diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index d1361fc81..2220eb282 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7886,3 +7886,58 @@ Update 212 02/10/24 18:01:43 vcfsort False Installed devteam ee60203e68d9 ee6020 Install 1645 03/10/24 15:00:53 kmc True Installed galaxy-australia 87ddc8ca7859 87ddc8ca7859 11/11 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1645/install_log.txt Install 1649 08/10/24 12:32:57 ctb_im_conformers True Installed bgruening a4b1474efada latest 1/1 ChemicalToolBox toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1649/install_log.txt Install 1649 08/10/24 13:04:04 gprofiler_gost True Tests failed iuc bf39cdd007f5 latest Staging Testing 0/2 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1649/install_log.txt +Update 213 09/10/24 11:24:40 arriba False Tests failed iuc 45c2ec061cf9 45c2ec061cf9 Staging Testing 1/2 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 11:40:19 augustus False Installed bgruening bd0e53f3a891 bd0e53f3a891 6/6 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 11:44:28 augustus_training False Installed bgruening f1e653756174 f1e653756174 1/1 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 11:47:57 cuffcompare False Installed devteam ad5d061fbdf2 ad5d061fbdf2 1/1 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 11:51:29 cufflinks False Installed devteam 6926716bbfb5 6926716bbfb5 1/1 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 11:54:59 cuffmerge False Installed devteam 22cf48ad7b16 22cf48ad7b16 1/1 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 11:58:45 cuffnorm False Installed devteam 28b94cfbfdb9 28b94cfbfdb9 1/1 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 12:02:15 cuffquant False Installed devteam 93148c05136f 93148c05136f 1/1 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 12:06:02 cutesv False Tests failed iuc 23d7e75d850e 23d7e75d850e Staging Testing 1/2 Variant Calling toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 13:10:40 data_manager_gtdbtk_database_installer False Errored iuc 3b1d503c6260 3b1d503c6260 Production Installation 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 13:15:25 fasta_compute_length False Tests failed devteam 5cbde03c1103 5cbde03c1103 Staging Testing 3/5 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 13:22:27 fastq_combiner False Installed devteam 9115b978ce10 9115b978ce10 6/6 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 13:31:50 fastq_filter False Installed devteam 144275714590 144275714590 9/9 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:00:19 fastq_groomer False Installed devteam e9f8633db0a2 e9f8633db0a2 35/35 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:13:49 fastq_manipulation False Installed devteam e30352e889fe e30352e889fe 15/15 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:18:27 fastq_masker_by_quality False Installed devteam 4e1d64e6385f 4e1d64e6385f 2/2 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:23:56 fastq_paired_end_deinterlacer False Installed devteam 523c2aff0376 523c2aff0376 4/4 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:30:46 fastq_paired_end_interlacer False Installed devteam b41c2c1bcfbf b41c2c1bcfbf 5/5 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:35:48 fastq_paired_end_joiner False Installed devteam 8d958759cf2a 8d958759cf2a 3/3 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:39:24 fastq_paired_end_splitter False Installed devteam 397dc333436b 397dc333436b 1/1 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:43:04 fastq_stats False Installed devteam f86c27295151 f86c27295151 1/1 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:47:47 fastqtofasta False Installed devteam ac3fed111eb6 ac3fed111eb6 3/3 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:53:06 fastq_to_tabular False Installed devteam 43807a65369f 43807a65369f 4/4 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 14:59:00 fastq_trimmer False Installed devteam f0b18efb97f1 f0b18efb97f1 5/5 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 15:04:45 gecko False Installed iuc 1de657a3198d 1de657a3198d 3/3 Multiple Alignments toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 15:05:23 gffcompare False Installed iuc 3c5e024a18cf 3c5e024a18cf RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 15:14:13 humann False Tests failed iuc c2803012bbb3 c2803012bbb3 Staging Testing 3/8 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 15:18:40 humann_regroup_table False Tests failed iuc 8237a0f225db 8237a0f225db Staging Testing 2/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 15:23:00 humann_rename_table False Tests failed iuc aabf8cfb8fef aabf8cfb8fef Staging Testing 2/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 15:58:00 idr_download_by_ids False Installed iuc f92941d1a85e f92941d1a85e 12/12 Imaging toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 15:58:44 intermine_galaxy_exchange False Installed iuc faef2b1622a3 faef2b1622a3 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:03:04 khmer_abundance_distribution False Installed iuc e699e2747356 e699e2747356 2/2 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:08:48 khmer_abundance_distribution_single False Installed iuc 65b382bf9b7c 65b382bf9b7c 2/2 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:12:07 khmer_count_median False Installed iuc 570505540a7b 570505540a7b 1/1 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:15:50 khmer_extract_partitions False Installed iuc 1061711538c6 1061711538c6 1/1 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:19:59 khmer_filter_abundance False Installed iuc 29a4d6e2ae9c 29a4d6e2ae9c 2/2 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:23:33 khmer_filter_below_abundance_cutoff False Installed iuc 00f7064c564b 00f7064c564b 1/1 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:28:21 khmer_normalize_by_median False Installed iuc 4d23ab83ea29 4d23ab83ea29 3/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:31:49 khmer_partition False Installed iuc 8388fe31d604 8388fe31d604 1/1 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:38:17 lofreq_call False Installed iuc b11e8e9c23bf b11e8e9c23bf 5/5 Variant Calling toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:42:46 pe_histogram False Installed iuc 594b85e4237a 594b85e4237a 2/2 Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 16:46:40 recentrifuge False Tests failed iuc 591175c0f051 591175c0f051 Staging Testing 0/4 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 17:20:40 scanpy_cluster_reduce_dimension False Installed iuc cb43c5d3acd3 cb43c5d3acd3 11/11 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 17:53:59 scanpy_filter False Installed iuc fc0321c000a3 fc0321c000a3 12/12 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 17:54:55 scanpy_inspect False Installed iuc 4338bf96809e 4338bf96809e Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 18:21:16 scanpy_normalize False Installed iuc 146ae5d70b47 146ae5d70b47 6/6 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 19:13:01 scanpy_plot False Installed iuc 40812a65a78b 40812a65a78b 38/38 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 19:40:39 scanpy_remove_confounders False Installed iuc fe8f16c594ec fe8f16c594ec 6/6 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 19:44:55 sinto_barcode False Installed iuc d0f56ac6bb60 d0f56ac6bb60 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 19:48:59 tabular_to_fastq False Installed devteam 78fb18899c99 78fb18899c99 2/2 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 20:02:48 umi_tools_count False Installed iuc 71ad4a56c40c 71ad4a56c40c 7/7 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 20:15:55 umi_tools_dedup False Installed iuc c5a2ee07c4e1 c5a2ee07c4e1 7/7 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 20:23:12 umi_tools_extract False Installed iuc 7a7e33d28f62 7a7e33d28f62 6/6 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 20:29:28 umi_tools_group False Installed iuc 428735be9764 428735be9764 5/5 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt +Update 213 09/10/24 20:35:18 umi_tools_whitelist False Installed iuc e4e12f0b3af1 e4e12f0b3af1 4/4 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 50b9d25a1..7402bed0d 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -3,10 +3,10 @@ tools: owner: iuc revisions: - 6e9aea89e388 - - 78c75f134c16 - - 3f3e247c053d - - c2ef298da409 - 4efdca267d51 + - c2ef298da409 + - 3f3e247c053d + - 78c75f134c16 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -26,8 +26,8 @@ tools: - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval @@ -40,23 +40,23 @@ tools: - name: annotatemyids owner: iuc revisions: + - f29602ae449e + - fe3ca740a485 + - cd2480f35935 - 133f36c29579 - - 3e1f6f6d557e - a79ee60b6926 + - 1aae04680c4b - 44018dd6b447 - - cd2480f35935 - - f29602ae449e - b5d8e5475247 + - 3e1f6f6d557e - 4f2967b27e67 - - fe3ca740a485 - - 1aae04680c4b 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 @@ -65,31 +65,33 @@ tools: - dc027fa56d55 - 7be22100e5e1 - 6519ebe25019 + - f1e653756174 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - - ca6d970d931c + - bd0e53f3a891 - 28433faa6e42 + - ca6d970d931c + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - 728dacaf08a9 - - da5f1924bb2e - d77802fe76f7 - 92eee5f31117 + - da5f1924bb2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: + - fe48aa4ccd5e - 8fd427007e93 - 7355bbf5e05f - - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -101,8 +103,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -114,9 +116,9 @@ tools: - name: cpat owner: bgruening revisions: - - 8e9e228c54c4 - 7ccc6234b54e - 1ac12c0cc7a0 + - 8e9e228c54c4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper @@ -148,61 +150,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 9c15ca7e764e + - 14f588312c56 + - 3bbe70fef6df - b6b5cd37f2a2 + - 582fd74dc2a1 - 756376aeb1ae - 9f2455341fac - - 14f588312c56 - - 9c15ca7e764e - - 582fd74dc2a1 - - 3bbe70fef6df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 8e1ace8f77c6 - a230ea445788 + - 30fb23d4c31c + - 73428a792541 - 1691af4a0d17 - - 8e1ace8f77c6 - 0ffe5be70caf - - 73428a792541 - - 30fb23d4c31c - 989f7c061f35 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 5a5ae61da69c + - 0418d28136de + - e94187d661df + - 57c6718cbfcc - 494f0bb4a993 - 563a19373357 - - 0418d28136de - 30f08d74024f - - 57c6718cbfcc - - e94187d661df + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - 4b96ced19f75 - - 2bba2ff070d9 - f31125bb85ea + - 7abc5f6dd595 - d6c7106b7b2e - f77d7b685bb3 - 1bc5a03faf2e - - 7abc5f6dd595 + - 2bba2ff070d9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - 520e30695ec3 - d3af38b9c7e1 - b3cf4684e9c7 - - 520e30695ec3 - 54961e026fe4 - d77fdcca400e - - fed64e676186 - 52af33194019 + - fed64e676186 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -214,9 +216,9 @@ 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 @@ -262,9 +264,9 @@ tools: - name: interproscan owner: bgruening revisions: + - 98cafcbd2578 - c55643c3d813 - 74810db257cc - - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -282,26 +284,26 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - 3c1a01127868 - - d46d803ca6cc - 370c210d9541 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 - - e95d52d295d7 - - b815ec682418 - c8ac28e8ac44 + - b815ec682418 + - 624606f7c996 + - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -343,11 +345,11 @@ tools: - name: prokka owner: crs4 revisions: - - a17498c603ec + - 8a22554cdde2 - d643e3b03500 - - bf68eb663bc3 + - a17498c603ec - eaee459f3d69 - - 8a22554cdde2 + - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -359,8 +361,8 @@ 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 @@ -391,14 +393,14 @@ tools: - name: snpeff owner: iuc revisions: - - 8f92c2b26e6d - - 5a29ab10dba6 + - cfcf33df7fc0 + - 5c7b70713fb5 - 68693743661e + - 5b80f544c67f - 6322be79bd8e - - cfcf33df7fc0 + - 5a29ab10dba6 - 268d162b9c49 - - 5b80f544c67f - - 5c7b70713fb5 + - 8f92c2b26e6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -418,8 +420,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -431,24 +433,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - d03af1c7002c + - ba6f87115e13 - 37213cf56392 - - e1a9d6fd258d - - ac8250086ac3 - 037a11682176 + - ac8250086ac3 + - e1a9d6fd258d + - 200c378d85f3 + - 45083d070fb8 - 51dd22484644 - - ba6f87115e13 - - 4839e590cb26 + - d03af1c7002c - 809dfc93d593 - - 45083d070fb8 - - 200c378d85f3 + - 4839e590cb26 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/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 0f732512c..82a1505f2 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,43 +2,43 @@ tools: - name: abyss owner: iuc revisions: - - 8f1b150a2487 + - 0124fce4654a - 841084c5fc46 - - 890b794c997d + - d6d5ccc2c581 + - a929ce596a34 + - 553bfe8bd0b5 - 0e93176640ac - fa5259cc561b - - 553bfe8bd0b5 - - 0124fce4654a - - d6d5ccc2c581 + - 890b794c997d - 7547fcab5d19 - - a929ce596a34 + - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b9e31c5c01c7 - 067592b6b312 - - 21e491ad532a - - 94fe43e75ddc - - ddddce450736 - b2860df42e16 + - ddddce450736 + - 94fe43e75ddc + - 21e491ad532a + - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - 3371c5bdc17a - - a7f16f24e9a1 + - 22286dab5aa1 - faee8629b460 + - a7f16f24e9a1 - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -52,31 +52,31 @@ tools: - name: busco owner: iuc revisions: + - 602fb8e63aa7 + - ea8146ee148f - bb935709506a - - 0d243f458b53 - - 4048d82f0c88 - - e824f5d958d0 - - 1e62c28ba91d - - 5ecdeca79a0d - 41030a6c03b7 - - 46ae58b1d792 - - 2babe6d5c561 + - cf13a1e03e5b + - e824f5d958d0 + - 1440ae06552f - 94170eee0ad8 + - 46ae58b1d792 - e4bd1e99bacf + - 2babe6d5c561 - 2dd755c1c6ff - - cf13a1e03e5b - - 1440ae06552f + - 1e62c28ba91d + - 4048d82f0c88 + - 5ecdeca79a0d - f18f0b887c31 - - ea8146ee148f - - 602fb8e63aa7 + - 0d243f458b53 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - c5b7390290b1 - - 86f150c8019d - 5732f959936a + - 86f150c8019d + - 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: - - 3e4f8642c77e - 1ce9b1d72ec3 - - e27815e82dd4 - 1f0769f0b56b - - 8d4f03b5fe9d - - 276f5d8712d5 - 291923e6f276 + - 3e4f8642c77e - cb8dfd28c16f + - e27815e82dd4 - 3ee0ef312022 + - 276f5d8712d5 + - 8d4f03b5fe9d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - - 01210c4e9144 - b2f674562a18 - 460fad600dce + - 01210c4e9144 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: + - 8b330a577046 - ba88bc5a6446 - 06bcf65179fb - 7348b69e5109 - - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: + - 3ef480892a9f + - 690c2caa367e - 3fba9c77550a - 5127a713de83 - - 690c2caa367e - - 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: - - 5bec28269d95 - - da9d8bf98802 - - 284a1cb82b61 - 60024a528cbd + - 366a11d316a7 + - 2061fb3b81b4 + - 6505bd37670d - ec9e21e9c71b - 5f625c63b8bc - - 366a11d316a7 - - f3c89da3af16 - - df25d4fb79b7 - - 0ee0c3089254 + - 9ef6920c3089 - 71740308d412 - - 2061fb3b81b4 - - 3f7be05a1597 - 41cea2aa2dce + - 5bec28269d95 + - 3f7be05a1597 + - 284a1cb82b61 - 045c7c3d8e59 - - 9ef6920c3089 - - 6505bd37670d + - 0ee0c3089254 + - da9d8bf98802 + - f3c89da3af16 + - df25d4fb79b7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -169,28 +169,28 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - 7518ee87b53d - - 14ddfc8ffb93 - de387b2b2803 + - a96f3ad4e0d8 + - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - 9d79beb19ac3 + - eb7b00ec347d + - 39edec572bae - 09c589057ee8 - - f8113c25bc6b - d7edbc9c3a07 - - 39edec572bae - - eb7b00ec347d + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - 29dabd8db6f2 + - eadfd71dde37 - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -198,14 +198,14 @@ tools: owner: nml revisions: - fd128c111ab0 + - 99ecfdafc64f + - f369ef5f210b - 2ecf5a570907 - eb7a370f6588 - f338e9942b27 - - 3ca2d2a9068c - - 99ecfdafc64f - - 606b09cc9860 - e731ea24e48d - - f369ef5f210b + - 606b09cc9860 + - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -218,10 +218,10 @@ tools: owner: iuc revisions: - 73a3846701e1 + - 8dee0218ac7d + - 8b6d0d85252b - b799a615995d - a7b889b90140 - - 8b6d0d85252b - - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -239,9 +239,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - - 64a1c751d99b - 15200570e926 + - 64a1c751d99b + - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -253,13 +253,13 @@ tools: - name: pretext_map owner: iuc revisions: + - 2b16ba799da9 - 79b48f02db49 - - dfb8a4497339 - - 8fef980d48b5 - bbe19ef04a74 - - 2b16ba799da9 - - d256a51a656b - 02831bf9e95f + - d256a51a656b + - 8fef980d48b5 + - dfb8a4497339 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups @@ -273,25 +273,25 @@ tools: - name: quast owner: iuc revisions: + - 875d0f36d66f + - 59db8ea8c845 - 7594365c546b - - 72472698a2df - 342a1d1fed7b - - 59db8ea8c845 - - 6fcbee531de6 - - 875d0f36d66f - - 3061c8b029e5 - 675488238c96 - ebb0dcdb621a + - 3061c8b029e5 + - 6fcbee531de6 + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - - 78c533842eeb - 39bed8de8017 - d865b62f501c + - 78c533842eeb - aa39b19ca11e + - cd06929b224b - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -311,11 +311,11 @@ tools: owner: iuc revisions: - 5c55448d0f33 - - 2b2a352488fa - - f8564b2d7f63 - 33b7d8481a76 - - f11b994b7eb2 - 3edba9afc9bc + - f11b994b7eb2 + - f8564b2d7f63 + - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -328,13 +328,13 @@ tools: - name: rnaspades owner: iuc revisions: - - ef69617ecb42 - - e122f9101584 - - 1d06c8b38e77 - - 378e55aeeb25 - - 53c2bc8c2ae3 - 28189050e437 + - 53c2bc8c2ae3 + - 378e55aeeb25 + - e122f9101584 + - ef69617ecb42 - 5fc94b3a4704 + - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -346,55 +346,55 @@ tools: - name: shovill owner: iuc revisions: - - d9f6a00b6db7 - - 865119fcb694 - - 83ead2be47b2 - ad80238462c1 - - 196a599ec43d - - ee17a294d3a3 + - 83ead2be47b2 - f698c7604b3b + - ee17a294d3a3 + - 196a599ec43d + - d9f6a00b6db7 + - 865119fcb694 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 015283de3004 - 24e471d13fe9 - 5e0825476fb7 + - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: + - 904bf932cf78 + - 051fd2db8a27 + - 1bb12736175c - 604782a8a53a - 1fc82fe7ebef - - 1bb12736175c - - 051fd2db8a27 - 7490b213baa9 - - 904bf932cf78 - c33a476f4001 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 655fa188c3cc - ad8b536d1caa - - 808b3a0a6716 - 9678993ca5bd - - d6e617c4e338 + - 808b3a0a6716 - 34305b013402 + - 655fa188c3cc + - d6e617c4e338 - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 7e27faaad80e - b8002c3f7141 - 037f9927c4ff - - e5a3b75a271f + - 7e27faaad80e - 21da31ed41a1 + - e5a3b75a271f - 6b5a5842531e - 8d4b90bf9caf tool_panel_section_label: Assembly @@ -402,135 +402,135 @@ tools: - name: spades_metaviralspades owner: iuc revisions: - - 86f66ab58e14 - - 7922870efcca - - 2a10645aeadd - f1532cb33c75 - - 5b26685e5d3b - - 9de69775f512 - 328aa71f0f3c + - 9de69775f512 + - 2a10645aeadd + - 86f66ab58e14 + - 5b26685e5d3b + - 7922870efcca tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 8cc856b935ee - - e41dcb0e913b - 340bc17f49cf + - 85fb02c43042 - 6aad515a5270 + - 8cc856b935ee - 1708851f8804 - - 85fb02c43042 + - e41dcb0e913b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - 249f6a28c751 + - de1260f8a300 + - b65a43f70b99 - b3490b036c5a + - 6357b127161e - d159735a6a9f - - 249f6a28c751 - d5fb354f745d - - 6357b127161e - - b65a43f70b99 - - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - b7829778729f - - a90db5dbaaf3 - - dd7ad84f3943 - - 7897763d14ec + - d5887ace0dd4 - 33368fec3b70 + - 7897763d14ec - d2d1df21dfb9 - - d5887ace0dd4 + - b7829778729f + - dd7ad84f3943 + - a90db5dbaaf3 - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 505a9833ab5d - - 8f631679571f - - ced385aa976d - - 189e837009c9 - ed2425b9fd27 + - 189e837009c9 + - ced385aa976d + - 505a9833ab5d - 6f4c8ad6ea01 + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - f31d376ce725 - 9ded6109434a - - d40ed4eb0c0e + - 19bdfd1e6fe3 - 356afed970b4 + - d40ed4eb0c0e + - f31d376ce725 - e59bee4565b3 - - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 4688ae3b49b5 - ebd801e712bc - - 80a17897564d - 6dd935e4984b - b23249f81bc4 + - 4688ae3b49b5 + - 80a17897564d - af40e971a8cc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b5e35a2ca4f3 - - b64696992ee9 - - bb11fefb23a3 - - 59bd28f6265d - cb1e3db43020 + - 59bd28f6265d - 937ea677d437 + - bb11fefb23a3 + - b5e35a2ca4f3 + - b64696992ee9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 2628f6790eda + - 383bb5ad32e2 - 6015aa0303f2 - 05bd7504fdb2 - - 6bfab4a4a988 - cb4768eeca3b - - 383bb5ad32e2 + - 2628f6790eda + - 6bfab4a4a988 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 0a3a602cd1e3 + - e92675014ac9 - 9e3e80cc4ad4 - - 6e26c9afd301 - 8f9f06995f98 - - e92675014ac9 - 3e44ef016b45 + - 0a3a602cd1e3 - e022dff952df + - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 5da9a0e2fb2d - - 8d09f8be269e - 920677cd220f + - 5da9a0e2fb2d - 