3c661e57a88f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 993b19f20c76 - 108db6635177 + - 993b19f20c76 - cb20f99fd45b - 1dfd95ee241e tool_panel_section_label: SAM/BAM @@ -25,8 +25,8 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 5325e44297b9 - 75d5afa09972 + - 5325e44297b9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag @@ -76,9 +76,9 @@ tools: owner: iuc revisions: - 5f8e69cc4c6e - - 30a201c9c310 - e7fd6754d093 - 19ece8afbaab + - 30a201c9c310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -103,15 +103,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - 890d97772e2a - a3b4ad6858ff + - 890d97772e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - 0e60e2dd20af - cf1ffd88f895 + - 0e60e2dd20af tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -123,15 +123,15 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 56c31114ad4a - 649a225999a5 + - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - 46c6639921f1 + - 9149ad20699a - 6856f8a01905 - 12749212f61b tool_panel_section_label: SAM/BAM @@ -140,8 +140,8 @@ tools: owner: devteam revisions: - 33208952b99d - - 06dc50b7b711 - 26b4f9f98aca + - 06dc50b7b711 - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -160,11 +160,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 66e23b11feae - a8d69aee190e - - b3d99709fe1a + - 66e23b11feae - 720217c23995 - b906586a6596 + - b3d99709fe1a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate @@ -177,64 +177,64 @@ tools: - name: samtools_flagstat owner: devteam revisions: + - fe34990e5ce7 + - db17d5321bad - cc61ade70eb8 - 22970df7a40e - fefd89ab563c - - fe34990e5ce7 - - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - 7a6034296ae9 + - 811fc2d75ad4 - 7def34e6cf4d - 88b8c2916784 - fa5d3e61e429 - - 811fc2d75ad4 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: - - b40e2d865d52 - - cae2794d2deb - - 740ce0a18f0d - 36677f429310 - 65a38e8c8e2a + - cae2794d2deb + - 740ce0a18f0d + - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: + - 9da0311ab1dd - 329deb17a9f7 + - b61f5d6a7f25 - 8da515fbc1bf - 583abf29fc8e - - b61f5d6a7f25 - - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c - 30388d878f81 - - 85e38b31e8b3 + - bb8cfc6f6e0c - db000c6007a0 + - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -247,53 +247,53 @@ tools: owner: devteam revisions: - 344fc91e1bfd - - b8beef827165 - a4a10c7924d1 + - b8beef827165 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - cab3f8d35989 - - 6c2c1836728b - d54a4df48867 + - 6c2c1836728b - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - 135c85f4cfaf - bd850490c7f1 - - 5d9ae78f34d3 - - b7f7826ef1cd - 818030fa6bbf + - 5d9ae78f34d3 - bcedabb53ddf + - 135c85f4cfaf + - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 5a08c09b9311 - 3a0efe14891f - - 24c5d43cb545 - - 145f6d74ff5e - 541082d03bef + - 24c5d43cb545 - 1cc79f49b8d5 + - 5a08c09b9311 + - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: + - c370440f901e + - 2dce91e11ca7 + - 0dbf49c414ae + - b72793637686 - bf328cec6a42 - - 5826298f6a73 - - 6be888be75f9 - 32dc5f781059 - b01db2684fa5 - - c370440f901e - - 2dce91e11ca7 + - 5826298f6a73 - 350bbc5c2ffd - - b72793637686 - - 0dbf49c414ae + - 6be888be75f9 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 a5a74eb99..0496b8840 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,13 +2,13 @@ tools: - name: ena_upload owner: iuc revisions: + - 480d9e9d156b - 5cb6146337d8 + - 4aab5ae907b6 - d147d6455873 - - a62c4a11a67d - 6f6537780379 - - 4aab5ae907b6 - - 480d9e9d156b - - ea5e944f447d - 59bb6d34fca6 + - ea5e944f447d + - a62c4a11a67d 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 3942690c9..08a102f2e 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -9,88 +9,88 @@ tools: owner: bgruening revisions: - f2000bc73102 - - e4c01dcece8b - e32b215b7c04 - - ecb9ea6269ee + - e4c01dcece8b - c9944a2600f1 + - ecb9ea6269ee tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - 707023fa62fe - - c0b037b12765 - e1c3c2f2a834 - cfaf5a405371 + - c0b037b12765 + - 707023fa62fe tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 55e35e9203cf - 32e547223c9e - cfc3f5a57dc6 - - fb9e030ffae4 - - 93dd15e13e6a - - 00712416fdaa - d330b3082107 + - 55e35e9203cf + - 00712416fdaa + - 93dd15e13e6a + - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - ee98d611afc6 - - 0bf7fddf90c7 + - 038e32885fec - 688357ad5e61 - - b9fac48532eb - 39e945f0b2c1 + - 0bf7fddf90c7 + - b9fac48532eb - 6f0d0c784f09 - - 038e32885fec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - b85871dd69f9 - - 7e8c677a7b71 - - ed4996a16f7f - - d4af736e7b83 - 3d748954434b + - ed4996a16f7f - 9bd945a03d7b - 43cb7b5a6fe7 + - d4af736e7b83 + - b85871dd69f9 + - 7e8c677a7b71 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - 2e8022f1923c - fe75d2414dc0 - a4774b7b2e85 + - 2e8022f1923c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 4fff5a293013 + - 0e70b2dfe4be - 02b1fe7aed76 - 769d815e4b0d - - 0e70b2dfe4be + - 4fff5a293013 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - a90f8efe08b4 - 344c2af50552 - - c29e7bb492bf - aa4a6f0916b4 + - c29e7bb492bf + - a90f8efe08b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - c32347702e12 - 5b7c81b35b89 + - c32347702e12 - b13d3e4c48e1 - 050cf43887d3 tool_panel_section_label: Single-cell @@ -98,9 +98,9 @@ tools: - name: baredsc_combine_2d owner: iuc revisions: + - 1d77986f9ddc - 02fc39c8610d - 239193b96d72 - - 1d77986f9ddc - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,11 +137,11 @@ tools: - name: dropletutils owner: iuc revisions: + - a9caad671439 + - 2c1200fba922 - cfe1e6c28d95 - - 8855361fcfc5 - cdf4443d5625 - - 2c1200fba922 - - a9caad671439 + - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -171,22 +171,22 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 9d42a6133690 - 57aeaf6b237d + - 9d42a6133690 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 163fd744e235 - 23b8d6b8960c + - 163fd744e235 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint @@ -206,22 +206,22 @@ tools: - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 640e0e45518a - 45a386d18509 + - 640e0e45518a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - 9d02f1819e81 - f963c251ac77 + - 9d02f1819e81 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - f881c94fb3b3 - 40fee49bc6c3 + - f881c94fb3b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix @@ -234,22 +234,22 @@ tools: - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - f0216498a666 - b05f662f9f35 + - f0216498a666 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - 8a11d70b6cd8 - c72fa6cb8817 + - 8a11d70b6cd8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization @@ -262,8 +262,8 @@ tools: - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - 2ba6cee8e4db - c0737631eea1 + - 2ba6cee8e4db tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix @@ -290,8 +290,8 @@ tools: - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 77d8e0fd162a - 5dfba24d7bdd + - 77d8e0fd162a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites @@ -318,15 +318,15 @@ tools: - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - c261b6b05ee3 - 55b013e59018 + - c261b6b05ee3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b6b8c8672756 - b376ef118807 + - b6b8c8672756 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops @@ -339,8 +339,8 @@ tools: - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - 6d042c96aceb + - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -367,15 +367,15 @@ tools: - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - - 58de3c7c8e89 - 8d203e74869b + - 58de3c7c8e89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - ea8fb5e899e8 + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices @@ -400,8 +400,8 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 27fe5cd1729c - f36828ebdc54 + - 27fe5cd1729c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations @@ -414,12 +414,12 @@ tools: - name: modify_loom owner: iuc revisions: - - 59be31ac9dc3 - - e98619de2776 - 0f1aaff9b22d - - eeab712b0b99 - - 4b0adaa31c95 + - e98619de2776 - 7784821452ac + - 4b0adaa31c95 + - 59be31ac9dc3 + - eeab712b0b99 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -431,16 +431,16 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 2cfd0db49bbc - 282819d09a4f - 7ffaa0968da3 + - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -466,45 +466,45 @@ tools: owner: iuc revisions: - 7e014059a88d - - f911a64454fb - - a4b734cd253b - 0bff0ee0683a + - f911a64454fb - c4f39bf4a068 + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: + - 7608d5faee41 - d45f092caf24 - 43c146e25a43 - b83fbc90161e - - 7608d5faee41 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - 2b0d3e2f402a - f3eb2291da05 + - 37a47c4fd84d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - df8e4e54d367 - a6821f856a1e + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: + - c92d0f9338c5 + - 72979cac22b2 - e93b008c637a - 44b935f2271b - - c92d0f9338c5 - 2af7c5086a96 - - 72979cac22b2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -522,92 +522,92 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - b2df381a6004 + - f9353ee6a0d4 - aaa5da8e73a9 - - 77b91b9bdf52 + - 38db3fef7aad - 4d8f983cd751 - 6f83f8fd381f - - 38db3fef7aad - - f9353ee6a0d4 - - b2df381a6004 + - 77b91b9bdf52 - 6acb08931836 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 72a6bebab2a5 + - a97abb8cd15b + - d636ce5cde16 - 8cb783c81905 + - 72a6bebab2a5 - b409c2486353 + - a03ff8633507 - 3c86f71498bc - 277313130da5 - - d636ce5cde16 - - a97abb8cd15b - - a03ff8633507 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 6bd82ed14acd - - f54f0f0598ad - - 5e9171dc8244 - d1cd8c147809 - - 3081ff5c84a3 - - 6c145a6868cc - - c5d3684f7c4c - 5c3ebe2adc77 + - 6c145a6868cc - c0a80a16560f + - f54f0f0598ad - 18262103fa61 + - 6bd82ed14acd + - c5d3684f7c4c + - 3081ff5c84a3 + - 5e9171dc8244 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 3bcd5445cd7a - - 7b9fafe32c86 - - 94c19fb1281c - ab55fe8030b6 + - 94c19fb1281c - c9cb76cf8d6c - - a407e7f8bdc1 - - 9f354c7c8c92 - - 56c0d4acef02 - d844935c906c + - 56c0d4acef02 + - 7b9fafe32c86 + - 3bcd5445cd7a + - 9f354c7c8c92 + - a407e7f8bdc1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - dbbe1ea8ecb1 - - 7647e5cd1b8b + - 95777145cb92 + - 1072ce66b426 + - 6f5349dd5c49 + - 9b0cdb8cf6be + - 0185bd174ea0 - aa0c474463c2 - 6adf98e782f3 - f7446fd8d5e7 - - 6f5349dd5c49 - - 1072ce66b426 - - 0185bd174ea0 - - 9b0cdb8cf6be - - 95777145cb92 + - 7647e5cd1b8b + - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 73ab2ac53d06 - - 9fb627495ec2 - 458e8f43a775 - - d18e7a6e5cd4 - a39040ae0a38 - - f2f6c703da06 + - d18e7a6e5cd4 - c65fce500915 - - 215733a383f2 + - 73ab2ac53d06 - bf2017df9837 + - 215733a383f2 + - f2f6c703da06 + - 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 - fd808de478b1 + - 8f333f90d8d6 - b834074a9aff tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -615,8 +615,8 @@ tools: owner: iuc revisions: - b7ea9f09c02f - - 7a365ec81b52 - 652923ce664f + - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -628,9 +628,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - ef4c80837bc5 - - 2e41b35b5bdd - 81e5bdff4853 + - 2e41b35b5bdd + - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_exprs_freq @@ -884,8 +884,8 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - 8f8bef61fd0b - afb90d3485df + - 8f8bef61fd0b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif @@ -905,8 +905,8 @@ tools: - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy @@ -918,8 +918,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 90e95e9ee190 - 883c33ef3372 + - 90e95e9ee190 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 914e4d7e1..731c74003 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -33,10 +33,10 @@ tools: owner: iuc revisions: - 2f3c6f2dcf39 + - 419027d822d6 - 746e8e4bf929 - - 562f3c677828 - 4c07ddedc198 - - 419027d822d6 + - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,8 +49,8 @@ tools: - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -71,8 +71,8 @@ tools: owner: devteam revisions: - 7a15159140d1 - - cb1c59d69557 - 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: - - 4c4ec859c31a + - 7442b94d6a1e - 9c3e1d3235c8 + - b1eda492f063 - 840f29aad145 - aef56d0e7a61 - - b1eda492f063 - - 7442b94d6a1e + - 4c4ec859c31a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 375bbd555f4a - - 30d21a6041f6 - - 07843f917990 - d0352e8b4c10 - 9fda0b82f419 + - 07843f917990 + - 375bbd555f4a + - 30d21a6041f6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 2c58b83c9bad - - 4cc980df6265 - - 7ae443e6217d - cd02bf168d23 + - 7ae443e6217d - 8b1b2b91f8d0 + - 2c58b83c9bad + - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - bb9fc9d46ea4 - - 4bbaf77573ef - - 1dd433d2c92c - - e10e776f2109 - ad7e0b4291ee + - 4bbaf77573ef + - bb9fc9d46ea4 - 7dd3fb35904f + - e10e776f2109 + - 1dd433d2c92c 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 a94d89bef..70330ed20 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -27,21 +27,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 02026300aa45 - 6595517c2dd8 - - be25c075ed54 - - 464b9305180e - aff5135563c6 + - 6e8d94597139 + - 02026300aa45 + - 464b9305180e - 9cd341095afd - 13b6f0007d9e - - 6e8d94597139 + - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 37cde8134c6a + - 90f657745fea - 34d29339abab - - 9cc411a62277 + - 37cde8134c6a - 557ec8d7087d - - 90f657745fea + - 9cc411a62277 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -115,20 +115,20 @@ tools: revisions: - 3a6b78c39dca - 623f3eb7aa48 + - 33d61c89fb8d + - 1ea4e668bf73 - cf34c344508d - cf4397560712 - - 33d61c89fb8d - 2e8f945f7285 - 83069b38aa85 - - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - ae8c4b2488e7 - 399da6b5ec21 - 503bcd6ebe4b - - 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: - - f768f6183386 + - c4d18aa4ec4a - b722161a845a - bce29ec10b78 - - c4d18aa4ec4a + - f768f6183386 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: + - f46f0e4f75c4 + - 74a8bef53a00 + - fbf99087e067 + - 86755160afbf - d698c222f354 - - 12615d397df7 - a6f147a050a2 - - fbf99087e067 - 9ff72e942410 - - 86755160afbf - - f46f0e4f75c4 - - 74a8bef53a00 + - 12615d397df7 - ddf54b12c295 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 476ac6db1..8d14e38bd 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: - - 82fb5e3bb93e - - 0d18a3ba2d1c - 85c57cc9b558 + - 0d18a3ba2d1c + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -34,57 +34,57 @@ tools: - name: freebayes owner: devteam revisions: - - 04fa42777df9 - - ef2c525bd8cd - a5937157062f - 156b60c1530f + - ef2c525bd8cd - 57def2d7c093 + - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - e61c9ac190ad - - 435b157bed6d - 09d6e4693887 - 791f73caa0c8 + - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - e1461b5c52a0 - - 3b4b2121842f - - 65432c3abf6c + - dfadc322b065 - 03627f24605f - 4805fe3d8fda - - dfadc322b065 + - 65432c3abf6c + - 3b4b2121842f - 074d44697036 + - e1461b5c52a0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - 9cb929f21cfa - - 7dfca164d2e3 - 701d134358ad + - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 - - c27549b9aa1f - f4473557ffc7 + - c27549b9aa1f + - 426d707dfc47 - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - cdaab621d454 - - aa35ee7f3ab2 - dbd9f2db9ed8 + - aa35ee7f3ab2 + - cdaab621d454 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -102,9 +102,9 @@ tools: - name: snippy owner: iuc revisions: - - d220115f882b - - fa016f1eea1a - 5bbf9eada9c2 + - fa016f1eea1a + - d220115f882b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -140,21 +140,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - ee4a90760848 - - e7aff4a85df5 - 32f14a2723ec - - 3b1e7c170b10 - 40f0591deda0 + - 3b1e7c170b10 + - e7aff4a85df5 + - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - 02d81b994ef5 - - adc0645b945c - 9793bc5d741b - - 4934c0ac6197 + - adc0645b945c - 42818629ec4c + - 4934c0ac6197 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 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