08256557922f + - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - d81360ea69d8 - - 37d88f41c810 - 0e2b4e3f9ca1 + - d81360ea69d8 - 82398ba86ba7 - 4a53b89fa703 + - 37d88f41c810 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 ca41eb5b1..b9ce76669 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: - - 4768f7f8e93f - - 1ae00120dd24 - 392f100eebcd - bfd290fe1588 + - 1ae00120dd24 + - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,10 +17,10 @@ tools: - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - - 1f5641a52664 - ded48b36f3b7 + - 8e8dc9a1e3e5 - 31812e7a1315 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 9ce523402..97a2d0048 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,13 +2,13 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 7beb76ffbc0f - - 204a131e47db - - d1f62024a08b - 1c427e24fb79 - 159b04e36791 - - a9c9d768b751 - 0840ba83860c + - 204a131e47db + - a9c9d768b751 + - 7beb76ffbc0f + - d1f62024a08b tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 1db0144ee..7914118f0 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: - - 0a5c785ac6db - - a1a923cd89e8 - - 87ee588b3d45 - - e19bebe96cd2 - - a8eabd2838f6 - - b28e0cfa7ba1 - 07e8b80f278c - - 589e7e57fd6d - dde39ba9c031 + - 0a5c785ac6db - a68aa6c1204a + - a1a923cd89e8 - 64e2edfe7a2c + - b28e0cfa7ba1 + - e19bebe96cd2 + - a8eabd2838f6 - ce3c7f062223 + - 87ee588b3d45 + - 589e7e57fd6d 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 2cd83209d..420d93d71 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: - - 62c9df8382c2 - - e8ac2b53f262 - 54f751e413f4 + - e8ac2b53f262 + - 62c9df8382c2 - f921014aba5a 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 - - 5edc472ec434 - - 2889433c7ae1 - - d999e774072a - 6f386c5dc4fb - - e25d3acf6e68 - - 0e3cf9594bb7 + - d999e774072a + - 2889433c7ae1 - acf4e47b734c + - 5edc472ec434 - a52d2d93e595 + - cbf3f518b668 + - e25d3acf6e68 + - 0e3cf9594bb7 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 9992cc575..9cee0987b 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 710301bc46fa - - 6ca543ec1bf8 - 27ee142314a9 - da6bd1975a71 - - f4230f116196 - 095ad4d096d1 - c8cdde00b105 + - 6ca543ec1bf8 + - f4230f116196 + - 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: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -130,32 +130,32 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 79cfd9ead848 - - bfb65cb551d8 - 88076940fa94 + - 79cfd9ead848 - 3b8a9d5ced85 - 0fac8e2afc13 + - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - eb6564a60136 + - 55918daa5651 + - d532b7e5f64b - 715cd0e87781 - b46d4b4d995c - - d532b7e5f64b - f5d979cb4b54 - - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - fdf2cc80adb5 - - 97872d87ba80 - d2f955aea23a - - f26afd1b7104 + - 97872d87ba80 - 5579659312e6 + - fdf2cc80adb5 + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files @@ -169,35 +169,35 @@ tools: - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - - 2c349b027a01 - 070e3ecc3fda - cac1886249a2 + - 2c349b027a01 - 4da9ee404eab + - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - 525ca7c8065f - - d1f803b5943c - - 73008ef1f487 - - 2e219a2d9327 - da8753545526 - 807aa4c9293d - - f197e34c33a9 - c0c9a5024177 + - d1f803b5943c + - f197e34c33a9 + - 2e219a2d9327 + - 73008ef1f487 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - 61094e01eff9 - - 27ea4e1a3f95 + - 1809414a9454 - c4fbab8e03c5 - - 2c8ed1b52bf7 - 7568ae18908a + - 2c8ed1b52bf7 + - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,18 +209,18 @@ tools: - name: md_converter owner: chemteam revisions: + - d7ec25187599 - 79e8ab8f1e81 - - ba83f0923369 - ccfbd956a2d3 - - d7ec25187599 - 730ef07b90ae + - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -270,8 +270,8 @@ tools: revisions: - e6011617c748 - b59c91adeac1 - - 4242b4d68e9c - 1400d1977e7b + - 4242b4d68e9c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -338,10 +338,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 85fad59f8168 + - d4c67ced6abc - 9b48456a96fe - bf99565cec1f - - d4c67ced6abc - - 85fad59f8168 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 83fe043ac..ec72543e1 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - fa56d93f7980 - - c97a786e8fb5 - 163688bb8f73 + - c97a786e8fb5 + - fa56d93f7980 - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -30,11 +30,11 @@ tools: - name: macs2 owner: iuc revisions: - - 640d3af5d833 - - 86e2413cf3f8 - - 495a4173006f - 424aefbd7777 + - 495a4173006f - f5d67c722d67 + - 86e2413cf3f8 + - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -54,8 +54,8 @@ tools: owner: devteam revisions: - 5c2cc3b58c7d - - 74c9214cc8e6 - 4a14714649b4 + - 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 da39336a4..d89569318 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - 705ebd286b57 - cd6da887a5f4 + - 705ebd286b57 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - 25136a2b0cfe - - 90981f86000f - 830961c48e42 - 33151a38533a + - 90981f86000f tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,10 +31,10 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 6cbe2f30c2d7 - - 2dae863c8f42 - baabc30154cd + - 6cbe2f30c2d7 - 0046692724f9 + - 2dae863c8f42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 300c44608..ba9e5bf13 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: - - e3cbd2287f63 + - 4a6ee918c13a + - 367b1ed91207 + - a3b86937ead6 + - 0b3c3ad92827 - 5e1240a87bcb - - 3b6f97e7094c - 6ef0b5664c69 - - 0b3c3ad92827 - - ab9350a8ab4d + - 3b6f97e7094c - f3a19509108a - - 367b1ed91207 - - a3b86937ead6 - - 4a6ee918c13a + - ab9350a8ab4d + - e3cbd2287f63 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 091bb5922a82 - bd46669113b9 - - 72ed72122deb - - 33c99804a32f - - d4d4e9febf5c - - e177a8ea0bf1 - - 584008e574b2 - - e525f9ffb9ac - 1b5fc03380d4 - 54ccb7e1f49a + - 091bb5922a82 + - e525f9ffb9ac + - e177a8ea0bf1 + - 584008e574b2 - 501c21cce614 + - d4d4e9febf5c + - 72ed72122deb + - 33c99804a32f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,23 +59,24 @@ 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 - - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 43807a65369f + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -100,9 +101,9 @@ tools: - name: gffread owner: devteam revisions: + - 3e436657dcd0 - 154d00cbbf2d - 4dea02886337 - - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -114,7 +115,7 @@ tools: - name: intermine_galaxy_exchange owner: iuc revisions: - - c24014d80001 + - faef2b1622a3 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: mz_to_sqlite @@ -134,23 +135,24 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0a7799698fe5 - 0b4e36026794 + - 0a7799698fe5 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - 2dcfbbf9071a + - 78fb18899c99 - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: + - 92ac8e086317 - 19e45916daf9 - b9b385097f13 - - 92ac8e086317 - 26c6706bfb07 - 63769c4217a7 tool_panel_section_label: Convert Formats @@ -171,8 +173,8 @@ tools: - 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/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 77423a5a0..aec7d700c 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,25 +2,25 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - c929a006727f + - a1ca9bccc7f2 + - 5f6d123679f4 - 268e91e540ee - 29451af70c52 - - 5f6d123679f4 - - de72ba3ed6f2 - - a1ca9bccc7f2 - e821645ef8fc - - c929a006727f + - de72ba3ed6f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - 12af64f93288 - - bb1e4f63e0e6 - 7a7fd0f5f15d - 0e143b4c3987 - - 0e49b109abc2 - - 5d11599b8a7d - 2d2cf5c1ea8a + - 5d11599b8a7d + - 0e49b109abc2 + - bb1e4f63e0e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize @@ -28,33 +28,33 @@ tools: revisions: - 7c1beb6d6eca - 195e98217334 - - 81b1e3e1fc6c - dc059492a995 - - 1d848bc4585f - c06951d10364 + - 1d848bc4585f + - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 3d211717a775 + - 26e7304d6737 - 93eb012d9eed - - 07418a30ed01 - - a67ac707496a - bfff7454b59a - - 26e7304d6737 + - a67ac707496a + - 07418a30ed01 - 71aa86af6762 + - 3d211717a775 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - 56d5b797ce84 + - dd0b7398bb96 + - b8858746dc1f - 2bc10a9ca58b - 5be24eba848d - 29fcfd36e90a - - b8858746dc1f - - dd0b7398bb96 - 26983857c91a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -62,47 +62,47 @@ tools: owner: bgruening revisions: - 7ef978dc1b8a - - 9384cd033f30 - - e6d0bff01239 + - c3e012dfe21f - 7e6bcd2e5128 + - e6d0bff01239 - ee3a1b0f45f1 + - 9384cd033f30 - 72bfafe3330b - - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - a60c359ec43c - 9470f29702f8 + - 514fa53b5efb + - b73e213add0c + - a60c359ec43c - d9a637e83828 + - 167788df3b46 - fd1275e01605 - fb9cf9c97ec4 - - b73e213add0c - - 514fa53b5efb - - 167788df3b46 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 86febdcc4283 - - e479c7ca5570 - ca0616bb2cdf - - 2c37ce318bc3 - - a02cfa31e9cb - - c34d11ea4ba6 + - e479c7ca5570 - 5bffaa8354a1 + - c34d11ea4ba6 + - a02cfa31e9cb + - 86febdcc4283 + - 2c37ce318bc3 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 2d466b530754 - 192ef85c0b0b - - 004aea905d4d - - 78f405266706 - 01fb6a7654e6 + - 2d466b530754 + - 78f405266706 + - 004aea905d4d - 69a8621ca2f0 - 1fcb7adc39b8 tool_panel_section_label: DeepTools @@ -110,97 +110,97 @@ tools: - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 137c4beed34b - - 3c9f0c486cca + - 459cfa861f0b + - 9ecba5e225a6 - d580d6acd1df + - d9ce4897dbb2 - 2f9e4843f480 + - 137c4beed34b + - 3c9f0c486cca - db940c262830 - - d9ce4897dbb2 - - 9ecba5e225a6 - - 459cfa861f0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - f264afa9fa6f - - bd7db9e2f2cb - - bad3ca889618 - fd408d755394 - fbe773640707 - - 32e451def88c + - bad3ca889618 - 2c66e43f1c86 + - f264afa9fa6f + - bd7db9e2f2cb + - 32e451def88c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 4e12ea27f788 - 56bce3c82278 - 7e361d147872 - 231994413f89 - - 9368fbc49c8b - 7fda5607e777 + - 9368fbc49c8b - 3b9d990a0a0e - - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: + - d9114ef1c8a5 - c03c3384cd81 - - e65d16fb2724 - 4431f39ede55 - - ce4ce3316f74 + - e65d16fb2724 - b1779366c8e9 - 94ca68515826 - - d9114ef1c8a5 + - ce4ce3316f74 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 2da482e408b8 - d57251071381 - - b88ebb3672a1 - 4ed32329e0ed - f8fc4e5aff9d + - b88ebb3672a1 - 793665fff0f8 - - 2da482e408b8 - 23f7c5f1fdaf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - ba6efa77fb79 + - a4dfb122e52b - 25d830337d31 - e4c7985d4585 - - c60570fa602f - - a4dfb122e52b - - 010e58e9d822 - a7849312d328 + - c60570fa602f - 512155688d98 + - ba6efa77fb79 + - 010e58e9d822 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 00d869ea03a1 - 69264da0ce77 - - 38e3f226248b - aa200e4f3939 + - 00d869ea03a1 + - 4d678170d29b + - 38e3f226248b - 443d9a9d6d11 - c899e0ccff8c - - 4d678170d29b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a - - 10301d137111 + - a2d70c4fd406 - 6662b1a8d326 - d806504e96d9 - - a2d70c4fd406 + - 10301d137111 - aac8444d6681 + - c361b12d207a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index ee87345b5..4e1f50c35 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -16,36 +16,36 @@ 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 owner: iuc revisions: - - 94f412098ac8 - 8cb6bd511879 + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -58,14 +58,14 @@ 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 owner: iuc revisions: - - c0f7b58b4ce4 - d4bea99366f9 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index 08bf8c016..2a6d2feda 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 - 63dd26468588 - - 832c20329690 - ce385837c160 + - 832c20329690 + - dba489bfcd62 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 da8dc7575..f1acc5abe 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 62f5fab76dfb - - d82648ad25a3 - 29bdbc353f20 - - 6da3972210ee + - d82648ad25a3 - cf1322aeb137 + - 6da3972210ee + - 62f5fab76dfb tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 371ffd65a..e04fed315 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 48f587c13075 - - b1c926deaa2d - - c5e2e5902201 + - c053d4cad713 - 44e2cc14f75b - - 093678460093 - - fe74900d6dc7 - 4e5056fefd88 - - de6cebe3c043 - - 64172f1c1202 - - 135b80fb1ac2 - - 288f97432497 - - 5eb7e84243f2 - - 8c0175e03cee - - 8665bcc8b847 - - c053d4cad713 - 660cffd8d92a + - 49370cb85f0f + - e4691e1589d3 - 5915ea1ec9b1 + - c5e2e5902201 + - 8665bcc8b847 + - 64172f1c1202 + - 8c0175e03cee + - 5eb7e84243f2 + - 135b80fb1ac2 + - 093678460093 + - fe74900d6dc7 - c4b82dce8335 - - e4691e1589d3 - - 49370cb85f0f + - de6cebe3c043 + - 288f97432497 + - b1c926deaa2d + - 48f587c13075 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: - - f666895cbebd - - 8889eb864cef - 9db07fd39f85 + - 8889eb864cef + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -53,15 +53,15 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - de2db1bdfbf8 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species owner: devteam revisions: - - 25b8736c627a - 717aee069681 + - 25b8736c627a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -80,9 +80,9 @@ tools: - name: fasta_formatter owner: devteam revisions: + - 9457a20156db - 516b97a23d7e - 859422bcb689 - - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -102,8 +102,8 @@ tools: owner: devteam revisions: - ec0b5076173a - - f81d4362b6c1 - f773e98b26cf + - f81d4362b6c1 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: + - 9c620a950d3a - cd0874854f51 - 0dbb995c7d35 - 56022eb50bbd - - 9c620a950d3a 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: + - c59d48774d03 - d60c3f704da0 - - 65b93b623c77 - 1d8fe9bc4cb0 - dbf9c561ef29 - - c59d48774d03 + - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -146,43 +146,85 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - 9115b978ce10 + - b05e39b9c170 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_combiner + owner: devteam + revisions: + - 9115b978ce10 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 10b75444feae + - '144275714590' - 81a9090d6df3 + - 10b75444feae + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_filter + owner: devteam + revisions: + - '144275714590' tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - - 8611b80a14d6 + - e9f8633db0a2 - 47e5dbc3e790 + - 8611b80a14d6 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_groomer + owner: devteam + revisions: + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: + - e30352e889fe - 5b87038565bb - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_manipulation + owner: devteam + revisions: + - e30352e889fe + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 + - 4e1d64e6385f - 9dfda4e310ed + - 9282652e7234 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_masker_by_quality + owner: devteam + revisions: + - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb + - 523c2aff0376 - 03d57fea6482 + - f3936d0632cb + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_deinterlacer + owner: devteam + revisions: + - 523c2aff0376 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -190,35 +232,50 @@ tools: revisions: - 2ccb8dcabddc - 3e396e702cea + - b41c2c1bcfbf + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_interlacer + owner: devteam + revisions: + - b41c2c1bcfbf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - c885369b207b + - 09a2199cd356 + - 8d958759cf2a + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_joiner + owner: devteam + revisions: + - 8d958759cf2a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - 249c8393f2d4 - e39cc71d3ed6 + - 397dc333436b + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - e39cc71d3ed6 + - 397dc333436b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -230,28 +287,43 @@ tools: - name: fastq_stats owner: devteam revisions: + - f86c27295151 - f0e7deab6518 - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_stats + owner: devteam + revisions: + - f86c27295151 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 + - f0b18efb97f1 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_trimmer + owner: devteam + revisions: + - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: + - ac3fed111eb6 - 297962e79f39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - - 567d5b3c52b1 - d5e9e83cd3d8 + - 567d5b3c52b1 - 09070cacefd8 - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ @@ -265,9 +337,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 0b7ec11b3c7c - 4bedca26c133 + - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -279,10 +351,10 @@ tools: - name: fastx_clipper owner: devteam revisions: + - bdf1ce174e39 - cb1e251cac37 - 90858c306551 - 736b8f6ee456 - - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -294,8 +366,8 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 - 07497255281e + - 7ce1891db6f5 - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -308,10 +380,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 02f8a17a4ebd - - 3599f5451ee2 - f984bb114520 + - 3599f5451ee2 - b29d37ca9e41 + - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -324,9 +396,9 @@ tools: owner: devteam revisions: - e246088b6e34 - - 0c2907307ba4 - - 6027ef51ef91 - 177f0621c266 + - 6027ef51ef91 + - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -339,9 +411,9 @@ tools: owner: devteam revisions: - 61b4cedc8934 - - 377ac2829eac - 73194cdd4f57 - 547e8d00f11c + - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -365,10 +437,10 @@ tools: - name: pear owner: iuc revisions: - - b4c6f054210a - f69501361cec - 037f0acc7830 - 2f804526f5fd + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -380,22 +452,22 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: - - 61eb4cfc7313 - fdc21382376d + - 61eb4cfc7313 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - - fe1ae2ebf63d - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -420,8 +492,8 @@ 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 @@ -441,52 +513,57 @@ tools: - name: umi_tools_count owner: iuc revisions: + - 8250ea3a1501 + - 71ad4a56c40c - e654095ab143 + - a535cf1e5da4 - b557acca0b56 - - 8250ea3a1501 - 24013bf85a6f - - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - a535cf1e5da4 + - 71ad4a56c40c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup owner: iuc revisions: - f1d33e4c7bd8 + - c5a2ee07c4e1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: - - 015cf18f4a15 - - 828dba98cdb4 + - 9fa7803d1c51 - 7accf7407811 + - 27ac32a22ad2 - f3759eec3018 - - 9fa7803d1c51 + - 015cf18f4a15 - 6a675c3aa610 - - 27ac32a22ad2 + - 828dba98cdb4 + - 7a7e33d28f62 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: - - 015cf18f4a15 + - 7a7e33d28f62 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group owner: iuc revisions: - d6255614afd7 + - 428735be9764 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist owner: iuc revisions: + - e4e12f0b3af1 - 4c8a1c7d3608 - 953b4821b183 tool_panel_section_label: FASTA/FASTQ diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index ba5bf222a..0ec3ee5a1 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -3,9 +3,9 @@ tools: owner: devteam revisions: - e41385662e5e - - 7b4468117008 - 64e9a6afdd0c - ce9cd02d5b88 + - 7b4468117008 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,28 +18,28 @@ tools: - name: fastqc owner: devteam revisions: + - f2e8552cf1d0 - 9da02be9c6cc - ff9530579d1f - - f2e8552cf1d0 - - e7b2202befea - 5ec9f6bceaee - 3d0c7bdf12f5 - - 2b0c9d9fc6ca + - e7b2202befea - 2c64fded1286 + - 2b0c9d9fc6ca tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - ad116ae3f4d9 - b6b54ba71bd8 + - ad116ae3f4d9 - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -47,38 +47,38 @@ tools: owner: devteam revisions: - cc0fd298cc17 - - 7306ec78632a - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - a72af9de6bf5 - - 8880fb74ef56 - 1f296803dfa3 + - 8880fb74ef56 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 75c93c70d094 - - f7985e0479b9 + - f7e2f1eb3a16 + - b2f1f75d49c4 + - 3d93dd18d9f8 - 9a913cdee30e - 1c2db0054039 - - b2f1f75d49c4 + - bf675f34b056 + - f7985e0479b9 - abfd8a6544d7 - - 3d93dd18d9f8 - - f7e2f1eb3a16 + - 75c93c70d094 - 5e33b465d8d5 - - bf675f34b056 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - cd7e644cae1d + - 084bbd8ba7b8 - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fetch_alignmentssequences.yml b/staging.gvl.org.au/fetch_alignmentssequences.yml index c01999d90..0dfc5355c 100644 --- a/staging.gvl.org.au/fetch_alignmentssequences.yml +++ b/staging.gvl.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index b248d7a64..ab23c208f 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -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 0e067e78f..9e3782808 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -9,8 +9,8 @@ tools: - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate @@ -31,29 +31,29 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -87,8 +87,8 @@ tools: owner: iuc revisions: - 45296e47d565 - - b2c25142267e - cf61daf064fe + - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -123,8 +123,8 @@ tools: owner: iuc revisions: - 840fb4850be3 - - 666f60a9331a - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,8 +137,8 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -151,21 +151,21 @@ tools: - 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 owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 28aa17fae..8627a5283 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,8 +2,8 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 2b3817d19..e598e12d4 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - 983bf725dfc2 + - c1b437242fee - b39347891609 - e9df53a75f3c - - c1b437242fee + - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,53 +17,53 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 1c58de56d587 - e063168e0a81 - 28587613264f + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 1ec814014652 - - c441583adae5 - - e407b9da183a - - 653e89d73fc4 + - 83c7d564b128 - 516a54ddf218 - - 4df8de2d0e48 - - 9a776b080193 - - ba931a59dd59 - - 69ebb7f46e45 - - f8054ea1c365 - - 7068f48d0ef9 - 8848455c0270 - - 83c7d564b128 - - 734abc7ac21d - - 6ea73833cf67 + - c441583adae5 - 4317d3cb6cba - - 1790dcf3c32d - 6591f049cf7e - - aad3885b3216 + - 6ea73833cf67 - f5ea3ce9b9b0 + - 734abc7ac21d + - aad3885b3216 + - 653e89d73fc4 + - 1790dcf3c32d - 5e6237d58b0c + - 1ec814014652 + - 7068f48d0ef9 + - e407b9da183a + - 4df8de2d0e48 + - 9a776b080193 + - f8054ea1c365 + - 69ebb7f46e45 - e08a7ad4378b + - ba931a59dd59 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 9aaa46d45472 - - 34758ab8aaa4 - 75b3b3d0adbf - 21a560af5913 + - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - af5eccf83605 - - bfdc6a7ffd3a - 468c71dac78a - 054483e27a35 + - bfdc6a7ffd3a 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 eaedea8b2..81b1e7381 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: - - 4b519282a05b + - df7356989ac1 - fd59d783248a - c4bde687c846 - - 7f13dc906cb9 - - a64dc31ab7f2 - 290a11559985 - - 740057a5126d - - df7356989ac1 + - 4b519282a05b - ae9994cf526f + - 740057a5126d + - 7f13dc906cb9 + - a64dc31ab7f2 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -48,8 +48,8 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 374e9062d874 - 3b37b1b1c3a7 + - 374e9062d874 - 53460afd5115 - ca7cb0eaad62 - '566197475670' @@ -58,19 +58,19 @@ tools: - name: ggplot2_heatmap owner: iuc revisions: - - 3d059e9c2fba - - 391a4cc45fea - 1a72f938213e - - 10515715c940 - da4c086cff5b + - 10515715c940 + - 3d059e9c2fba - d3a9e32672ec + - 391a4cc45fea tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - b0d96516e6a5 - 6fc8bab811da + - b0d96516e6a5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca @@ -83,12 +83,12 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 5fe1dc76176e - - d0fc8b746d57 - - 1acf88921176 - 5298e06f14f9 - - 299307abd804 + - d0fc8b746d57 + - 5fe1dc76176e - e3a675da7fd0 + - 299307abd804 + - 1acf88921176 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -107,8 +107,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -121,8 +121,8 @@ tools: - name: histogram owner: devteam revisions: - - 6f134426c2b0 - cdb9e89e2970 + - 6f134426c2b0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse2 @@ -134,17 +134,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 17359b808b01 - - 1cfc579079a6 - - 836d1aa3e89a + - a6e57ff585c0 + - 2bb2e07a7a21 - 112eb40ba6cf - fd5dbf0f732e + - 836d1aa3e89a + - 6cd09d7b5f37 - 4542035c1075 - - a6e57ff585c0 - - 2bb2e07a7a21 - ca2def38369c + - 1cfc579079a6 + - 17359b808b01 - 667e17248bfe - - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -163,22 +163,23 @@ tools: owner: iuc revisions: - 03c13085aecc - - fe154a7af404 - f1691de443a7 + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: + - 594b85e4237a - bd1416eea1f0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: + - 1c5dcef5ce0f - 62e3a4e8c54c - 85da91bbdbfb - - 1c5dcef5ce0f - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -198,9 +199,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 - 44c66e8d21e6 - 6c571966cfb9 + - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -212,22 +213,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 326a3db8d9d1 - - 14e7c35f3d00 + - 4ac4e7083b7e - 36b848d5f3ec - - 2824d77cd8f8 - a1abfa420d9d - - 4ac4e7083b7e - - 7dd841a32245 + - 14e7c35f3d00 - 360df4999907 + - 2824d77cd8f8 + - 7dd841a32245 + - 326a3db8d9d1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - 44608d0193ed - - 73b8cb5bddcd - 2f557f6abbfb + - 73b8cb5bddcd - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -240,7 +241,7 @@ tools: - name: xy_plot owner: devteam revisions: - - 319fa5a9fc1b - ecb437f1d298 + - 319fa5a9fc1b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index e9f6c47c0..af1a981ce 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,29 +21,29 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 7779b9dcf040 - 22bd5861706d + - 7779b9dcf040 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -63,22 +63,22 @@ 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 owner: ebi-gxa revisions: - - c9da9192eee5 - 9d76c3d6dff6 + - c9da9192eee5 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony @@ -91,8 +91,8 @@ tools: - 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 @@ -120,15 +120,15 @@ tools: - 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 owner: ebi-gxa revisions: - - 4a74b45c1ce4 - 6f5509cf3176 + - 4a74b45c1ce4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory @@ -141,22 +141,22 @@ tools: - name: scanpy_read_10x owner: ebi-gxa revisions: - - 078aa23c9374 - 287503c35cb4 + - 078aa23c9374 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable owner: ebi-gxa revisions: - - d18ed15697bb - 0bab2ae44e7a + - d18ed15697bb 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 @@ -169,15 +169,15 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - 65c3ec07502b - be019b069e31 + - 65c3ec07502b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga 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: - - ea91cfd0444e - - 0f98603d0116 - 767a675b5254 + - 0f98603d0116 + - ea91cfd0444e tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index e6c75aac2..7d63509ce 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: - - ed2cca6b5de4 + - 29f66c353bcb - 921a2da49a0c - a4c13ddcc8ee - - 29f66c353bcb + - ed2cca6b5de4 - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 755df866ad0c + - 78fb5e286609 - d404277cc87a - - ec4b948dc6f0 - 5746d61f0a91 - - 78fb5e286609 + - ec4b948dc6f0 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 977dc15add20 + - 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: - 3b5b54ed6392 + - 41dbf4d162a2 + - 0ba4f56a3613 - 77919cc3618e - c3e5e2cf12b7 - - 0ba4f56a3613 - - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: + - 9939786dd9c9 - 12d51d7be66f - - 5308ca68ef3d - b63363075c2e - 7babd8a46fe0 - - 9939786dd9c9 + - 5308ca68ef3d 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 94115c1d6..ae6739981 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,19 +2,19 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 0c777d708acc - - 8bccb36e055a + - 7db4fc31dbee - 699a5e9146b3 - 81f0cbca04a7 - - 7db4fc31dbee + - 0c777d708acc + - 8bccb36e055a - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - 0a53256b48c6 + - 5791a7f65275 - 2436a8807ad1 - 5bc8cdc17fd0 tool_panel_section_label: Imaging @@ -30,27 +30,27 @@ tools: - name: 2d_histogram_equalization owner: imgteam revisions: - - b1c2c210813c - - 70316d792fc9 - 77f7159d775a + - 70316d792fc9 + - 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 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 - - 85edbb7a436b - - 10eed33aa9b2 - fcadded98e61 + - 85edbb7a436b - b07f4839ca77 + - 10eed33aa9b2 + - f3360fbeda64 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -63,48 +63,48 @@ tools: - name: count_objects owner: imgteam revisions: - - b58447a2eed2 - - 664232d2a3f7 - 5bf8eb50b280 + - 664232d2a3f7 + - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - 0e4dccaafef5 - eb6c08714244 + - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - 6070780813d9 - e7273daa5ae2 - 670975e92458 + - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - cdf8e3c57dae - - df3ad3ba5c6f - ef4aed1d34c4 + - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - - 2484086dee41 - 5d28ac336861 + - 2484086dee41 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -118,25 +118,25 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - - f8fa0f6718a3 - f24c370e5ea4 + - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 3245681b2f6d - ad271f78a87a - 31d195bedf6d + - 3245681b2f6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - 993faa34333b - - 87d4d92d7487 - b6eec6087271 + - 87d4d92d7487 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -150,25 +150,25 @@ tools: - name: cp_mask_image owner: bgruening revisions: + - b178453ea8d1 - 667a513e67e4 - 3a05117669cf - - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - 2564f461de62 + - a1a961c46d4b - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - 91e03287f285 - a32c3f810ade + - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity @@ -190,17 +190,17 @@ tools: - name: cp_measure_object_intensity owner: bgruening revisions: - - 407925835dd9 - - 980aed9e8fd5 - e52c75a28c4b + - 980aed9e8fd5 + - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - d85f11570109 - - acf3aa487283 - 79e10d12d90a + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture @@ -220,16 +220,16 @@ tools: - name: cp_relate_objects owner: bgruening revisions: + - 8083a87d2fdf - 48102a685037 - 3a3033222f61 - - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -249,15 +249,16 @@ tools: - name: idr_download_by_ids owner: iuc revisions: + - f92941d1a85e - 4b794652dcdc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: + - 236ec78b2e53 - f8b4eada923c - 7b6d9412c7f8 - - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index 9834aff8d..192dca83f 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,31 +2,31 @@ tools: - name: ivar_consensus owner: iuc revisions: + - 78bbd17d0703 - 3e4f434a69c6 - 40737febe339 + - f362150bef41 + - e319b5b65879 + - e4ee04da1c19 - a38934e303b9 - 3a72fede57ce - - e4ee04da1c19 - - e319b5b65879 - - f362150bef41 - 1069f6db0a0e - - 78bbd17d0703 - d6e72da3ec35 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - fcbeda41d0ac - - 9537184d421f + - 8f8df367470d - f91cfb73d369 + - 0135f1d487a0 - 7fe36019c073 - - 2b95d5c04908 - c88553ec696e - 618297d23022 + - 9537184d421f + - fcbeda41d0ac - 72ddd32392cd - - 0135f1d487a0 - - 8f8df367470d + - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked @@ -41,54 +41,54 @@ tools: - name: ivar_removereads owner: iuc revisions: - - 8d36959b000d - - bd2a7d1316b9 - - 5dc33613c288 - - 7f1cfa4c0e32 - - 3d18f8c3c0f6 - - 9eaadf03e0df - - 94df24c6bc00 - - 28a6f1908fcc - 6a1515bb0687 - - a1c2aecd7a0d + - 8d36959b000d - 43aac8d29685 - ee2beb764a7b + - 9eaadf03e0df + - 94df24c6bc00 + - 3d18f8c3c0f6 - 8c05afb547fa + - bd2a7d1316b9 - ee29337f905c + - 28a6f1908fcc + - a1c2aecd7a0d + - 7f1cfa4c0e32 + - 5dc33613c288 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - cb903c9dc33d - - 5d6ed46cc101 - - a250929be21b - - bcaa0d571ce2 + - c092052ed673 + - db536ad45f28 - 9f978da6528a - 8858fa037a15 - - 5671e1d3d5ee + - e3bb03cf207a + - a250929be21b - 364f4ffec275 - d37ede8589b2 - - db536ad45f28 - - c092052ed673 + - cb903c9dc33d - 86a20ae274fc - - e3bb03cf207a + - 5671e1d3d5ee + - 5d6ed46cc101 + - bcaa0d571ce2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - f95f403841ad - - 194e3ceee923 + - 3b6a16d82c1b - c5c9f02b6167 - e1a015876aa9 - - abbc8041e8ec - - 49236b03e4fd - - 3b6a16d82c1b - - ed28dd32141c - 584beffa972b + - 49236b03e4fd + - f95f403841ad - 230b05597996 - - 12d66d0d05ac + - ed28dd32141c + - abbc8041e8ec - 38b91a3190cd + - 194e3ceee923 + - 12d66d0d05ac tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index 29fb32c4e..11b754e7c 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,9 +2,9 @@ tools: - name: datamash_reverse owner: iuc revisions: + - f198773344e4 - 17e3b698dd52 - 0f1724dd59d2 - - f198773344e4 - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu @@ -12,9 +12,9 @@ tools: owner: iuc revisions: - 374cb875d38a - - ac092723240d - ba0c40780ecf - 22c2a1ac7ae3 - a513e3fbb4c5 + - ac092723240d tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index 16722bb8a..fe9aaaecc 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -3,55 +3,55 @@ tools: owner: bgruening revisions: - 522137aaa9c4 - - 66d7efc06000 - 772e0e89fc68 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - 8a794e6d3388 - - f22a9297440f - 4d81e3e2fb63 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - 818f9b69d8a0 - - e1317b5502fa - 2af1346e68c9 - - f1b9a42d6809 + - e1317b5502fa - b6ef6d0cb6b7 + - f1b9a42d6809 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - 05143043ca13 - - 947c2eacccb8 - - 8334dc98c48e - 1588f9076e32 + - 947c2eacccb8 - c80db5d6fd8c + - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - 1552b8cb4a94 - - 9991c4ddde14 - - 83228baae3c5 - 25b46af53232 + - 9991c4ddde14 - 29e4122c90de + - 83228baae3c5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - f3dfa4bdf87e + - 060ca94ac049 - 1a53edc4b438 - a07ab242b0b5 - - 060ca94ac049 + - f3dfa4bdf87e - 53616c8b0865 - 841a6cc5fc58 tool_panel_section_label: Machine Learning @@ -59,42 +59,42 @@ tools: - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 - - 927586a18553 - dc4b5fd604a6 - - d4808d5b83da - 40f4447733b2 + - 927586a18553 + - 2fc89dcd41c8 - 91c4e3331208 + - d4808d5b83da tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - 7626ea9c2e1b - - c6ae57f774c6 - - 25ab6b4e376e - 301e07345c93 + - c6ae57f774c6 - 36e8d6d5d01b - e5a5ad882f1f + - 25ab6b4e376e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: + - 80852884053f - 4ed102b922cb + - b7c3e9a3b954 - 0630258dcf35 - - 80852884053f - f9639b488779 - - b7c3e9a3b954 - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - ec69cbe34b73 - - caeb57858702 - - 61634a87efc7 - 14180f9c831e + - 61634a87efc7 + - caeb57858702 + - ec69cbe34b73 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 1a9e5ff1d..0ef1d70a6 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - d5ceb9f3c25b - - 017aba02828d - - 937aa69e715f - - a6d65b0c67af - 3ba8d4563129 + - 17062a0decb7 + - a6d65b0c67af + - 749c918495f7 + - 937aa69e715f - f6877ad76b00 - 0d4acadabb04 - cd659e8cc5fa + - d5ceb9f3c25b - 03e9b2fbc005 - - 749c918495f7 - - 17062a0decb7 + - 017aba02828d tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 53646aaaafef - - dfd8b7f78c37 - - 3fe632431b68 - e188dc7a68e6 - - 2477830927ec + - dfd8b7f78c37 + - 53646aaaafef - 64f11cf59c6e + - 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: - - 60afcc2c1d05 - - 37b497aa133f - - 3e1ea2facca6 - 2ff111fac1d7 + - 3e1ea2facca6 + - 60afcc2c1d05 - e7f19d6a9af8 + - 37b497aa133f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - be1d967337e4 + - 8c6cd2650d1f + - 77b2770508f6 + - 3f4d6399997b - 11a0d50a54e6 - f54f5baedfdd - - 53c0b7a1a0c3 - - 037c6e54df11 + - be1d967337e4 - 09b53c1d4ab1 - - 8c6cd2650d1f - - b3eab4b67562 - - 3f4d6399997b - c0c2d0941de8 - - 5cc34c3f440d + - 53c0b7a1a0c3 + - 037c6e54df11 - 6b1e195506a3 - - 77b2770508f6 + - 5cc34c3f440d + - b3eab4b67562 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 45795f582ae9 - - 9ee34ba73ebf - - 5ef7ec16b04f + - e403d27e8f24 + - 42ce70172b72 - 1cd2511a396e - 79b885ce78d7 - ec9cbd6b9a49 - - 00fbfac99d39 - - 178bdbdb6d24 - b8f5f6e87f5c - - e403d27e8f24 + - 178bdbdb6d24 + - 00fbfac99d39 - 13022c3d3076 - - 42ce70172b72 + - 9ee34ba73ebf + - 45795f582ae9 + - 5ef7ec16b04f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index f2b80eb76..339c7d83b 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: - - 90dc951da294 - 6cd2a9e6ac49 + - 90dc951da294 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -93,22 +93,22 @@ tools: - name: matchms_convert owner: recetox revisions: - - b9cc12600553 - c990df6afc24 + - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - 00e66c401366 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - - 84af792d3a78 - d7b517f2c5fe + - 84af792d3a78 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter @@ -141,8 +141,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 1d74ae228df3 - 8147d93d372d + - 1d74ae228df3 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 @@ -192,8 +192,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - b5467dead5b1 - 90745ecc5e9f + - b5467dead5b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -241,38 +241,38 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - f2c1d0bbb074 - 5f2b58dadb39 + - f2c1d0bbb074 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr owner: recetox revisions: - - da7722f665f4 - 9b716db0a786 + - da7722f665f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - 79ad928a0dae - c53a97599181 + - 79ad928a0dae - 7b42ee54d757 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - 149b9cc7499b - - 18ec7635bac6 - f3a18e020cdd + - 18ec7635bac6 + - 149b9cc7499b tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - 134be5abb208 - 481d769e2f7a + - 134be5abb208 - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -280,40 +280,40 @@ tools: owner: recetox revisions: - 51332c2520c7 - - 9064aecc78a7 - 02c772a49998 + - 9064aecc78a7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: + - b341cfd4baf8 - b3413f335327 - e7305ba0dd38 - - b341cfd4baf8 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - dd7bbc2b99d1 - cf061712a184 + - dd7bbc2b99d1 - 17a48d0a80f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - 24278c6b6d1c - 99d118321d5f - d7f5878a98c3 + - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - d90187b0f247 - ffbabefbd2e2 - ea0758b41473 + - d90187b0f247 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: - - 6b5dec818827 - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -375,8 +375,8 @@ tools: - name: use_theoretical_mz_annotations owner: recetox revisions: - - b3d41b1fcb18 - e0cac9994a72 + - b3d41b1fcb18 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: w4mclassfilter diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index f41ba92a3..2f67c8846 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -9,8 +9,8 @@ tools: owner: iuc revisions: - 18676df0cb3a - - 0e63d03c8790 - 0094893f5001 + - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -95,121 +95,121 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 63f86089423e - - 7c2100246a2f - - 5b5a7af9fbb4 - 76d3d2b10738 + - 5b5a7af9fbb4 - 65db807336bc + - 63f86089423e + - 7c2100246a2f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - 18a502a9d287 - - 96336c6a2bb7 - - 1c35dadbe76f - - 00f5005840fa - 84fd33a60b35 + - 00f5005840fa + - 1c35dadbe76f + - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - e8fba04706d3 - - 34e55239e68b - - f732237754fc - a9f4a217dcd6 - addaf9d22850 + - 34e55239e68b + - e8fba04706d3 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 04c15826a0b8 - 5fe3edf19b9c + - 0776d824d896 - 8c202e741d68 - - 04c15826a0b8 - 75403243703a - - 0776d824d896 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - e96bbb9e24ea + - 75c8945b0da2 - 8470de786d47 - - 1c9b3bcd4261 - 43c99742158b - - 75c8945b0da2 + - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 306a40d4bb8f - 35176674168c + - 306a40d4bb8f + - 5c865a382933 - 84743da21318 - 1d75bd0595e2 - - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - - 32c9ea835770 - 555ccac8a4c5 + - 8daf4564ccda - 78faebd0879c + - 32c9ea835770 - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - a58e4a43f49c + - d60df8727f59 - 7b8cb2b02978 - f947b4bb5107 - cae017b76acb - - d60df8727f59 + - a58e4a43f49c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - 073608a50ac3 - - 7136e9ab70db + - 04144473e59e - 1bc3657cd694 - 7f3b59dee073 - - 04144473e59e + - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - d943081510da - - 0a1224c4b781 - - 19299bb1c6af - a7817705348e - 9058d8943303 + - 0a1224c4b781 + - 19299bb1c6af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - e005e659ae21 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - b907a3c0434f + - f8f56dd6449f + - c4db8c4de66f - 4d9445dff47b - 65d52c693b8e - - 5c7ba3d85a01 - dbf1798c0dcc - a68b985913ab - - c4db8c4de66f - - f8f56dd6449f + - 5c7ba3d85a01 + - b907a3c0434f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -222,9 +222,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6c84982ee6f7 - 6d364c65c946 - 654548ae1357 + - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -236,8 +236,8 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - e66ab198ec15 - 6aad8ca3918b + - e66ab198ec15 - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -245,16 +245,16 @@ 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 owner: iuc revisions: - - 9704f1a3b32d - cad93abecac9 - 7f208f1eb64f + - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -272,52 +272,52 @@ tools: - name: humann_barplot owner: iuc revisions: - - 5fea25ee6275 - 523ae8314ef5 + - 5fea25ee6275 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables owner: iuc revisions: - - f01ca38fb6c5 - 6bf703133209 + - f01ca38fb6c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table owner: iuc revisions: - - 60749924ad62 - 6552df6efe6b + - 60749924ad62 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - - c409a495841f - e88b731dad59 - - 31c6d107e7a5 - 79706f10d680 + - c409a495841f + - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - 71ea608ddfa3 + - 714d5a28cc5c - 172920f67a84 - - d24841f5c3d2 - 094ad9c068af - - 714d5a28cc5c + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 4137b492233e - - a4d7148ccee4 - - 12fb63b5f63f - a293a742194f - - 2bdd84912a2b + - a4d7148ccee4 - d7e9a3c41657 + - 4137b492233e + - 2bdd84912a2b + - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -329,12 +329,12 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 6fcb8ac37a3e - - cf87759761eb - a92c06a3afa7 + - cf87759761eb + - 6fcb8ac37a3e - 75bedfb2078b - - 64bc7acc22a9 - e2c71b852aba + - 64bc7acc22a9 - 97f7bb0851e7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -354,20 +354,20 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c - c82508e76ad1 - - 5e5a999ffaa9 - - 2d35528d2141 - 4033827c76b8 - 4e5e73d03f0d + - 080ea153677c + - 2d35528d2141 + - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - 6b7622dda516 - - 2cd76b089570 - fc6c328c292f + - 2cd76b089570 - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -380,13 +380,14 @@ tools: - name: jellyfish owner: iuc revisions: - - dcd30574a456 - 11658afb8c87 + - dcd30574a456 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single owner: iuc revisions: + - 65b382bf9b7c - 385a965c6f87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -394,23 +395,27 @@ tools: owner: iuc revisions: - 7624945cacd3 + - e699e2747356 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median owner: iuc revisions: - b3d513c7093e + - 570505540a7b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions owner: iuc revisions: - adb3dd5a899f + - 1061711538c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance owner: iuc revisions: + - 29a4d6e2ae9c - b86562b4f3fd tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -418,18 +423,21 @@ tools: owner: iuc revisions: - 19607c740d19 + - 00f7064c564b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median owner: iuc revisions: - b1fe2ef3d244 + - 4d23ab83ea29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition owner: iuc revisions: - 5a0fa29951ae + - 8388fe31d604 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kmc @@ -441,17 +449,17 @@ tools: - name: kraken2 owner: iuc revisions: + - cdee7158adf3 + - 328c607150ff - 4a9da2b6c2e3 - 20e2f64aa1fe - - 328c607150ff - - cdee7158adf3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -470,15 +478,15 @@ tools: - name: kraken_report owner: devteam revisions: - - 1c677354ab18 - 6c09bed3444f + - 1c677354ab18 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report owner: iuc revisions: - - 27d65c78863c - bfae8da6082c + - 27d65c78863c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -490,8 +498,8 @@ tools: - name: kraken owner: devteam revisions: - - 8ba2174315aa - 766d5f63b0f4 + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -509,8 +517,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 4960abe31b4d + - 073c867c5244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -522,8 +530,8 @@ 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 @@ -559,14 +567,14 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 3cc4a60615c0 - - 2cff76cf35c6 - - 27250f92a01a - - 7f5d7b0e9884 - 327d9f4cc95f - - e073891b2afc - 4fd3b5d8706b + - 7f5d7b0e9884 + - e073891b2afc - 0270541aaf46 + - 27250f92a01a + - 2cff76cf35c6 + - 3cc4a60615c0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 @@ -647,19 +655,19 @@ tools: - name: metaphlan owner: iuc revisions: - - 1a037928504c - - ec368db926f4 - - 1a6cdf55390f - - a92a632c4d9b + - 289b3807e80c - 2131d7dca455 - - fd69c607b43f - a16313517e55 - - 289b3807e80c - - b89b0765695d - ef65b083bd0c - - 6dee4abadccb - - ff8f55893e7d + - fd69c607b43f - 740fd2d16a28 + - ff8f55893e7d + - 6dee4abadccb + - a92a632c4d9b + - 1a6cdf55390f + - ec368db926f4 + - b89b0765695d + - 1a037928504c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -684,8 +692,8 @@ 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 @@ -698,29 +706,29 @@ tools: - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - 540aedfc81c7 - d6bb2e3febda + - 540aedfc81c7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 680fb3eb574c - 73b56418e7f4 + - 680fb3eb574c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -801,13 +809,13 @@ tools: - name: staramr owner: nml revisions: - - 4d83eccf5f81 - - be818ae858e4 - - 4b9a8031ab74 - - 141afacabcfa - 2fd4d4c9c5c2 + - 141afacabcfa - 3b22de20bd4b + - 4d83eccf5f81 - aeaa20b96ef2 + - be818ae858e4 + - 4b9a8031ab74 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -837,8 +845,8 @@ tools: - name: vsearch owner: iuc revisions: - - 9495df9dd6ef - b3c7199d8786 + - 9495df9dd6ef - 576963db5f1b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index d64c813ba..0e15febb9 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index a54c8c4bb..7365d5c47 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: + - 2263989660f5 - 9baa871cb1d1 - - 48c13389050d - - 80f03df2e2ce - - 8b67dd48fec1 - 94b8c6013083 + - 80f03df2e2ce - bdfbaf0c10aa - - 2263989660f5 - 9eeb13a92d79 + - 8b67dd48fec1 + - 48c13389050d - cd07731e4434 + - a74dbfee5a86 - 6ae5a7b5a0a2 - 098506c54016 - - a74dbfee5a86 - 9422c5a87ee2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f14193ec1f50 - - 2e093badc689 - - fc2e49f91e52 + - d7ce0ec78e51 - '764845535798' - - 4a60927aaca5 - - aaa0d6a8b808 + - c18157c68134 - bc3831dd65c1 - - d390fe1567dc - - f0af8936ed41 - be78f13134e2 - - 3ff17bad4006 + - aaa0d6a8b808 - 5abf2c2249aa - - d7ce0ec78e51 + - 2e093badc689 + - f14193ec1f50 + - d390fe1567dc + - 4a60927aaca5 + - 3ff17bad4006 - c44f824c051a - - c18157c68134 + - fc2e49f91e52 + - f0af8936ed41 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -53,13 +53,14 @@ tools: - name: clustalw owner: devteam revisions: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: + - 1de657a3198d - 5efbd15675ca tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -67,53 +68,53 @@ tools: owner: rnateam revisions: - f0d493f8f84f - - c5908940967d - - 8e649f27aa0d - f1a5908ea2cb - - 15974dd17515 - - 6f28e90db932 + - 8e649f27aa0d - bf28a8cff401 + - 6f28e90db932 + - c5908940967d + - 15974dd17515 - a65296ffb4a0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: + - e8fdceffea4c - b3acbb3a6af0 - fbca557a4847 - - e8fdceffea4c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - c9685bc0407c - 5561a1193611 + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 57f042937ba7 + - bcd65de9725b - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: + - ebe3b0f84de9 - fb43e8887350 - 4fc0cb2ac8ae - - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 7cd7a55a678d - - e18267f90096 - 636b049e6141 + - e18267f90096 + - 7cd7a55a678d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index 454d16183..1d03b7621 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,9 +8,9 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 7c47b3c9e493 - 18a8d140ec6f - 28928576e1ea + - 7c47b3c9e493 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado @@ -29,12 +29,12 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - 72b5e9dda577 - 79e9a869f40e - - a7228a7ea146 + - cb34f00cc10f - 0e9e7fcdd543 - - 72b5e9dda577 - fc8804320156 - - cb34f00cc10f + - a7228a7ea146 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus @@ -42,8 +42,8 @@ tools: revisions: - fa11aa8103b2 - 18505fe2bdb1 - - d6cddc06aeae - db25ec99c3ea + - d6cddc06aeae 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 - 222669c4afb6 + - edf6d4003fad + - cc36773a3681 + - 0f5f4a208660 - eb746fa6f514 - 43815fa60f3a - 19f3b583a9b3 - 2bf63b38ee9b - - cc36773a3681 - ec699520444c - - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -82,13 +82,13 @@ tools: - name: nanoplot owner: iuc revisions: + - 7b379e98b9a9 + - a3c4fe6f49ab - a38bdcec9e4c + - 0f1c34698076 - edbb6c5028f5 - - a02b8b3f5a0c - - a3c4fe6f49ab - 645159bcee2d - - 7b379e98b9a9 - - 0f1c34698076 + - a02b8b3f5a0c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -110,38 +110,37 @@ tools: - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - 449e9aeded2d - 4857d5bcce52 + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - de5b3d8f5b90 - - bec636361cfd - a3afc5f0a96c + - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 5f76b20953e5 - 93d623d9979c - 543cbeef3949 + - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - daf8518d243a - 1d835c691480 + - daf8518d243a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract owner: iuc revisions: - - 7e4f1ed70187 - 08064da7b7fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -155,23 +154,20 @@ tools: - name: poretools_nucdist owner: iuc revisions: - - a57b6350fd5d - 5c4fa65f5733 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_occupancy owner: iuc revisions: - - 0433aad600e9 - - 338d15b8d6fb - 336791b5665f + - 0433aad600e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist owner: iuc revisions: - 72dfdbfab3cc - - ae9060e764b5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualpos @@ -186,7 +182,6 @@ tools: revisions: - 26e6c9362b7b - ce8af9373061 - - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -199,7 +194,6 @@ tools: owner: iuc revisions: - 5f5f1da94d7f - - 2cb2feb94f0e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_times @@ -212,7 +206,6 @@ tools: owner: iuc revisions: - 6d93709247c7 - - 79c1ac92f31b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_yield_plot diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 9fea002f1..8b830380d 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 @@ -59,19 +59,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - 3e73c97f025d - - adfd6bf710bd - baceff842902 - 97b1b5ad1cda - d74850cf4e42 + - 3e73c97f025d + - adfd6bf710bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 9dd107db92c2 - - 83da94c0e4a6 - 1586b111d2a3 + - 83da94c0e4a6 + - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -114,22 +114,22 @@ tools: owner: iuc revisions: - 38ccd4589990 - - 48a42ca61006 - 5711fc06a63e + - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -155,31 +155,31 @@ 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 - 5bcf0e24f42c - - 172815da3d41 - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - 10232d2b5062 - df84aaed4769 + - 10232d2b5062 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d210e1f185bd - d74c740bdb25 + - d210e1f185bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -191,9 +191,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 19bbd19b74b3 - 87febc68b45b - fea85c467896 + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -206,8 +206,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 4c7ebbad42cf - 15c2fc266540 + - 4c7ebbad42cf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -225,36 +225,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 0cb27ea69dc1 + - 4ba60cb14cb0 - d8dc037e3c13 - - 5fe20c915fa6 - 9c43baa60906 - - 4ba60cb14cb0 - 2c61c30a57e7 + - 0cb27ea69dc1 + - 5fe20c915fa6 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: - - 0db22932bc39 - - aec831b54a5b - 9d09724f2bf1 + - aec831b54a5b + - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - - 6e24e79d3d69 - ed7a967cb11b - 29c738066906 + - df30a2f1db55 + - 6e24e79d3d69 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 - 1865e693d8b2 + - ad90c2da4f38 - 3e4d45aca422 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -294,8 +294,8 @@ tools: owner: iuc revisions: - 64deddb6a8ec - - c520a52b5174 - d63c1442407f + - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder @@ -1053,22 +1053,22 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - 544f6d2329ac - d64562a4ebb3 + - 544f6d2329ac 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: - - a22969b08177 - e4b7d1507a75 + - a22969b08177 - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1081,9 +1081,9 @@ tools: - name: salsa owner: iuc revisions: + - 9a22227bb6d0 - 58a870ef434c - ba7b0f11e470 - - 9a22227bb6d0 - ab5b7f6b7198 - f77f7a7f3b83 tool_panel_section_label: None diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index d70d63285..c7c7f5c80 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: - - d7c7ef3353fe - - 3f59ebfbfe3d - - d033ffc1c161 - - 8834daeb9892 - 3b8b5bde0bd9 - - cce7b18495e4 - - 6a457678efcb - - f73435dc282b - - 81e66674859e - - 26de3a7b1cb9 - - a6619171428e - - 5a7c56a5cc08 + - d033ffc1c161 + - b89cac5156ec + - d7c7ef3353fe - c78f3d7dd1db + - 5a7c56a5cc08 - f04a1264e2a2 - - b89cac5156ec - 107d3ba7024a + - 81e66674859e + - f73435dc282b + - a6619171428e + - cce7b18495e4 - '841557158611' + - 6a457678efcb + - 8834daeb9892 + - 26de3a7b1cb9 + - 3f59ebfbfe3d tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 7a2092844346 - - 3b96e92e8ec3 - - b0af57c1a968 - - e75442c7f4da - - 6223845127ea - - 88c4aa435ded - - df47d4845b62 - - 4755f52427c4 - a185b079b095 - - 02b8758214b0 + - aa8cc71438cf - 6a726db04d4b - - 5fcd1ece3a6e + - 88c4aa435ded - 5b777002c2de - - aa8cc71438cf + - 3b96e92e8ec3 + - 5fcd1ece3a6e + - df47d4845b62 - 6283babe736e + - 4755f52427c4 + - 6223845127ea + - 7a2092844346 + - 02b8758214b0 - 659517798cc4 + - e75442c7f4da + - b0af57c1a968 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 70acec670c30 - - d1c340a5664b - - 111bd54f6bc4 - - 524d31add34a - - 24d024316465 - f97743d52b87 - - b8476e82ac20 + - 24d024316465 + - 524d31add34a - 0878b7fd5260 + - b8476e82ac20 + - 111bd54f6bc4 + - 70acec670c30 + - d1c340a5664b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - feb40665d7cd - - 4f6349228462 - daddf188c13f - 9e10ba792be2 + - 4f6349228462 + - feb40665d7cd 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: - - ca337cce3888 - - 03ed9524dcd1 - - a2099fb98cdb + - 42a174224817 - 2f1019071464 - - 81804a978fc0 - 36912871ccdc + - ca337cce3888 + - 2fa9d4f1b48f + - 7bb8726be37c - b6abccb1f25b - - 42a174224817 - - abf6dbe8c9d7 - - 5f8727ff21e7 + - 03ed9524dcd1 - 83a69484cb87 + - 437e28791761 + - b7e297c2ede6 + - 81804a978fc0 + - abf6dbe8c9d7 + - ca0d8cf80567 + - a2099fb98cdb - 14ae456b8cc5 - - 9d61d3fa046c - 8ad84c5753ea - - 437e28791761 + - 9d61d3fa046c - 3a43c3982401 - - 2fa9d4f1b48f - - 7bb8726be37c - - ca0d8cf80567 - - b7e297c2ede6 + - 5f8727ff21e7 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 @@ -149,22 +149,22 @@ tools: owner: iuc revisions: - b1e68bbe4cef - - 73a469f7dc96 - - a4b71be30c3c - - ea30d3089354 - 29ff6a849eac + - ea30d3089354 - ba29b5e2a4be + - 73a469f7dc96 + - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - 9b2b122d0415 - - 91887494eb97 - e88a7de55d6e + - f1ccc8a6eb05 + - 91887494eb97 + - dbe2b2204555 - 15ac71df11a0 - 809e42326fc2 - - dbe2b2204555 - - 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 a0000981c..2d7de491f 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - f9242e01365a - 3f254c5ced1d - - a1f0b3f4b781 - - fc288950c3b7 - f6ced08779c4 + - 1aac2a13842a + - f9242e01365a + - fc288950c3b7 - b502c227b5e6 - 7d34178f2812 - - 1aac2a13842a + - a1f0b3f4b781 - 881d7645d1bf tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index 751ad97ca..ba18ba522 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: - - 2f7702fd0a4c - - 6ab1a261520a - - eb085b3dbaf8 - - 3bd420ec162d - - d00e15139065 - a58f7eb0df2c - ca90d17ff51b + - 6ab1a261520a - 7fbec959cf2b - e4a053d67e24 - - c0e71cb2bd1b - 5b85006245f3 + - 2f7702fd0a4c + - d00e15139065 + - c0e71cb2bd1b + - eb085b3dbaf8 + - 3bd420ec162d 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 0d6dddd3c..88812c6bc 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,23 +2,23 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 0a18ac48ac53 + - ece627528a78 + - 4c177985028a - 277dc652246e + - f28ad96b76dc - b574b84afc4d - b18329a8ac14 - - 4c177985028a - - f28ad96b76dc - - ece627528a78 + - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - bf06d196e23d + - 525f201b86c1 - e988563cc6e5 - e215f71d7983 - - bf06d196e23d - b41107d8fe89 - - 525f201b86c1 - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -34,22 +34,22 @@ tools: - name: cardinal_filtering owner: galaxyp revisions: - - f23d67e28cc8 - - 528fb09022be - - b8c79e70516d - a8157342d9a3 + - b8c79e70516d - 890845926d4b + - 528fb09022be + - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 25b83cbd596a - 59e85306eae5 - 80600735685d + - 25b83cbd596a - ae304a72db7b - - a95a82eb4d50 - a69865da6f80 + - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing @@ -57,39 +57,39 @@ tools: revisions: - 83aac7741200 - e0669b1854b1 + - 611d80c0e29d - 798da6bdff3d - f1897eb07081 - ed9ed1e6cca2 - - 611d80c0e29d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - - d426a9107a6c - - 5a35e3a8d013 - 74b61bf5bc4b + - 5a35e3a8d013 + - d426a9107a6c + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - 82f6c2f4332d + - 91f0f5922011 - df2187f9013b - cc430977c8ff - - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: + - 10566783d718 - 043f9c91f686 - c5aa9fca18c6 - - ba92b59cd529 - 1693b2126f30 + - ba92b59cd529 - d2483487e077 - - 10566783d718 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -108,8 +108,8 @@ tools: owner: galaxyp revisions: - bf0728e000cd - - 9fa3dbf06f17 - ae4dc0c041f9 + - 9fa3dbf06f17 - ff8c9e0e8a7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -130,15 +130,15 @@ tools: owner: galaxyp revisions: - 1c5cbf8f79ce - - 4081e4faa4ab - 0fa397f4f40b + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - 36880dfd9fa7 - fb192dd6658a + - 36880dfd9fa7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut @@ -158,16 +158,16 @@ 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: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -180,16 +180,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - f522c08e900c - - 2133b0be850a - - e42225f8a659 - 9c52362ae7bb - - 7f432d87c82c - - 1f39c833f65f - 837224ad1694 + - 1f39c833f65f - 4d17fcdeb8ff + - f522c08e900c - 97a7f34fcb6a + - 2133b0be850a - 37d669de2828 + - 7f432d87c82c + - e42225f8a659 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,17 +201,17 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - 85b8866f06d7 - - 0ed07016d668 - e63db1aa82ee + - 0ed07016d668 - a72ac2c7cc5b + - 85b8866f06d7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 990b4560ead7 - 767c1d761aaf + - 990b4560ead7 - 352b37c66d97 - 1974224d63c2 tool_panel_section_label: Proteomics @@ -219,44 +219,44 @@ tools: - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f + - 99450519d727 - 4f359549383c - 35cc7ca0bdc7 - - 99450519d727 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c1343e3389ca - - e79958768a2c - - c7745841de24 - 06f6826d380c + - c7745841de24 + - e79958768a2c + - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 - b9d453dca8d3 - da986f83631b + - d2eac53666f0 - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 944b43462104 - - 1199751329b0 - 9bf325045235 + - 1199751329b0 - 8bd7734309f6 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - e0104a9f20f0 - 8295d959ca28 + - e0104a9f20f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert @@ -269,10 +269,10 @@ tools: - name: msstats owner: galaxyp revisions: - - de7593c29499 - 593839e1f2c3 - - 28434abe6c5c + - de7593c29499 - 8212e342e482 + - 28434abe6c5c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -285,8 +285,8 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 01dbaf6a57e0 - 8960fb791701 + - 01dbaf6a57e0 - f4be248c3d47 - 4e77b8f12cd3 tool_panel_section_label: Proteomics @@ -294,26 +294,26 @@ tools: - name: openms_decoydatabase owner: galaxyp revisions: - - 06cca574e337 - - 25529df60a81 - 370141bc0da3 + - 25529df60a81 + - 06cca574e337 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - 518b1730cf2a - - 6ccbf9a2072c - - f7fef900f5b2 - - 9cdf15d3cfc8 - c9eff69a7c62 + - 9cdf15d3cfc8 + - f7fef900f5b2 + - 6ccbf9a2072c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 5e948629bc73 - dff6c756eee5 + - 5e948629bc73 - 9876bda3ec53 - ca88bd28f116 tool_panel_section_label: Proteomics @@ -321,64 +321,64 @@ tools: - name: openms_fidoadapter owner: galaxyp revisions: - - 1595601708ec - - 41859bbdc16e - 890025d6e426 + - 41859bbdc16e + - 1595601708ec - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 2a93a25f0599 - 6634cad7d797 - 5ad0b5bf1deb - 9b7977080f6d + - 2a93a25f0599 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 0bb5056cb775 - - fe4e4587d265 - d6878d27f051 - 05d5e1ddc985 + - fe4e4587d265 + - 0bb5056cb775 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - - 52ba9695e752 - - febd569ad26f - 4af67edd5aef + - febd569ad26f + - 52ba9695e752 + - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: + - b2fc8da99bcc - 92352a475eed - 39e8fde08881 - - b2fc8da99bcc - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - d413dc49d650 - 0efbc235f314 - 9e26f5c770f8 + - d413dc49d650 - d3546bb9fd8e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - - ca1740533b59 - 3720e349ba2a - c28f13cab67a + - 8a04ed1c1d1b + - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter @@ -386,46 +386,46 @@ tools: revisions: - ca799a7246e7 - 382cde407f81 - - a5d785af0ad8 - c55dddc5844a - c427a8628cbe + - a5d785af0ad8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - b5d0905419da - - 8ddb7bab1138 - - adca857b4884 - 39caaa778d2e + - adca857b4884 + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - f817513840a9 + - 8d4db262964c + - 18f93351f8b6 - 34e7afee141d - 1c5f31b8d632 - - 18f93351f8b6 - - 8d4db262964c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 5d9f175dff81 - c69f69d7867a - 986e03d3201e + - 5d9f175dff81 - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 476b5e296979 + - 4204882495f2 - be74a8cd7d66 + - 476b5e296979 - 0e52c85f3b15 - - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -438,35 +438,35 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - c18d8efa4474 - - f5ec766d80cf - 2b2a7551a857 + - f5ec766d80cf - a407b6790342 + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - d0304fb829c0 - - 4e66c4e73909 - 021fdb80f204 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - 8098330f6d91 - 2735db4dd8d9 - ee860980edc6 - bf32e0bcf554 - - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - a2a6e9551046 - - 08488066d588 - 0ced5bc9f4dd + - 08488066d588 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator @@ -480,49 +480,49 @@ tools: - name: openms_openswathconfidencescoring owner: galaxyp revisions: + - e8f64a7dc470 - c1809c05ae8c - 1bf940c18d93 - - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: + - f861ec9fbe59 - 496cf619e311 - 9f505cd4428f - - f861ec9fbe59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - c99d5004b74f - - d4396637b9f5 - 0bddef8d144e + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 89254095cbf6 - 8b814eafce2c - 4bb198c0bd3e - - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f9ed7e074900 - f82b320ceb90 - 05ec9fb05ed1 + - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 18826fb8e5db - 6e8cc5ed2a9b - d31426ef20f6 + - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -537,43 +537,43 @@ tools: owner: galaxyp revisions: - 3d8d4ada5405 - - 6b01678ec2fc - - 5ae104d0da6e - decc397c3b7e + - 5ae104d0da6e + - 6b01678ec2fc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - 5182338d5e7c + - e039cc5c7aed - dd173849c3d8 - - d6aca689dd48 - 539a3a4dcc9e + - d6aca689dd48 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - 16026cdb1330 - - d426affe977c - 8a45fd5a608a + - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - dd71e020e2aa - - 9c70a651a53e - 43b9ed22e8ce + - 9c70a651a53e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - 1b03536aa3c9 - 9020199dba0a - d063e2fe4ba4 - - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator @@ -587,10 +587,10 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - 7f6a1f27553e - c8b225c69a7f - - 5c2a97a234d6 - fb52e95a370c + - 5c2a97a234d6 + - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -616,14 +616,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 1beff3ddce58 - - 943a34df6047 - - a72c48001f7c - - da885ca16cb2 - - 7fdd9119cc4f - 3634c90301af - 3ec27b4cee7c + - 1beff3ddce58 - 07ff622ec007 + - a72c48001f7c + - 943a34df6047 + - 7fdd9119cc4f + - da885ca16cb2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator diff --git a/staging.gvl.org.au/qiime_2.yml b/staging.gvl.org.au/qiime_2.yml index bf015d3f9..52697721b 100644 --- a/staging.gvl.org.au/qiime_2.yml +++ b/staging.gvl.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/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index cbdf887f5..d3e79b944 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 289b7d6b69a4 - 110a346daf36 - - 42201b90e3f4 - - cd5f98911089 - - 2f1d464ebfd2 - e345aadf914f + - 2f1d464ebfd2 + - cd5f98911089 + - 289b7d6b69a4 + - 42201b90e3f4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -20,11 +20,11 @@ tools: owner: iuc revisions: - 0cd2df8af811 - - fcce77c09289 - - c207119ba5f6 - 0345dbaaa79b - - 8501601a118d + - c207119ba5f6 - 42d9087b4789 + - 8501601a118d + - fcce77c09289 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: + - 04db7fd6b238 - 33486216eec0 - 405a212b32ab - - 04db7fd6b238 - - ad5ab22ffe24 - - 421c33b8bf17 - 89eb29319bf4 + - 421c33b8bf17 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - 1d839ead7ad3 - - 7b72fde3d27e - - 7370bb65bad4 - - eb784fa07f80 - fa51dc5e8386 + - 7370bb65bad4 + - 7b72fde3d27e - f6e91108b7b1 + - 1d839ead7ad3 + - 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 + - 8a55d29c8fcf + - c9b77ced9a78 - 1544278c272e - a3e86cd9cac7 - - 3d70c2996730 - d30e36c48c93 - - c9b77ced9a78 - - 8a55d29c8fcf 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 - - 564c33e5c3e3 - e2db212d64ad + - b242deb58952 - a5969aa9347e + - 887cf585cafc + - 564c33e5c3e3 - 7b881f5f5ad5 - - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,9 +104,9 @@ tools: - name: stacks2_procrad owner: iuc revisions: + - 9a171f9a450b - bd5ff77e2036 - e897c74a48bb - - 9a171f9a450b - 8cff84759bf6 - b4bab607eb05 tool_panel_section_label: RAD-seq @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 6dafad990086 + - 887e0991eb24 - 33f0793edf93 + - 6dafad990086 + - 5e10f396979e - 4f65e343ecdf - adc7a7610d4f - - 5e10f396979e - - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,11 +137,11 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - 97575d01f06b - - 17d39bf0a63a - 43e3eeb2e0ec - 4e280b27a831 + - 97575d01f06b - c5d7050e4ad7 + - 17d39bf0a63a - c287418eb288 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: - - d9bf483266a1 + - a819ec3b362d - 9586f08634c0 - cd034465d4a4 - - a819ec3b362d - - 0b8c84a7fdb5 - 09b8edb56d80 + - 0b8c84a7fdb5 + - d9bf483266a1 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: + - a9c34a289493 - 2645575d1bf2 - - 95351dd0fd3f + - 69842dd5aa48 - a4b4bd84f69e + - 95351dd0fd3f - bf0e43ab0416 - - 69842dd5aa48 - - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - - d033e1ccb386 - d1fda11e602f + - bb0475c884ff - 8a35a3bc6752 - 912f904a6e1e - - bb0475c884ff + - d033e1ccb386 + - cfb504394ae1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d504d945a655 - 95286af4139b - d1fad35bdb4a + - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 9aba65372..fdbdf0f03 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,26 +2,26 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 7acb00fc980a - 2d4e3aff9dc7 - - 31f8063eedea - cf01dd6c6b1f + - 7acb00fc980a + - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: + - 32e542c2a773 + - 7a5a2d28c539 - 703a2cb3fb38 - 125d20cb23d7 - - 7a5a2d28c539 - - 32e542c2a773 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 @@ -70,42 +70,71 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - e66b9b5b8580 + - ad5d061fbdf2 + - f648e5180e40 + tool_panel_section_label: RNA-seq + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cuffcompare + owner: devteam + revisions: + - ad5d061fbdf2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - d080005cffe1 - e04dbae2abe0 + - d080005cffe1 + - 6926716bbfb5 + tool_panel_section_label: RNA-seq + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cufflinks + owner: devteam + revisions: + - 6926716bbfb5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - 86285ddd4512 - cf747d1bd79a + - 22cf48ad7b16 - 6a6717a5f421 + - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - 86285ddd4512 + - 22cf48ad7b16 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - 6cbfede05833 + - 28b94cfbfdb9 - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu +- name: cuffnorm + owner: devteam + revisions: + - 28b94cfbfdb9 + tool_panel_section_label: RNA-seq + tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant owner: devteam revisions: - 679d93c99757 + - 93148c05136f + tool_panel_section_label: RNA-seq + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cuffquant + owner: devteam + revisions: + - 93148c05136f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cummerbund @@ -123,10 +152,10 @@ tools: - name: describe_samples owner: iuc revisions: - - e3b16fd7dd08 - - 3b36efd62b3e - 0693ccd171c4 - 8f0181aacb7a + - e3b16fd7dd08 + - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -138,13 +167,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 0696db066a5b - - d027d1f4984e - 24a09ca67621 - - 9a882d108833 - - 6a3a025714d3 - cd9874cb9019 + - 0696db066a5b + - 6a3a025714d3 + - 9a882d108833 - 8fe98f7094de + - d027d1f4984e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -156,11 +185,11 @@ tools: - name: dexseq owner: iuc revisions: - - b47c006d90c5 - - 62adf13b86ea - 2872c633f07e - - 9a7c5b6d8f1e - df929f257179 + - 9a7c5b6d8f1e + - b47c006d90c5 + - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -172,18 +201,18 @@ tools: - name: edger owner: iuc revisions: - - df0c8d0a5992 - 0cb907a2a810 - - 6e53e565fc6a + - 5bf899c13979 - 9bdff28ae1b1 - - ae2aad0a6d50 - - f2843df56434 - a8305cf0c951 + - df0c8d0a5992 + - 070900306913 - 3d89af8a44f0 - - 334ce9b1bac5 - 555659de7321 - - 070900306913 - - 5bf899c13979 + - 6e53e565fc6a + - ae2aad0a6d50 + - 334ce9b1bac5 + - f2843df56434 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -195,8 +224,8 @@ tools: - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -214,17 +243,17 @@ tools: - name: featurecounts owner: iuc revisions: - - f3a5f075498f - - a37612abf7f9 - - a56fbe2d6ba7 - - 38b6d12edc68 + - 7db9d3ea71c9 + - 90d16db017d7 - af814359d244 - e6a2a912677a - - 90d16db017d7 - - 6f66ae7c5f7a - ea04b737afa0 + - f3a5f075498f + - a37612abf7f9 + - 38b6d12edc68 - f9d49f5cb597 - - 7db9d3ea71c9 + - a56fbe2d6ba7 + - 6f66ae7c5f7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -254,15 +283,15 @@ tools: - name: gffcompare owner: iuc revisions: - - f99dd58de04f - - 0f710191a66d + - 3c5e024a18cf - 3c97c841a443 + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare owner: iuc revisions: - - f99dd58de04f + - 3c5e024a18cf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -274,13 +303,13 @@ tools: - name: hisat2 owner: iuc revisions: - - f4af63aaf57a - - 26371a1df031 - - 3fb01a8c902d - - 6c19daec423d - 6ab42baa56e9 - d4b55e2beb12 + - 6c19daec423d + - 26371a1df031 + - 3fb01a8c902d - a86e80d3c09c + - f4af63aaf57a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -298,9 +327,9 @@ tools: - name: htseq_count owner: lparsons revisions: - - 4418229c501e - 67b0b160903a - 916cb26bd9d3 + - 4418229c501e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -318,11 +347,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 5ae5c312d718 - - ce5d418183c5 - 87c11c05d238 - - 1c75aa5de15e + - 5ae5c312d718 - 01247aaf0a10 + - 1c75aa5de15e + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -335,9 +364,9 @@ tools: owner: iuc revisions: - 40985510cd98 + - c971db6f0fe5 - 4f9c4e6566e5 - 10c98fab6c5a - - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -349,14 +378,14 @@ tools: - name: limma_voom owner: iuc revisions: - - 0921444c832d - 58c35179ebf0 - - e827f9aae031 - - 97e06a4c7c75 - - 119b069fc845 + - 708348a17fa1 - d6f5fa4ee473 + - 119b069fc845 + - 97e06a4c7c75 - 32511f586472 - - 708348a17fa1 + - 0921444c832d + - e827f9aae031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -374,8 +403,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -405,8 +434,8 @@ 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 @@ -424,21 +453,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 5ec75f5dae3c - - e132e7d02a3e + - c772497b2c32 - 79de45b5069b - - 4df95e2d7f61 + - c7c55b694974 + - b0f2be869d6d - 7ed2edc1337f + - e132e7d02a3e + - 4014de1b6daf + - 0a563fd2f22e + - 5ec75f5dae3c + - 3ea5a2a63fa2 - 99b17b74a8cd - b9e04854e2bb - 980d2a2e1180 - - 4014de1b6daf - - c7c55b694974 - - 3ea5a2a63fa2 - - b0f2be869d6d - 4074fc1940e2 - - c772497b2c32 - - 0a563fd2f22e + - 4df95e2d7f61 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -462,14 +491,14 @@ tools: - name: salmon owner: bgruening revisions: - - ebab418107f5 - - e3d32471da11 - - 15cd64d7c58b - cc05793bb896 + - e3d32471da11 + - 49121db48873 - f4d5237a84f6 - 2c0ca397d302 - 53e9709776a0 - - 49121db48873 + - ebab418107f5 + - 15cd64d7c58b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -481,9 +510,9 @@ tools: - name: seurat owner: iuc revisions: - - c0fd285eb553 - - 56242ff81c84 - 8c28affc7c48 + - 56242ff81c84 + - c0fd285eb553 - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -491,13 +520,13 @@ tools: owner: iuc revisions: - 258d696dbd7e - - 76d290331481 - - 914cfcba0ec8 - - cbf488da3b2c - ae618321f34a - - 1ebd14235b92 + - cbf488da3b2c + - 914cfcba0ec8 - cef79931dda5 + - 76d290331481 - dd4df992d93d + - 1ebd14235b92 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -533,10 +562,10 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 - 0db979fead3a - - ffd1300599a1 - c6334cb383ff + - d0d4cef4f967 + - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -548,10 +577,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - 74217fbfba4d - ba3720d7e68b - - bcc5f03f1900 + - 74217fbfba4d - d6a479fd4281 + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -578,9 +607,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - 3f4094b6a565 - 9ff3765e7172 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -592,9 +621,9 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e - 4687ecf0eb2d - 34a018cbee9c + - 870ac06dff8e - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -609,9 +638,9 @@ tools: revisions: - 05ab8d5e04a2 - 5192f657f305 - - c5fbddcac63a - 65e7dea767ea - 33406f5a445c + - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -623,10 +652,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - a35cba31d904 - e406ac71165d - 1fdb25a8384d - 6f0fb35b799c + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -639,8 +668,8 @@ tools: owner: iuc revisions: - 7c7fbf13aadd - - c2c039e421af - 964b7efe2639 + - c2c039e421af - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -653,10 +682,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - eafea3083352 - - 24e94d84adc9 - 047c22569787 + - 24e94d84adc9 - 1d689e4e1caf + - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -668,10 +697,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: + - 9871104ea630 - 3a4ac03d1266 - - 04bb8bb7c198 - 1812dbc5bb7b - - 9871104ea630 + - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -695,15 +724,15 @@ tools: - name: trinity owner: iuc revisions: - - d84caa5a98ad - c9cfec002f71 + - 48636f857c4b + - 9fa24d5aac68 + - d84caa5a98ad - 32b86cd8eb50 - d2bc35f3d1c5 - cee61b3fcf78 - - 8f1c3df4dd49 - db1f362cca3e - - 48636f857c4b - - 9fa24d5aac68 + - 8f1c3df4dd49 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -716,9 +745,9 @@ tools: owner: iuc revisions: - 9e61bc67866f - - 4383070d29ed - 6fd16fad465d - 2b093007fab9 + - 4383070d29ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index 636b5a8af..13cadf889 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 27e16a30667a - 080fd5739bb4 - 1a052c827e88 + - 27e16a30667a - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index c5c1fde5c..e9471988f 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 88eedb4abea0 - - 3c661e57a88f - 10184eaa85fc + - 3c661e57a88f + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,9 +16,9 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - - 993b19f20c76 - 1dfd95ee241e + - 993b19f20c76 + - cb20f99fd45b - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 30a201c9c310 + - e7fd6754d093 - 19ece8afbaab + - 30a201c9c310 - 5f8e69cc4c6e - - e7fd6754d093 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 @@ -123,15 +123,15 @@ 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: - - cf1ffd88f895 - 0e60e2dd20af + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -163,10 +163,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - - 9149ad20699a - 6856f8a01905 - 46c6639921f1 + - 12749212f61b + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -179,9 +179,9 @@ tools: owner: devteam revisions: - 26b4f9f98aca - - 06dc50b7b711 - - 92ec40abcdcf - 33208952b99d + - 92ec40abcdcf + - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -205,10 +205,10 @@ tools: - name: samtools_fastx owner: iuc revisions: + - 720217c23995 + - a8d69aee190e - b3d99709fe1a - b906586a6596 - - a8d69aee190e - - 720217c23995 - 66e23b11feae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -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: - - fe34990e5ce7 + - 22970df7a40e - db17d5321bad + - fe34990e5ce7 - cc61ade70eb8 - fefd89ab563c - - 22970df7a40e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -245,10 +245,10 @@ tools: owner: devteam revisions: - 811fc2d75ad4 + - 7a6034296ae9 - 88b8c2916784 - - 7def34e6cf4d - fa5d3e61e429 - - 7a6034296ae9 + - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -267,10 +267,10 @@ tools: - name: samtools_merge owner: iuc revisions: - - 36677f429310 + - 740ce0a18f0d - cae2794d2deb - b40e2d865d52 - - 740ce0a18f0d + - 36677f429310 - 65a38e8c8e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -278,10 +278,10 @@ tools: owner: devteam revisions: - 9da0311ab1dd - - 329deb17a9f7 - 583abf29fc8e - - b61f5d6a7f25 + - 329deb17a9f7 - fa7ad9b89f4a + - b61f5d6a7f25 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c - db000c6007a0 - 30388d878f81 - 85e38b31e8b3 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -327,9 +327,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: + - 344fc91e1bfd - b8beef827165 - a4a10c7924d1 - - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - cab3f8d35989 + - d54a4df48867 - 6c2c1836728b - e613c1ad4c4c - - d54a4df48867 + - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,11 +356,11 @@ tools: - name: samtools_split owner: devteam revisions: - - bcedabb53ddf - - 135c85f4cfaf - - bd850490c7f1 - b7f7826ef1cd + - 135c85f4cfaf - 5d9ae78f34d3 + - bd850490c7f1 + - bcedabb53ddf - 818030fa6bbf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - 24c5d43cb545 - 145f6d74ff5e - - 1cc79f49b8d5 + - 5a08c09b9311 - 3a0efe14891f - 541082d03bef - - 5a08c09b9311 + - 24c5d43cb545 + - 1cc79f49b8d5 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: - - b72793637686 - - 5826298f6a73 + - 32dc5f781059 - 2dce91e11ca7 + - 5826298f6a73 - 350bbc5c2ffd - - 32dc5f781059 - 6be888be75f9 - - bf328cec6a42 - - c370440f901e - b01db2684fa5 - 0dbf49c414ae + - c370440f901e + - b72793637686 + - bf328cec6a42 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 4c2cfd112..356aa6aa8 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,13 +2,13 @@ tools: - name: ena_upload owner: iuc revisions: - - 59bb6d34fca6 - - ea5e944f447d - - d147d6455873 - a62c4a11a67d - 6f6537780379 + - 4aab5ae907b6 - 5cb6146337d8 + - d147d6455873 - 480d9e9d156b - - 4aab5ae907b6 + - 59bb6d34fca6 + - ea5e944f447d 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 dec52b62a..22e057c13 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 - - ecb9ea6269ee - c9944a2600f1 - - e32b215b7c04 + - ecb9ea6269ee - e4c01dcece8b + - e32b215b7c04 + - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: + - c0b037b12765 - cfaf5a405371 - - 707023fa62fe - e1c3c2f2a834 - - c0b037b12765 + - 707023fa62fe tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 55e35e9203cf - fb9e030ffae4 - 32e547223c9e - - 93dd15e13e6a + - cfc3f5a57dc6 - d330b3082107 + - 55e35e9203cf - 00712416fdaa - - cfc3f5a57dc6 + - 93dd15e13e6a 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: - - 038e32885fec - - 0bf7fddf90c7 + - 688357ad5e61 - 39e945f0b2c1 - - ee98d611afc6 - b9fac48532eb - - 688357ad5e61 + - 0bf7fddf90c7 - 6f0d0c784f09 + - ee98d611afc6 + - 038e32885fec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -63,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - b85871dd69f9 - - 43cb7b5a6fe7 - d4af736e7b83 - - ed4996a16f7f - - 7e8c677a7b71 - 9bd945a03d7b + - 43cb7b5a6fe7 + - b85871dd69f9 - 3d748954434b + - 7e8c677a7b71 + - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -81,16 +81,16 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: - - a4774b7b2e85 - - 2e8022f1923c - fe75d2414dc0 + - 2e8022f1923c + - a4774b7b2e85 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 769d815e4b0d - 4fff5a293013 + - 769d815e4b0d - 0e70b2dfe4be - 02b1fe7aed76 tool_panel_section_label: Single-cell @@ -99,18 +99,18 @@ tools: owner: iuc revisions: - aa4a6f0916b4 - - c29e7bb492bf - - 344c2af50552 - a90f8efe08b4 + - 344c2af50552 + - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 050cf43887d3 - b13d3e4c48e1 - c32347702e12 - 5b7c81b35b89 + - 050cf43887d3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d @@ -155,11 +155,11 @@ tools: - name: dropletutils owner: iuc revisions: + - a9caad671439 - 2c1200fba922 - cdf4443d5625 - - a9caad671439 - - 8855361fcfc5 - cfe1e6c28d95 + - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -209,8 +209,8 @@ tools: - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - 163fd744e235 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint @@ -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 @@ -265,22 +265,22 @@ tools: - 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: - - e03780179ee5 - 3ee5332bf57c + - e03780179ee5 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 @@ -300,22 +300,22 @@ tools: - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2b4d6a8dab36 - 2786a931cad2 + - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - 0410b6aada45 - ffc33339cd3e + - 0410b6aada45 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -328,15 +328,15 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 7f7c6ead2d0d - 409396ea5cf0 + - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - 51e40e9b6c3c - e4f8fceab96a + - 51e40e9b6c3c 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: - - ed900cd4a0a9 - 1511a8ebe906 + - ed900cd4a0a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -377,8 +377,8 @@ tools: - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 6326cd29c1c3 - 11f39d7f6c64 + - 6326cd29c1c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl @@ -391,15 +391,15 @@ 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 @@ -424,8 +424,8 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - f36828ebdc54 - 27fe5cd1729c + - f36828ebdc54 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations @@ -439,11 +439,11 @@ tools: owner: iuc revisions: - 7784821452ac - - eeab712b0b99 - 4b0adaa31c95 - - 59be31ac9dc3 - 0f1aaff9b22d + - eeab712b0b99 - e98619de2776 + - 59be31ac9dc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -455,8 +455,8 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -489,11 +489,11 @@ tools: - name: raceid_clustering owner: iuc revisions: + - 7e014059a88d + - 0bff0ee0683a - c4f39bf4a068 - - a4b734cd253b - f911a64454fb - - 0bff0ee0683a - - 7e014059a88d + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -520,8 +520,8 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - f3eb2291da05 + - 37a47c4fd84d - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -534,9 +534,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: + - a6821f856a1e - 69018f285aa3 - df8e4e54d367 - - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -548,11 +548,11 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - 72979cac22b2 - e93b008c637a - 44b935f2271b - - c92d0f9338c5 - 2af7c5086a96 + - 72979cac22b2 + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -576,130 +576,135 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 6acb08931836 - - 4d8f983cd751 + - edec35114f72 - 6f83f8fd381f - - aaa5da8e73a9 - f9353ee6a0d4 + - b2df381a6004 + - cb43c5d3acd3 + - aaa5da8e73a9 - 77b91b9bdf52 + - 4d8f983cd751 + - 6acb08931836 - 38db3fef7aad - - b2df381a6004 - - edec35114f72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 38db3fef7aad + - cb43c5d3acd3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - a97abb8cd15b + - d636ce5cde16 - 3c86f71498bc - 277313130da5 - - 8cb783c81905 + - a97abb8cd15b - b409c2486353 - 72a6bebab2a5 - - d636ce5cde16 + - 8cb783c81905 - a03ff8633507 + - fc0321c000a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 8cb783c81905 + - fc0321c000a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 18262103fa61 + - 4338bf96809e + - 5c3ebe2adc77 + - 6bd82ed14acd + - c5d3684f7c4c - 6c145a6868cc - c0a80a16560f - - f54f0f0598ad - - 3081ff5c84a3 - 5e9171dc8244 - - 6bd82ed14acd - - c5d3684f7c4c - - 5c3ebe2adc77 - - d1cd8c147809 - cc0deb593fc8 + - 3081ff5c84a3 + - f54f0f0598ad + - 18262103fa61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - d1cd8c147809 + - 4338bf96809e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: + - 3bcd5445cd7a + - 56c0d4acef02 + - 146ae5d70b47 + - 9f354c7c8c92 - a407e7f8bdc1 - ab55fe8030b6 - - 9f354c7c8c92 - d844935c906c - - 56c0d4acef02 - - 7b9fafe32c86 - c9cb76cf8d6c - - 3bcd5445cd7a + - 7b9fafe32c86 - 94c19fb1281c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 56c0d4acef02 + - 146ae5d70b47 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 95777145cb92 - - 7647e5cd1b8b - 6adf98e782f3 - - f7446fd8d5e7 - - 0185bd174ea0 - 6f5349dd5c49 - dbbe1ea8ecb1 - - 9b0cdb8cf6be - - aa0c474463c2 + - 0185bd174ea0 + - 95777145cb92 - 1072ce66b426 + - aa0c474463c2 + - 7647e5cd1b8b + - f7446fd8d5e7 + - 40812a65a78b + - 9b0cdb8cf6be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 2dfb2227a16c + - 40812a65a78b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - a39040ae0a38 - - c65fce500915 - - d18e7a6e5cd4 - 73ab2ac53d06 - - 458e8f43a775 - - 9fb627495ec2 + - fe8f16c594ec - 215733a383f2 + - c65fce500915 - f2f6c703da06 + - d18e7a6e5cd4 - bf2017df9837 + - 458e8f43a775 + - 9fb627495ec2 + - a39040ae0a38 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 9fb627495ec2 + - fe8f16c594ec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - b834074a9aff - 8f333f90d8d6 + - b834074a9aff - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -712,9 +717,9 @@ tools: - name: scater_filter owner: iuc revisions: + - 652923ce664f - 7a365ec81b52 - b7ea9f09c02f - - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -732,9 +737,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: + - 2e41b35b5bdd - ef4c80837bc5 - 81e5bdff4853 - - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -752,9 +757,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 46fc6751d746 - - 9e5c0bb18d08 - c99ba278dfa9 + - 9e5c0bb18d08 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -977,13 +982,14 @@ tools: owner: iuc revisions: - d1b34ac42b8f + - d0f56ac6bb60 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: sinto_fragments owner: iuc revisions: - - 03a04f48b922 - 29e6bfb2cf49 + - 03a04f48b922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image @@ -995,8 +1001,8 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - afb90d3485df - 8f8bef61fd0b + - afb90d3485df tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif @@ -1016,8 +1022,8 @@ 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 diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index df0f80463..ff0ae7d6c 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: + - 2f3c6f2dcf39 - 562f3c677828 - - 746e8e4bf929 - 4c07ddedc198 - 419027d822d6 - - 2f3c6f2dcf39 + - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: + - 6c29c7e347e8 - cb1c59d69557 - 7a15159140d1 - - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 9c3e1d3235c8 - - aef56d0e7a61 - - 4c4ec859c31a + - b1eda492f063 - 7442b94d6a1e - 840f29aad145 - - b1eda492f063 + - aef56d0e7a61 + - 9c3e1d3235c8 + - 4c4ec859c31a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: + - 07843f917990 + - d0352e8b4c10 - 375bbd555f4a - 30d21a6041f6 - 9fda0b82f419 - - d0352e8b4c10 - - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - 8b1b2b91f8d0 + - 4cc980df6265 - cd02bf168d23 - 2c58b83c9bad - - 4cc980df6265 - 7ae443e6217d - - 8b1b2b91f8d0 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: + - ad7e0b4291ee - 4bbaf77573ef - bb9fc9d46ea4 - e10e776f2109 - 1dd433d2c92c - 7dd3fb35904f - - 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 decd70463..2a7697187 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -27,22 +27,22 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - f18f67056946 - 6c6d26ff01ff + - f18f67056946 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 464b9305180e - - 6e8d94597139 - - be25c075ed54 - 6595517c2dd8 + - 9cd341095afd - aff5135563c6 - - 02026300aa45 + - 464b9305180e - 13b6f0007d9e - - 9cd341095afd + - 02026300aa45 + - 6e8d94597139 - 626658afe4cb + - be25c075ed54 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: + - 34d29339abab + - 9cc411a62277 + - 90f657745fea - 557ec8d7087d - 37cde8134c6a - - 90f657745fea - - 9cc411a62277 - - 34d29339abab tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,30 +107,30 @@ tools: - name: merge_cols owner: devteam revisions: + - dd40b1e9eebe - ae7843d06f8f - f2aac0c5c60d - - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 2e8f945f7285 - - 1ea4e668bf73 - - cf4397560712 - cf34c344508d - - 33d61c89fb8d - - 83069b38aa85 - 623f3eb7aa48 + - 83069b38aa85 + - 1ea4e668bf73 + - cf4397560712 - 3a6b78c39dca + - 2e8f945f7285 + - 33d61c89fb8d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - ae8c4b2488e7 - - 503bcd6ebe4b - 399da6b5ec21 + - 503bcd6ebe4b + - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -143,29 +143,29 @@ tools: owner: iuc revisions: - f768f6183386 - - b722161a845a - c4d18aa4ec4a + - b722161a845a - bce29ec10b78 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 3bf5661c0280 - 60ff16842fcd + - 3bf5661c0280 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - d698c222f354 - - 74a8bef53a00 - - 0a8c6b61f0f4 - - f46f0e4f75c4 - 9ff72e942410 + - f46f0e4f75c4 + - 0a8c6b61f0f4 + - d698c222f354 - ddf54b12c295 - - 86755160afbf + - 74a8bef53a00 - a6f147a050a2 + - 86755160afbf - fbf99087e067 - 12615d397df7 tool_panel_section_label: Text Manipulation diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index e1eea58eb..5335dc472 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -14,9 +14,9 @@ tools: - name: breseq owner: iuc revisions: - - 82fb5e3bb93e - 85c57cc9b558 - 0d18a3ba2d1c + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -34,57 +34,58 @@ tools: - name: freebayes owner: devteam revisions: - - a5937157062f + - 57def2d7c093 - 156b60c1530f - - 04fa42777df9 + - a5937157062f - ef2c525bd8cd - - 57def2d7c093 + - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - 791f73caa0c8 - - 09d6e4693887 - 435b157bed6d - e61c9ac190ad + - 09d6e4693887 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - e1461b5c52a0 - - 3b4b2121842f - - 074d44697036 - 65432c3abf6c - - 03627f24605f - - dfadc322b065 + - 074d44697036 - 4805fe3d8fda + - dfadc322b065 + - 03627f24605f + - e1461b5c52a0 + - 3b4b2121842f + - b11e8e9c23bf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 701d134358ad - 7dfca164d2e3 + - 701d134358ad - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - c27549b9aa1f - 971e07ca4456 - - f4473557ffc7 - 426d707dfc47 + - f4473557ffc7 + - c27549b9aa1f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - aa35ee7f3ab2 - cdaab621d454 - dbd9f2db9ed8 + - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -103,9 +104,9 @@ tools: - name: snippy owner: iuc revisions: - - d220115f882b - fa016f1eea1a - 9bccc8404a3c + - d220115f882b - c9a8ef2aa380 - 5bbf9eada9c2 tool_panel_section_label: Variant Calling @@ -152,17 +153,17 @@ tools: - ee4a90760848 - e7aff4a85df5 - 3b1e7c170b10 - - 40f0591deda0 - 32f14a2723ec + - 40f0591deda0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - 4934c0ac6197 - 02d81b994ef5 - 9793bc5d741b - 42818629ec4c - - 4934c0ac6197 - adc0645b945c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 423fab309..e30a52ca6 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -3,13 +3,13 @@ tools: owner: iuc revisions: - 6a88248893c4 + - b7ea370b8f5d - 8a2e296c07ef + - 265fe0f9ea64 - 95815a0bb307 - 2c372041ed8c - - b7ea370b8f5d - ebe5fc018e72 - e075b1be5abb - - 265fe0f9ea64 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -22,12 +22,12 @@ tools: owner: iuc revisions: - 1001172b5089 + - 0fba2c15b40d - c37b684e7f4e - - 22637b1a55bf - 544cb432072b - - b03984136ce4 - - 0fba2c15b40d - 21687e35f066 + - b03984136ce4 + - 22637b1a55bf 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: - - 8ca3647c90fd - 3a7084316a6e - - 143796b504eb - - 01d6b7d6365e + - 8ca3647c90fd - ccb83bf54de0 - - 8408bffd5616 - - 8627b2b383b4 - bf1f4994f104 - 0238f68ad641 + - 8627b2b383b4 + - 8408bffd5616 + - 143796b504eb + - 01d6b7d6365e 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: - - 62ca6da715bf - - d144af39073a - - 9b5abbf50d23 - - abd489215f73 - 03e0645395d2 + - d144af39073a - 81426b3cf18b - - f430a1ec7ee4 + - abd489215f73 - 6b6c992d3a14 + - 9b5abbf50d23 + - 62ca6da715bf + - f430a1ec7ee4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - d3081540d175 - - 95c6f3f4c77f - 1829900b5dcd - - d37e313a41be - - 2363ef414c9b - - 8aa352093d73 - e522022137f6 + - 8aa352093d73 + - 2363ef414c9b + - 95c6f3f4c77f + - d37e313a41be - 1171446da5db + - d3081540d175 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 012656fd329f + - 348cd212dbad - 09f37afb3621 - - 1137ce8efc1e - - 9b29129fb491 + - 012656fd329f - b14ff40958cb - - 348cd212dbad - - d58d2e8c7a57 - 92c0aff8b53e + - d58d2e8c7a57 + - 9b29129fb491 + - 1137ce8efc1e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - 7291189e98b4 + - cfd81f17580b - 1f2183a23823 + - 367ba501b6eb + - ecc9192912b8 + - 7291189e98b4 - 55c0e906c14c - - cfd81f17580b - de68c11034f6 - - ecc9192912b8 - - 367ba501b6eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,13 +134,13 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 7cbf3c66d4ad - - 64a8f7dae3ad - 6c790a091c7c - - e6f4badbe6f3 + - d237eaef451f + - 7cbf3c66d4ad - ae68ceb4cca3 + - e6f4badbe6f3 + - 64a8f7dae3ad - 039ea3f1dea9 - - d237eaef451f 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: - - 963a3635b2e1 - - 6ea7170a016d - 5d6653c989cb - 277719af4dd7 - - cdb7b4927742 - e7452697afd9 + - 6ea7170a016d + - cdb7b4927742 - 33bd9301568c - 46fcafba49ec + - 963a3635b2e1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 26d97cdd5410 - - 91c1e57d5c7f - - a1213a0b7b66 - - 7b4454382d39 - b7f0f59baa7e - - 501bfb078342 - 5a321fab1fe4 + - 91c1e57d5c7f + - 501bfb078342 + - 7b4454382d39 + - 26d97cdd5410 - a29a2f40b665 + - a1213a0b7b66 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: + - d7d1663559e9 + - c803c34361e0 - 15da1ddcfeff - - 97d19c008d15 - 39bca000353d - - c803c34361e0 - - 5f27e814a119 + - 81e4014fa809 - 709dd8291b83 + - 97d19c008d15 + - 5f27e814a119 - 768d04526638 - - 81e4014fa809 - - d7d1663559e9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -210,14 +210,14 @@ tools: - name: bcftools_merge owner: iuc revisions: - - 5b006286a458 - - b931e65638b8 + - b1eba148b35b - 2215287d5cc9 + - 5b006286a458 + - 7ba36babba2d - 85ee7e6c4204 - - 86296490704e + - b931e65638b8 - b84fda8ebef0 - - 7ba36babba2d - - b1eba148b35b + - 86296490704e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -229,15 +229,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - f506df85c652 - cf06b44624c7 - - 31ea13dfe5e6 - 56556e1267de + - 37757ffb4c5f - 9c711df3258d - - 4e1d23e5c691 + - f506df85c652 + - 31ea13dfe5e6 - 5660b21a0dbd - ce9396ddcb2b - - 37757ffb4c5f + - 4e1d23e5c691 - 0a5dcc9a8ec2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -250,13 +250,13 @@ tools: - name: bcftools_norm owner: iuc revisions: - - a404f786a94c - - 271965b55437 - - 19905c025d2a - - 1ca7418e46ee - 021693fdadaa - 6deb4d549bc9 - 48291658fdf6 + - 271965b55437 + - 19905c025d2a + - a404f786a94c + - 1ca7418e46ee tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 97e8145d7e30 - - 3f6fadf8b8ff - - c450406f722b + - dadbd61dc4cf - f7879f1e77f9 - - 69d8b7567281 - 71c78e0eea52 + - 97e8145d7e30 - 5ad5d4243987 - - dadbd61dc4cf + - c450406f722b + - 69d8b7567281 + - 3f6fadf8b8ff 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: - - 0fe007201caf + - 283911fe7e1a + - 2514e684f8a3 + - 6cf13a657cf6 - d31a2e310a52 + - 0fe007201caf - 79f7a1acc2cd - cc7f9a4e186b - - 6cf13a657cf6 - - 283911fe7e1a - 52f9e4a660e3 - - 2514e684f8a3 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: - - 6963a6841d22 - - 230e424bde67 - - 026a989b7cee + - 80e6e399ccd0 + - 0a62420cb9cd - a12844ca467a + - 230e424bde67 - 75ddd081f608 + - 026a989b7cee - 1411bef27a75 - - 80e6e399ccd0 - - 0a62420cb9cd + - 6963a6841d22 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - bca7ce81688f - - b10d1510fa84 - - 5acfca5a76af + - ba20340426fe - 5808f77b2bb6 + - b10d1510fa84 + - 444e6a756c35 + - bca7ce81688f - e493702b19eb - 450a265f92e8 - - 444e6a756c35 - - ba20340426fe + - 5acfca5a76af tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -344,14 +344,14 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - dd72ff87cfd0 - 157ffcdd3fa7 - d52b8947b269 - - f2482aa4862e - c43399f161f4 - 12152af85697 - - 4d236c696844 + - f2482aa4862e - 68fec03a63b7 + - dd72ff87cfd0 + - 4d236c696844 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 - - 0e5d11004815 - - 8f2fc0ab30fb - cbe39e530cbf + - 75becf493cd3 - 8dbce095986c + - 0e5d11004815 - 6f8e223f78f3 - 29ba253e2e05 + - 8f2fc0ab30fb 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: - - 3ff5654b4e7d + - 8f5962c43868 + - a367a15c6de5 + - e0a856def0b0 - a8630d4fbaf8 - f544f71adb73 - - e0a856def0b0 - - 8f5962c43868 - 9708e3086f32 + - 3ff5654b4e7d - 88bb477f45f7 - - a367a15c6de5 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: - - 34dc0bbc7e93 - - 5c9729d54721 + - 8b260d252ff4 - 31c096c6b156 - 6ce175385dd9 - 4ed46189d6c6 - - 03e30f06f15f - 96d0145c041a - - 8b260d252ff4 + - 5c9729d54721 + - 34dc0bbc7e93 + - 03e30f06f15f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -420,13 +420,13 @@ tools: owner: iuc revisions: - 11af7fce71cf - - a730269af659 - - 09f5e45a8212 + - 40daf124be88 - 2c4941386820 - - 46eb13bc2c73 + - 09f5e45a8212 - a1aad8b559c6 - 681bdf1e22ff - - 40daf124be88 + - a730269af659 + - 46eb13bc2c73 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: - - 743cd1472aeb + - f272b8ba0983 - 8cb121b6a1d2 - - 3897eaadfbff - - 882b2e649602 - 6cbb9c47795c + - 3897eaadfbff - b74b8cbfc1f1 + - 743cd1472aeb - 12038f59c0f4 + - 882b2e649602 - 0594ea1417c8 - - f272b8ba0983 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 - - adee7e8b746f - dba06328556a - - cced6715f926 - - 238f78e38a8b - 18cf9de1cf73 + - eccb508bb678 - a9826db86d9a + - 238f78e38a8b + - adee7e8b746f + - cced6715f926 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: - - 3ce32adc55b2 - - e53501abf992 - e0ad88dec40d - - c9935c9e8a24 - - fdec14f69010 - 9f36041495a3 - - 31a1b89eab9b + - c9935c9e8a24 + - 3ce32adc55b2 - f64e7ca2efd2 + - 31a1b89eab9b + - e53501abf992 + - fdec14f69010 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: + - d68c43202172 + - 4db0695a6fc7 - d43eb39b989e - fd3539749127 - - d68c43202172 - - b7be725976b6 - 79489d5685dd - - 4db0695a6fc7 - - 3b7b1fe7b937 - 2331ddcbd5aa + - 3b7b1fe7b937 + - b7be725976b6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,10 +514,10 @@ tools: - name: bcftools_roh owner: iuc revisions: + - 58091e1be01b - 6a636d58dfc2 - - 1a989b4110da - 78cd8b69da4c - - 58091e1be01b + - 1a989b4110da - b0d39ef600a7 - 5296d26b0373 - 1ccf0e7fb4f6 @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: - - bf8325a07ce7 - - baa8823f8073 - - e8af591435d1 - - 4d3ce9dc1525 - - b641062a2587 - - b17394940c7a - '388983871932' - 591cc8518033 + - b641062a2587 + - b17394940c7a + - e8af591435d1 + - bf8325a07ce7 + - 4d3ce9dc1525 + - 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 - - 38d75661c235 - - c2ab91a0d506 - - e6b5cbbf449b - d1f8f55f564d - - 3a233c8eb814 - - 3ca3de4e5291 - 59fa8742285e + - 3ca3de4e5291 + - 3a233c8eb814 + - c2ab91a0d506 + - 38d75661c235 + - e6b5cbbf449b + - 1a2ef636f48e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -577,8 +577,8 @@ tools: - name: vcfaddinfo owner: devteam revisions: - - 6ea73d6151ec - afc0ba768690 + - 6ea73d6151ec tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives @@ -619,8 +619,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -633,8 +633,8 @@ tools: - name: vcfcommonsamples owner: devteam revisions: - - 254f285dbaaa - f1852ecef841 + - 254f285dbaaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance @@ -647,10 +647,9 @@ tools: - name: vcffilter owner: devteam revisions: + - 6b935ab36d7b - eae7c08ebb6f - 4bdc111b2470 - - 6b935ab36d7b - - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -684,8 +683,8 @@ tools: - name: vcfhethom owner: devteam revisions: - - 8254e0fe7358 - b07ef36cf7e6 + - 8254e0fe7358 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign @@ -705,23 +704,22 @@ tools: - name: vcfrandomsample owner: devteam revisions: - - 12b570dd0bc5 - 6257ee3b50d3 + - 12b570dd0bc5 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: - - f0580efedada - - ee60203e68d9 - 5b7120c66efc + - ee60203e68d9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/staging.gvl.org.au/viral_tools.yml b/staging.gvl.org.au/viral_tools.yml index 06370d956..15250eab7 100644 --- a/staging.gvl.org.au/viral_tools.yml +++ b/staging.gvl.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 18aad692772a - 9def47f3c1e4 + - 18aad692772a tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 9cbcfa975..04af652dc 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 78c75f134c16 - - c2ef298da409 - - 6e9aea89e388 - 3f3e247c053d + - 6e9aea89e388 + - 78c75f134c16 - 4efdca267d51 + - c2ef298da409 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -33,23 +33,23 @@ tools: - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - 3e1f6f6d557e - a79ee60b6926 - - fe3ca740a485 - - f29602ae449e - - cd2480f35935 - 4f2967b27e67 + - f29602ae449e + - fe3ca740a485 + - 3e1f6f6d557e + - 133f36c29579 - 44018dd6b447 - - b5d8e5475247 - 1aae04680c4b - - 133f36c29579 + - b5d8e5475247 + - cd2480f35935 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,33 +62,35 @@ tools: - name: augustus_training owner: bgruening revisions: - - 6519ebe25019 - dc027fa56d55 + - 6519ebe25019 + - f1e653756174 - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 + - bd0e53f3a891 - 28433faa6e42 + - 09855551d713 - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - da5f1924bb2e - - 728dacaf08a9 - 92eee5f31117 + - da5f1924bb2e - d77802fe76f7 + - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 8fd427007e93 - fe48aa4ccd5e + - 8fd427007e93 - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -115,16 +117,16 @@ tools: owner: bgruening revisions: - 7ccc6234b54e - - 8e9e228c54c4 - 1ac12c0cc7a0 + - 8e9e228c54c4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - 63662ae295d6 - - 9d1fbff733cf - d9c3016f7283 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -148,61 +150,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - b6b5cd37f2a2 + - 582fd74dc2a1 - 3bbe70fef6df - 9c15ca7e764e - 14f588312c56 - 9f2455341fac + - b6b5cd37f2a2 - 756376aeb1ae - - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 989f7c061f35 - 73428a792541 - - 0ffe5be70caf + - 30fb23d4c31c + - 989f7c061f35 + - a230ea445788 - 8e1ace8f77c6 + - 0ffe5be70caf - 1691af4a0d17 - - a230ea445788 - - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 0418d28136de - 57c6718cbfcc - - 494f0bb4a993 + - e94187d661df - 30f08d74024f + - 494f0bb4a993 + - 0418d28136de - 563a19373357 - - e94187d661df - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f77d7b685bb3 - - 4b96ced19f75 - - f31125bb85ea - d6c7106b7b2e - 1bc5a03faf2e + - f77d7b685bb3 - 2bba2ff070d9 + - 4b96ced19f75 + - f31125bb85ea - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - d3af38b9c7e1 + - 520e30695ec3 + - 54961e026fe4 - d77fdcca400e + - d3af38b9c7e1 + - b3cf4684e9c7 - 52af33194019 - fed64e676186 - - b3cf4684e9c7 - - 54961e026fe4 - - 520e30695ec3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -214,8 +216,8 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 79261884facd + - 2aea122fbd25 - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -228,10 +230,10 @@ tools: - name: goseq owner: iuc revisions: - - 43798b4caee0 - 602de62d995b - 8b3e3657034e - ef2ad746b589 + - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -255,15 +257,15 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - - 74810db257cc - 98cafcbd2578 + - 74810db257cc - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -282,26 +284,26 @@ tools: - name: maker_map_ids owner: iuc revisions: - - 326f9c294b09 - e906fa778440 + - 326f9c294b09 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - - 3c1a01127868 - d46d803ca6cc - 370c210d9541 + - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 + - 624606f7c996 + - c8ac28e8ac44 - e95d52d295d7 - b815ec682418 - - c8ac28e8ac44 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -349,9 +351,9 @@ tools: - name: prokka owner: crs4 revisions: + - a17498c603ec - 8a22554cdde2 - bf68eb663bc3 - - a17498c603ec - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -371,8 +373,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -396,14 +398,14 @@ tools: - name: snpeff owner: iuc revisions: - - 6322be79bd8e - - cfcf33df7fc0 - - 268d162b9c49 - 8f92c2b26e6d - - 5a29ab10dba6 + - 268d162b9c49 + - 5b80f544c67f - 5c7b70713fb5 + - cfcf33df7fc0 - 68693743661e - - 5b80f544c67f + - 5a29ab10dba6 + - 6322be79bd8e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -430,17 +432,17 @@ tools: - name: tbprofiler owner: iuc revisions: - - 200c378d85f3 + - d03af1c7002c + - ba6f87115e13 - 809dfc93d593 + - 37213cf56392 - e1a9d6fd258d - - 45083d070fb8 - - 51dd22484644 - - ba6f87115e13 - - ac8250086ac3 - - d03af1c7002c + - 200c378d85f3 - 037a11682176 + - ac8250086ac3 + - 51dd22484644 - 4839e590cb26 - - 37213cf56392 + - 45083d070fb8 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 5d151a55b..a4775b47f 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,42 +2,42 @@ tools: - name: abyss owner: iuc revisions: - - 841084c5fc46 - - fa5259cc561b - - d6d5ccc2c581 - - 0e93176640ac - - 7547fcab5d19 - 553bfe8bd0b5 + - 7547fcab5d19 + - 841084c5fc46 - a929ce596a34 - 890b794c997d - - 8f1b150a2487 + - 0e93176640ac + - d6d5ccc2c581 - 0124fce4654a + - fa5259cc561b + - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - ddddce450736 - - b2860df42e16 - - b9e31c5c01c7 - 21e491ad532a - - 067592b6b312 + - ddddce450736 - 94fe43e75ddc + - 067592b6b312 + - b9e31c5c01c7 + - b2860df42e16 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: - 3371c5bdc17a - - a7f16f24e9a1 - 22286dab5aa1 + - a7f16f24e9a1 - 5258e18bbe23 - faee8629b460 tool_panel_section_label: Assembly @@ -45,29 +45,29 @@ tools: - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - 8c2167481e72 + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - bb935709506a - - 41030a6c03b7 + - 5ecdeca79a0d + - e4bd1e99bacf - 2dd755c1c6ff - - 2babe6d5c561 - - 1e62c28ba91d - e824f5d958d0 - - 1440ae06552f - - e4bd1e99bacf + - 41030a6c03b7 - cf13a1e03e5b - - 94170eee0ad8 - - 4048d82f0c88 - - 46ae58b1d792 - - 5ecdeca79a0d + - 1e62c28ba91d + - 2babe6d5c561 - 602fb8e63aa7 - ea8146ee148f + - 46ae58b1d792 - 0d243f458b53 + - 4048d82f0c88 + - 1440ae06552f + - bb935709506a + - 94170eee0ad8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu @@ -87,42 +87,42 @@ tools: - name: flye owner: bgruening revisions: - - 3e4f8642c77e - - 8d4f03b5fe9d - - 1ce9b1d72ec3 - 291923e6f276 + - 3ee0ef312022 + - 8d4f03b5fe9d - e27815e82dd4 + - 1ce9b1d72ec3 - 276f5d8712d5 - - 1f0769f0b56b - - 3ee0ef312022 - cb8dfd28c16f + - 3e4f8642c77e + - 1f0769f0b56b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - b2f674562a18 - 01210c4e9144 + - 3169a38c2656 - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - ba88bc5a6446 + - 7348b69e5109 - 06bcf65179fb + - ba88bc5a6446 - 8b330a577046 - - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 3fba9c77550a - 3ef480892a9f - - 690c2caa367e + - 3fba9c77550a - 5127a713de83 + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -134,23 +134,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - df25d4fb79b7 - - 3f7be05a1597 - - 2061fb3b81b4 - - 60024a528cbd - - 0ee0c3089254 - - da9d8bf98802 - - 5bec28269d95 - 284a1cb82b61 - - f3c89da3af16 - 6505bd37670d + - 5bec28269d95 - 045c7c3d8e59 - - 5f625c63b8bc + - 9ef6920c3089 + - f3c89da3af16 - 71740308d412 - - 41cea2aa2dce - - ec9e21e9c71b - 366a11d316a7 - - 9ef6920c3089 + - da9d8bf98802 + - 0ee0c3089254 + - 2061fb3b81b4 + - ec9e21e9c71b + - 60024a528cbd + - 41cea2aa2dce + - 5f625c63b8bc + - df25d4fb79b7 + - 3f7be05a1597 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: - - 7518ee87b53d + - de387b2b2803 - a96f3ad4e0d8 - 14ddfc8ffb93 - - de387b2b2803 + - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: + - d7edbc9c3a07 - 09c589057ee8 - - eb7b00ec347d - 39edec572bae - - d7edbc9c3a07 - f8113c25bc6b - 9d79beb19ac3 + - eb7b00ec347d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - 29dabd8db6f2 - eadfd71dde37 + - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - eb7a370f6588 - - 99ecfdafc64f - f369ef5f210b - - 3ca2d2a9068c - fd128c111ab0 + - 99ecfdafc64f + - 3ca2d2a9068c - 606b09cc9860 - - e731ea24e48d - - f338e9942b27 - 2ecf5a570907 + - f338e9942b27 + - e731ea24e48d 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: + - 8dee0218ac7d + - 8b6d0d85252b - a7b889b90140 - 73a3846701e1 - b799a615995d - - 8b6d0d85252b - - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -244,9 +244,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - - 64a1c751d99b - 15200570e926 + - 64a1c751d99b + - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -258,13 +258,13 @@ tools: - name: pretext_map owner: iuc revisions: - - bbe19ef04a74 - - 2b16ba799da9 - - 8fef980d48b5 - d256a51a656b + - 02831bf9e95f + - bbe19ef04a74 - 79b48f02db49 + - 2b16ba799da9 - dfb8a4497339 - - 02831bf9e95f + - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups @@ -278,26 +278,26 @@ tools: - name: quast owner: iuc revisions: - - 7594365c546b - - ebb0dcdb621a + - 72472698a2df + - 342a1d1fed7b - 675488238c96 - 875d0f36d66f - 59db8ea8c845 - - 6fcbee531de6 - - 72472698a2df - - 342a1d1fed7b + - ebb0dcdb621a - 3061c8b029e5 + - 6fcbee531de6 + - 7594365c546b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 78c533842eeb - - d865b62f501c - a199cd7ac344 - cd06929b224b - aa39b19ca11e - 39bed8de8017 + - 78c533842eeb + - d865b62f501c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -310,30 +310,30 @@ tools: owner: iuc revisions: - 2b2a352488fa - - f11b994b7eb2 - - f8564b2d7f63 - 33b7d8481a76 - 5c55448d0f33 + - f11b994b7eb2 - 3edba9afc9bc + - f8564b2d7f63 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: - 1d06c8b38e77 - - 53c2bc8c2ae3 - - e122f9101584 - - 28189050e437 - 378e55aeeb25 - - 5fc94b3a4704 - ef69617ecb42 + - 28189050e437 + - 5fc94b3a4704 + - 53c2bc8c2ae3 + - e122f9101584 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -346,113 +346,113 @@ tools: owner: iuc revisions: - 865119fcb694 - - ee17a294d3a3 - - ad80238462c1 - 83ead2be47b2 + - ee17a294d3a3 + - d9f6a00b6db7 - f698c7604b3b - 196a599ec43d - - d9f6a00b6db7 + - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: + - 015283de3004 - 24e471d13fe9 - 5e0825476fb7 - - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 051fd2db8a27 + - 604782a8a53a - 1fc82fe7ebef + - 051fd2db8a27 + - c33a476f4001 - 1bb12736175c - - 904bf932cf78 - 7490b213baa9 - - 604782a8a53a - - c33a476f4001 + - 904bf932cf78 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - ad8b536d1caa + - fee85957cebe - 34305b013402 + - ad8b536d1caa + - d6e617c4e338 + - 808b3a0a6716 - 9678993ca5bd - - fee85957cebe - 655fa188c3cc - - 808b3a0a6716 - - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 7e27faaad80e - - 8d4b90bf9caf - - e5a3b75a271f - - 6b5a5842531e - 21da31ed41a1 + - 8d4b90bf9caf + - 7e27faaad80e - 037f9927c4ff - b8002c3f7141 + - 6b5a5842531e + - e5a3b75a271f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: + - 7922870efcca - 2a10645aeadd - - f1532cb33c75 - 5b26685e5d3b - - 7922870efcca - - 9de69775f512 + - f1532cb33c75 - 328aa71f0f3c - 86f66ab58e14 + - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 6aad515a5270 + - 85fb02c43042 + - e41dcb0e913b - 1708851f8804 + - 6aad515a5270 - 340bc17f49cf - - 85fb02c43042 - 8cc856b935ee - - e41dcb0e913b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b65a43f70b99 - - 6357b127161e - d5fb354f745d + - d159735a6a9f + - 6357b127161e - b3490b036c5a - - de1260f8a300 - 249f6a28c751 - - d159735a6a9f + - b65a43f70b99 + - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 7897763d14ec - - d5887ace0dd4 - a90db5dbaaf3 - 9006e5836729 - - 33368fec3b70 - b7829778729f - - dd7ad84f3943 - d2d1df21dfb9 + - dd7ad84f3943 + - 33368fec3b70 + - d5887ace0dd4 + - 7897763d14ec tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - ced385aa976d - - 8f631679571f - 505a9833ab5d - ed2425b9fd27 + - 8f631679571f - 189e837009c9 - 6f4c8ad6ea01 tool_panel_section_label: Assembly @@ -460,43 +460,43 @@ tools: - name: trycycler_consensus owner: iuc revisions: + - d40ed4eb0c0e - 9ded6109434a - 356afed970b4 - - d40ed4eb0c0e - - 19bdfd1e6fe3 - f31d376ce725 + - 19bdfd1e6fe3 - e59bee4565b3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 4688ae3b49b5 - af40e971a8cc - - ebd801e712bc - - b23249f81bc4 - 80a17897564d - 6dd935e4984b + - 4688ae3b49b5 + - b23249f81bc4 + - ebd801e712bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - b5e35a2ca4f3 - - 937ea677d437 - - cb1e3db43020 - bb11fefb23a3 - - b64696992ee9 + - cb1e3db43020 - 59bd28f6265d + - 937ea677d437 + - b64696992ee9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - cb4768eeca3b + - 05bd7504fdb2 - 6bfab4a4a988 - 2628f6790eda - - 05bd7504fdb2 + - cb4768eeca3b - 383bb5ad32e2 - 6015aa0303f2 tool_panel_section_label: Assembly @@ -504,20 +504,20 @@ tools: - name: unicycler owner: iuc revisions: - - e92675014ac9 - - 3e44ef016b45 - - 8f9f06995f98 - - 9e3e80cc4ad4 + - 0a3a602cd1e3 - 6e26c9afd301 - e022dff952df - - 0a3a602cd1e3 + - 3e44ef016b45 + - 9e3e80cc4ad4 + - 8f9f06995f98 + - e92675014ac9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 5da9a0e2fb2d - 8d09f8be269e + - 5da9a0e2fb2d - 08256557922f - 920677cd220f tool_panel_section_label: Assembly @@ -525,9 +525,9 @@ tools: - name: velvetoptimiser owner: simon-gladman revisions: + - 37d88f41c810 - 82398ba86ba7 - 4a53b89fa703 - - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko @@ -540,7 +540,7 @@ tools: owner: iuc revisions: - 425e63adcc5d - - 39495e107274 - ff4031bfaa22 + - 39495e107274 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index 10e54112a..8b8abc905 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 - - 392f100eebcd - 4768f7f8e93f + - bfd290fe1588 - 1ae00120dd24 + - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - ded48b36f3b7 + - 1f5641a52664 - 31812e7a1315 - 8e8dc9a1e3e5 - - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 17fcac7ddf54 - 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 b198fca64..1c8a62b33 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: - - d1f62024a08b + - 204a131e47db - 159b04e36791 - - 0840ba83860c - 1c427e24fb79 - - 204a131e47db - 7beb76ffbc0f - a9c9d768b751 + - d1f62024a08b + - 0840ba83860c 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 13e54546d..a4b827c7e 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 589e7e57fd6d - - ce3c7f062223 - 64e2edfe7a2c - - a68aa6c1204a - - a8eabd2838f6 - 07e8b80f278c - - a1a923cd89e8 + - b28e0cfa7ba1 - e19bebe96cd2 - - 87ee588b3d45 - - dde39ba9c031 - 0a5c785ac6db - - b28e0cfa7ba1 + - dde39ba9c031 + - a8eabd2838f6 + - 589e7e57fd6d + - a68aa6c1204a + - a1a923cd89e8 + - 87ee588b3d45 + - ce3c7f062223 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml index fc0bebec7..3f256080a 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,30 +8,30 @@ tools: - name: diamond owner: bgruening revisions: - - 54f751e413f4 - - e8ac2b53f262 - f921014aba5a + - e8ac2b53f262 - 62c9df8382c2 + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - 5edc472ec434 - - a52d2d93e595 - - 2889433c7ae1 - - 0e3cf9594bb7 + - acf4e47b734c + - e25d3acf6e68 - 6f386c5dc4fb + - 0e3cf9594bb7 + - 2889433c7ae1 - cbf3f518b668 - d999e774072a - - acf4e47b734c - - e25d3acf6e68 + - a52d2d93e595 + - 5edc472ec434 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 242082a20..9fbe356e7 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - c8cdde00b105 - 710301bc46fa + - 095ad4d096d1 - da6bd1975a71 - 27ee142314a9 + - c8cdde00b105 - f4230f116196 - 6ca543ec1bf8 - - 095ad4d096d1 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_conformers @@ -130,62 +130,62 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 3b8a9d5ced85 - 88076940fa94 - - 0fac8e2afc13 - 79cfd9ead848 - bfb65cb551d8 + - 0fac8e2afc13 + - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - 715cd0e87781 - - d532b7e5f64b - eb6564a60136 + - d532b7e5f64b - b46d4b4d995c - - 55918daa5651 - f5d979cb4b54 + - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - dae135dfd519 - 5579659312e6 - - f26afd1b7104 - d2f955aea23a - fdf2cc80adb5 + - dae135dfd519 + - f26afd1b7104 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: + - 070e3ecc3fda - 2c349b027a01 - 4da9ee404eab - - ed736e6eee39 - cac1886249a2 - - 070e3ecc3fda + - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 807aa4c9293d + - 73008ef1f487 - c0c9a5024177 + - 807aa4c9293d + - da8753545526 + - 2e219a2d9327 - d1f803b5943c - f197e34c33a9 - - 73008ef1f487 - - 2e219a2d9327 - - da8753545526 - 525ca7c8065f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -193,11 +193,11 @@ tools: owner: chemteam revisions: - 2c8ed1b52bf7 - - 27ea4e1a3f95 + - 7568ae18908a - c4fbab8e03c5 - - 61094e01eff9 + - 27ea4e1a3f95 - 1809414a9454 - - 7568ae18908a + - 61094e01eff9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: - - 79e8ab8f1e81 + - 730ef07b90ae - ccfbd956a2d3 + - 79e8ab8f1e81 - ba83f0923369 - d7ec25187599 - - 730ef07b90ae tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -268,9 +268,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e6011617c748 - - 4242b4d68e9c - b59c91adeac1 + - 4242b4d68e9c + - e6011617c748 - e2c36f62e22f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -350,9 +350,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 9b48456a96fe - d4c67ced6abc - 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 d3ab19cbb..95508a2e1 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,11 +2,11 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - - fa56d93f7980 - - c97a786e8fb5 - - 2605cbdaa7d8 - f907216064f6 + - 2605cbdaa7d8 + - c97a786e8fb5 + - fa56d93f7980 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -25,18 +25,18 @@ tools: - name: macs2 owner: iuc revisions: - - 86e2413cf3f8 - - f5d67c722d67 - 640d3af5d833 - - 495a4173006f + - f5d67c722d67 + - 86e2413cf3f8 - 424aefbd7777 + - 495a4173006f 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 9baa0ab20..8b37b2b01 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,17 +9,17 @@ tools: - name: collapse_collections owner: nml revisions: - - 830961c48e42 - 25136a2b0cfe - - 90981f86000f - 33151a38533a + - 90981f86000f + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -32,9 +32,9 @@ tools: owner: bgruening revisions: - 2dae863c8f42 - - 0046692724f9 - 6cbe2f30c2d7 - baabc30154cd + - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 454e987e5..2899ce9ea 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: - - 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: - - a3b86937ead6 - - f3a19509108a - - 367b1ed91207 - 0b3c3ad92827 + - ab9350a8ab4d + - 367b1ed91207 - 4a6ee918c13a - 6ef0b5664c69 + - f3a19509108a + - 3b6f97e7094c - 5e1240a87bcb + - a3b86937ead6 - e3cbd2287f63 - - 3b6f97e7094c - - ab9350a8ab4d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: + - e177a8ea0bf1 + - 584008e574b2 + - d4d4e9febf5c + - 091bb5922a82 - 72ed72122deb - e525f9ffb9ac - - bd46669113b9 - 1b5fc03380d4 - - 54ccb7e1f49a - - d4d4e9febf5c - - 091bb5922a82 - - 33c99804a32f - - e177a8ea0bf1 + - bd46669113b9 - 501c21cce614 - - 584008e574b2 + - 33c99804a32f + - 54ccb7e1f49a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -58,22 +58,23 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 186b8d913e6c - 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 + - 43807a65369f - 4b347702c4aa tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -108,6 +109,7 @@ tools: owner: iuc revisions: - c24014d80001 + - faef2b1622a3 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: mz_to_sqlite @@ -120,8 +122,8 @@ tools: - name: samtools_bam_to_cram owner: iuc revisions: - - b9ea85dfaf45 - 18dbde5680c0 + - b9ea85dfaf45 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -133,18 +135,19 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 + - 78fb18899c99 - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - 19e45916daf9 + - 63769c4217a7 + - 92ac8e086317 - 26c6706bfb07 - b9b385097f13 - - 92ac8e086317 - - 63769c4217a7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 800517b4a..c78b0fedf 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,24 +2,24 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - e821645ef8fc - 5f6d123679f4 - de72ba3ed6f2 - - 268e91e540ee + - c929a006727f - a1ca9bccc7f2 + - 268e91e540ee - 29451af70c52 - - c929a006727f - - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 2d2cf5c1ea8a - - 0e143b4c3987 - - 7a7fd0f5f15d - 0e49b109abc2 - - bb1e4f63e0e6 + - 7a7fd0f5f15d - 12af64f93288 + - 0e143b4c3987 + - bb1e4f63e0e6 + - 2d2cf5c1ea8a - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -28,34 +28,34 @@ tools: revisions: - c06951d10364 - dc059492a995 - - 195e98217334 - - 7c1beb6d6eca - 81b1e3e1fc6c - 1d848bc4585f + - 195e98217334 + - 7c1beb6d6eca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 26e7304d6737 - - bfff7454b59a - - 71aa86af6762 - a67ac707496a - - 93eb012d9eed - 07418a30ed01 + - bfff7454b59a + - 71aa86af6762 + - 26e7304d6737 - 3d211717a775 + - 93eb012d9eed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 5be24eba848d - - 2bc10a9ca58b + - dd0b7398bb96 + - b8858746dc1f - 26983857c91a - 29fcfd36e90a - - dd0b7398bb96 + - 2bc10a9ca58b - 56d5b797ce84 - - b8858746dc1f + - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations @@ -64,96 +64,96 @@ tools: - 72bfafe3330b - 7e6bcd2e5128 - 7ef978dc1b8a + - ee3a1b0f45f1 - e6d0bff01239 - c3e012dfe21f - 9384cd033f30 - - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - a60c359ec43c - - b73e213add0c + - 514fa53b5efb - 167788df3b46 - - 9470f29702f8 - fd1275e01605 + - a60c359ec43c + - 9470f29702f8 + - b73e213add0c - fb9cf9c97ec4 - d9a637e83828 - - 514fa53b5efb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 5bffaa8354a1 - - e479c7ca5570 - - 2c37ce318bc3 - a02cfa31e9cb - c34d11ea4ba6 - - 86febdcc4283 + - e479c7ca5570 + - 5bffaa8354a1 - ca0616bb2cdf + - 86febdcc4283 + - 2c37ce318bc3 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - 78f405266706 - - 192ef85c0b0b - - 69a8621ca2f0 + - 01fb6a7654e6 - 1fcb7adc39b8 + - 192ef85c0b0b - 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: + - db940c262830 + - 137c4beed34b - 2f9e4843f480 - - 9ecba5e225a6 - 459cfa861f0b + - 9ecba5e225a6 + - d9ce4897dbb2 - d580d6acd1df - - db940c262830 - - 137c4beed34b - 3c9f0c486cca - - d9ce4897dbb2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 32e451def88c - f264afa9fa6f + - fd408d755394 + - 32e451def88c - fbe773640707 - - bad3ca889618 - bd7db9e2f2cb - - fd408d755394 + - bad3ca889618 - 2c66e43f1c86 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 4e12ea27f788 + - 3b9d990a0a0e + - 231994413f89 - 7e361d147872 + - 9368fbc49c8b - 7fda5607e777 - 56bce3c82278 - - 231994413f89 - - 9368fbc49c8b - - 3b9d990a0a0e + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - c03c3384cd81 - - ce4ce3316f74 + - 94ca68515826 + - b1779366c8e9 - d9114ef1c8a5 - e65d16fb2724 - - b1779366c8e9 - - 94ca68515826 - 4431f39ede55 + - ce4ce3316f74 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint @@ -161,46 +161,46 @@ tools: revisions: - 4ed32329e0ed - 793665fff0f8 - - b88ebb3672a1 - - d57251071381 - f8fc4e5aff9d - 2da482e408b8 + - b88ebb3672a1 - 23f7c5f1fdaf + - d57251071381 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 25d830337d31 - - e4c7985d4585 - - a4dfb122e52b + - 010e58e9d822 - c60570fa602f - - 512155688d98 + - e4c7985d4585 - a7849312d328 - - 010e58e9d822 + - 25d830337d31 + - a4dfb122e52b - ba6efa77fb79 + - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - c899e0ccff8c + - 443d9a9d6d11 - aa200e4f3939 + - 38e3f226248b + - 69264da0ce77 - 4d678170d29b - 00d869ea03a1 - - 443d9a9d6d11 - - 69264da0ce77 - - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a - - aac8444d6681 - - 10301d137111 - 6662b1a8d326 - a2d70c4fd406 + - 10301d137111 + - c361b12d207a + - aac8444d6681 - d806504e96d9 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 83a0942c9..ce8b0ccc8 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -30,8 +30,8 @@ tools: - name: obi_illumina_pairend owner: iuc revisions: - - 94f412098ac8 - 8cb6bd511879 + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 5f4544915893 - 39320fee9d70 + - 5f4544915893 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab @@ -65,7 +65,7 @@ tools: - name: obi_uniq owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 2a6d2feda..fe227f636 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,8 +2,8 @@ tools: - name: emboss_5 owner: devteam revisions: - - 63dd26468588 - ce385837c160 + - 63dd26468588 - 832c20329690 - dba489bfcd62 tool_panel_section_label: EMBOSS diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 68f49c8e3..e310dc4ac 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,10 +8,10 @@ tools: - name: bwameth owner: iuc revisions: - - 6da3972210ee - - 62f5fab76dfb - d82648ad25a3 + - 62f5fab76dfb - 29bdbc353f20 + - 6da3972210ee - cf1322aeb137 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 4da737153..0b387e7cd 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,34 +8,34 @@ tools: - name: cutadapt owner: lparsons revisions: - - 5915ea1ec9b1 - - 64172f1c1202 - - 4e5056fefd88 - - 288f97432497 - - de6cebe3c043 - - 135b80fb1ac2 - - 660cffd8d92a - - 44e2cc14f75b - - 8665bcc8b847 - - b1c926deaa2d - 8c0175e03cee - - c5e2e5902201 + - 48f587c13075 + - de6cebe3c043 + - c053d4cad713 - 49370cb85f0f + - 135b80fb1ac2 + - 288f97432497 + - 4e5056fefd88 - e4691e1589d3 - - c053d4cad713 - - 48f587c13075 - - fe74900d6dc7 + - 44e2cc14f75b - 093678460093 - 5eb7e84243f2 - c4b82dce8335 + - 660cffd8d92a + - b1c926deaa2d + - c5e2e5902201 + - 8665bcc8b847 + - 5915ea1ec9b1 + - 64172f1c1202 + - fe74900d6dc7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - f666895cbebd - - 9db07fd39f85 - 8889eb864cef + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -60,9 +60,9 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - - 516b97a23d7e - 9457a20156db + - 516b97a23d7e + - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -75,28 +75,28 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - ec0b5076173a - f81d4362b6c1 + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - 9c620a950d3a - - cd0874854f51 - - 56022eb50bbd - 0dbb995c7d35 + - 56022eb50bbd + - cd0874854f51 + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - d60c3f704da0 - - dbf9c561ef29 - 65b93b623c77 - c59d48774d03 - 1d8fe9bc4cb0 + - d60c3f704da0 + - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -104,11 +104,13 @@ tools: revisions: - f1dc2a761c30 - b05e39b9c170 + - 9115b978ce10 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: + - '144275714590' - 81a9090d6df3 - 10b75444feae tool_panel_section_label: FASTA/FASTQ @@ -118,11 +120,13 @@ tools: revisions: - 8611b80a14d6 - 47e5dbc3e790 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: + - e30352e889fe - 7861f3b10c68 - 5b87038565bb tool_panel_section_label: FASTA/FASTQ @@ -130,20 +134,23 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 + - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - 03d57fea6482 + - 523c2aff0376 - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: + - b41c2c1bcfbf - 3e396e702cea - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ @@ -151,6 +158,7 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: + - 8d958759cf2a - c885369b207b - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ @@ -159,21 +167,23 @@ tools: owner: devteam revisions: - 249c8393f2d4 - - e39cc71d3ed6 - 35e38452bb3f + - 397dc333436b + - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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_stats owner: devteam revisions: + - f86c27295151 - b1cea1b2fcd0 - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ @@ -183,12 +193,14 @@ tools: revisions: - b63b2bfb3ea3 - 33794bdb7fe0 + - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: - 297962e79f39 + - ac3fed111eb6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -196,60 +208,60 @@ tools: revisions: - 09070cacefd8 - 529bccd5e4a1 - - d5e9e83cd3d8 - 567d5b3c52b1 + - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 4bedca26c133 - 0b7ec11b3c7c + - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - bdf1ce174e39 - 736b8f6ee456 - - 90858c306551 - cb1e251cac37 + - bdf1ce174e39 + - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: + - 421f0af4ee95 - 07497255281e - 7ce1891db6f5 - - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - f984bb114520 - - b29d37ca9e41 - 02f8a17a4ebd - 3599f5451ee2 + - b29d37ca9e41 + - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - e246088b6e34 - - 0c2907307ba4 - 6027ef51ef91 + - 0c2907307ba4 + - e246088b6e34 - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 547e8d00f11c - 73194cdd4f57 - 377ac2829eac - 61b4cedc8934 + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -261,17 +273,17 @@ tools: - name: pear owner: iuc revisions: - - b4c6f054210a - 2f804526f5fd - 037f0acc7830 - f69501361cec + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort @@ -284,8 +296,8 @@ tools: - name: seqkit_stats owner: iuc revisions: - - fe1ae2ebf63d - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -305,49 +317,54 @@ tools: - name: ucsc_fasplit owner: iuc revisions: + - d3f58a0dc09d - bf04bd405d5b - 71f649c23021 - - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - 8250ea3a1501 + - b557acca0b56 - 24013bf85a6f - - a535cf1e5da4 - e654095ab143 - - b557acca0b56 + - a535cf1e5da4 + - 71ad4a56c40c + - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup owner: iuc revisions: - f1d33e4c7bd8 + - c5a2ee07c4e1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: + - 828dba98cdb4 + - 6a675c3aa610 - 015cf18f4a15 - 7accf7407811 + - 7a7e33d28f62 - f3759eec3018 - - 9fa7803d1c51 - - 6a675c3aa610 - 27ac32a22ad2 - - 828dba98cdb4 + - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group owner: iuc revisions: - d6255614afd7 + - 428735be9764 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist owner: iuc revisions: - - 4c8a1c7d3608 - 953b4821b183 + - e4e12f0b3af1 + - 4c8a1c7d3608 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index f77470fa4..2540444d1 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -11,68 +11,68 @@ tools: - 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: + - 2b0c9d9fc6ca + - e7b2202befea - 9da02be9c6cc - - 2c64fded1286 - - 3d0c7bdf12f5 + - 5ec9f6bceaee - ff9530579d1f + - 3d0c7bdf12f5 - f2e8552cf1d0 - - e7b2202befea - - 5ec9f6bceaee - - 2b0c9d9fc6ca + - 2c64fded1286 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - c1a33f603da2 - - a252d8415583 - 89d299153577 + - a252d8415583 + - c1a33f603da2 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: + - ad116ae3f4d9 - b6b54ba71bd8 - 18a51655db17 - - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: + - cc0fd298cc17 - 7306ec78632a - 59003d0543cd - - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - 1f296803dfa3 - 8880fb74ef56 - a72af9de6bf5 - - 1f296803dfa3 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - 75c93c70d094 + - f7e2f1eb3a16 + - abfd8a6544d7 - 1c2db0054039 - - 5e33b465d8d5 + - 3d93dd18d9f8 - 9a913cdee30e - - c1a4b5f3b432 + - 5e33b465d8d5 - b2f1f75d49c4 - - abfd8a6544d7 - - f7e2f1eb3a16 - bf675f34b056 - - 3d93dd18d9f8 + - c1a4b5f3b432 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/usegalaxy.org.au/fetch_alignmentssequences.yml b/usegalaxy.org.au/fetch_alignmentssequences.yml index 0dfc5355c..c01999d90 100644 --- a/usegalaxy.org.au/fetch_alignmentssequences.yml +++ b/usegalaxy.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 19f42b3ea391 - 9e776e7fab4f + - 19f42b3ea391 tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 950bfb9dc..61c50f0b5 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -16,8 +16,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 85ef5f5a0562 - 83a19df00eab - 141612f8c3e3 + - 85ef5f5a0562 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 38fbbf8dc..6cc2ad082 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,37 +9,37 @@ tools: - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - 8f53b238a360 - - f2f3bc622a16 - 0c8f7322f8fc + - f2f3bc622a16 + - 8f53b238a360 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 owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: + - b2c25142267e - cf61daf064fe - 45296e47d565 - - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,23 +108,23 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc owner: iuc revisions: - - 86e46972e183 - 9e83673fa6d2 + - 86e46972e183 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: + - da74170c55c7 - 840fb4850be3 - 666f60a9331a - - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -158,14 +158,14 @@ tools: - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 2e186f768..aade5505c 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -9,15 +9,15 @@ tools: - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 2214cf40b..16f971e71 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: - - b39347891609 - - 983bf725dfc2 - e9df53a75f3c + - b39347891609 - c1b437242fee + - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -26,45 +26,45 @@ tools: owner: iuc revisions: - e08a7ad4378b - - 4df8de2d0e48 - - e407b9da183a - - aad3885b3216 + - 8848455c0270 + - f5ea3ce9b9b0 + - 653e89d73fc4 + - f8054ea1c365 + - 4317d3cb6cba + - 1790dcf3c32d + - 83c7d564b128 - 5e6237d58b0c - 6591f049cf7e - - 516a54ddf218 + - e407b9da183a + - 4df8de2d0e48 + - aad3885b3216 - 1ec814014652 - - 8848455c0270 - - f5ea3ce9b9b0 + - 516a54ddf218 + - 69ebb7f46e45 - 734abc7ac21d + - ba931a59dd59 - 6ea73833cf67 - - 83c7d564b128 - 7068f48d0ef9 - - ba931a59dd59 - - 4317d3cb6cba - - 69ebb7f46e45 - - f8054ea1c365 - - c441583adae5 - - 653e89d73fc4 - 9a776b080193 - - 1790dcf3c32d + - c441583adae5 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - 21a560af5913 - 9aaa46d45472 - 34758ab8aaa4 + - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 95fb5712344f + - 054483e27a35 - 468c71dac78a - - bfdc6a7ffd3a + - 95fb5712344f - af5eccf83605 - - 054483e27a35 + - bfdc6a7ffd3a 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 0ed8ad3ef..0bed69f99 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 + - c4bde687c846 - 290a11559985 - - 4b519282a05b - 740057a5126d - - a64dc31ab7f2 - - fd59d783248a - - df7356989ac1 - - c4bde687c846 - 7f13dc906cb9 - - ae9994cf526f + - df7356989ac1 + - fd59d783248a + - 4b519282a05b + - a64dc31ab7f2 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -29,8 +29,8 @@ tools: owner: devteam revisions: - 867ab348287d - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,22 +42,22 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 374e9062d874 - - '566197475670' - - ca7cb0eaad62 - 53460afd5115 + - ca7cb0eaad62 - 3b37b1b1c3a7 + - '566197475670' + - 374e9062d874 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 10515715c940 - - 391a4cc45fea - 3d059e9c2fba - - d3a9e32672ec - - 1a72f938213e - da4c086cff5b + - 391a4cc45fea + - 1a72f938213e + - d3a9e32672ec + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -70,26 +70,26 @@ tools: - name: ggplot2_pca owner: iuc revisions: - - ae344ccf9d62 - b1268b7544d3 + - ae344ccf9d62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - 1acf88921176 - - e3a675da7fd0 - - 299307abd804 + - d0fc8b746d57 - 5fe1dc76176e + - e3a675da7fd0 - 5298e06f14f9 - - d0fc8b746d57 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 0e7290688b50 - 17b666467c32 + - 0e7290688b50 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -101,15 +101,15 @@ 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: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -127,17 +127,17 @@ tools: - name: jbrowse owner: iuc revisions: + - 667e17248bfe + - a6e57ff585c0 + - 17359b808b01 - 4542035c1075 - - 1cfc579079a6 - fd5dbf0f732e - - 2bb2e07a7a21 - - a6e57ff585c0 - - 836d1aa3e89a - 6cd09d7b5f37 - - 667e17248bfe - - 17359b808b01 + - 2bb2e07a7a21 - 112eb40ba6cf - ca2def38369c + - 1cfc579079a6 + - 836d1aa3e89a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -155,24 +155,25 @@ tools: - name: pathview owner: iuc revisions: + - 03c13085aecc - f1691de443a7 - fe154a7af404 - - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - bd1416eea1f0 + - 594b85e4237a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - 62e3a4e8c54c - - 1c5dcef5ce0f - - f234e2e59d76 - 85da91bbdbfb + - f234e2e59d76 + - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -191,8 +192,8 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 6c571966cfb9 - 44c66e8d21e6 + - 6c571966cfb9 - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -205,23 +206,23 @@ tools: - name: pygenometracks owner: iuc revisions: + - 2824d77cd8f8 - 360df4999907 - - 4ac4e7083b7e - - 7dd841a32245 - - a1abfa420d9d - 326a3db8d9d1 - - 2824d77cd8f8 - - 14e7c35f3d00 - 36b848d5f3ec + - 7dd841a32245 + - 4ac4e7083b7e + - 14e7c35f3d00 + - a1abfa420d9d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 83c573f2e73c - - 73b8cb5bddcd - 2f557f6abbfb + - 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 12b14dea9..04444a4b9 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,57 +21,57 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph 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 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: - - fc4b3b46dc9d - 36735850e461 + - fc4b3b46dc9d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - 0a8e527d1517 - d8f5224005bb + - 0a8e527d1517 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - c9da9192eee5 - 9d76c3d6dff6 + - c9da9192eee5 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat @@ -91,8 +91,8 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - ff6decc0f432 - 9a2f72d7dbd2 + - ff6decc0f432 - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -113,8 +113,8 @@ tools: - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 73d43034c860 - 0387a2179f88 + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed @@ -134,15 +134,15 @@ tools: - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x owner: ebi-gxa revisions: - - 287503c35cb4 - 078aa23c9374 + - 287503c35cb4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable @@ -155,15 +155,15 @@ tools: - 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 @@ -176,8 +176,8 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - b2768cae00a1 - 6d4f88995e40 + - b2768cae00a1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca @@ -197,15 +197,15 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - 767a675b5254 - ea91cfd0444e + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - 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 b495975e0..a863b15c9 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,51 +2,51 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 9edf8894a22d - - 29f66c353bcb + - ed2cca6b5de4 - a4c13ddcc8ee - 921a2da49a0c - - ed2cca6b5de4 + - 29f66c353bcb + - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - 5746d61f0a91 - - 755df866ad0c + - 78fb5e286609 - ec4b948dc6f0 - d404277cc87a - - 78fb5e286609 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 - - 03dd3c16ae4e - - 11fa44ee0603 - 9e357a8b2ec3 + - 11fa44ee0603 - 4d511437b1e5 + - 977dc15add20 + - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - - 41dbf4d162a2 - 77919cc3618e - - 0ba4f56a3613 + - 3b5b54ed6392 - c3e5e2cf12b7 + - 0ba4f56a3613 + - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 12d51d7be66f + - 5308ca68ef3d - 7babd8a46fe0 - 9939786dd9c9 + - 12d51d7be66f - b63363075c2e - - 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 9a5f1c6e6..d0bcbee27 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,12 +2,12 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 3df9f0a4bf34 - - 81f0cbca04a7 - - 7db4fc31dbee - - 0c777d708acc - 8bccb36e055a + - 3df9f0a4bf34 - 699a5e9146b3 + - 0c777d708acc + - 7db4fc31dbee + - 81f0cbca04a7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction @@ -22,17 +22,17 @@ tools: - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - e576b73a2e2f - 9d47aabda459 - 6ad1d3cfdea1 + - e576b73a2e2f 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 @@ -52,11 +52,11 @@ tools: - name: bfconvert owner: imgteam revisions: - - 85edbb7a436b - b07f4839ca77 - - fcadded98e61 - - f3360fbeda64 + - 85edbb7a436b - 10eed33aa9b2 + - f3360fbeda64 + - fcadded98e61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -77,9 +77,9 @@ tools: - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - - eb6c08714244 - e917a2424690 + - eb6c08714244 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -93,32 +93,32 @@ tools: owner: bgruening revisions: - 6070780813d9 - - e7273daa5ae2 - 670975e92458 + - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image 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 + - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet @@ -132,25 +132,25 @@ tools: - name: cp_gray_to_color owner: bgruening revisions: + - ad271f78a87a - 3245681b2f6d - 31d195bedf6d - - ad271f78a87a 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: + - ff1a86a87364 - 6100a22bf4f2 - c09dcda1143f - - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -164,17 +164,17 @@ tools: - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - 2564f461de62 + - a1a961c46d4b - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - a32c3f810ade - - 91e03287f285 - 20dbb1f7ec7b + - 91e03287f285 + - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity @@ -189,55 +189,55 @@ tools: owner: bgruening revisions: - e972e07c7845 - - 6f4715b8540a - d3890df07463 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 980aed9e8fd5 - e52c75a28c4b - 407925835dd9 + - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - acf3aa487283 - d85f11570109 - 79e10d12d90a + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - 80b200ae516b - b76841ee5560 - 035a58c7f54a - - 80b200ae516b 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 + - 48102a685037 - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: + - 27edbb90ab2b - 4ecf93628f97 - 33f4fa1413fb - - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -249,22 +249,23 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids owner: iuc revisions: - 4b794652dcdc + - f92941d1a85e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - 7b6d9412c7f8 - - 236ec78b2e53 - f8b4eada923c + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 964459c6e..a09de5315 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 40737febe339 + - d6e72da3ec35 + - 1069f6db0a0e + - f362150bef41 - e4ee04da1c19 + - 3a72fede57ce + - e319b5b65879 - 78bbd17d0703 - - a38934e303b9 - - f362150bef41 + - 40737febe339 - 3e4f434a69c6 - - e319b5b65879 - - 3a72fede57ce - - d6e72da3ec35 - - 1069f6db0a0e + - a38934e303b9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 7fe36019c073 - - 618297d23022 - - fcbeda41d0ac - - 9537184d421f - - 0135f1d487a0 - f91cfb73d369 - - 72ddd32392cd - 2b95d5c04908 - - c88553ec696e + - 9537184d421f - 8f8df367470d + - fcbeda41d0ac + - 0135f1d487a0 + - c88553ec696e + - 7fe36019c073 + - 72ddd32392cd + - 618297d23022 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 + - fafb3d685fa9 - d7e79eb3bcb3 - ad0dc9f4c9e2 - - fafb3d685fa9 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 43aac8d29685 - - 3d18f8c3c0f6 + - ee2beb764a7b + - 94df24c6bc00 - 28a6f1908fcc + - 43aac8d29685 - ee29337f905c + - 3d18f8c3c0f6 - 6a1515bb0687 - - 94df24c6bc00 - - 7f1cfa4c0e32 - - 8d36959b000d - 9eaadf03e0df - - bd2a7d1316b9 - - ee2beb764a7b - 5dc33613c288 - - 8c05afb547fa + - 8d36959b000d + - bd2a7d1316b9 - a1c2aecd7a0d + - 7f1cfa4c0e32 + - 8c05afb547fa tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - d37ede8589b2 - - bcaa0d571ce2 - - 8858fa037a15 - - 9f978da6528a - - c092052ed673 - - 86a20ae274fc - db536ad45f28 - - 5d6ed46cc101 + - 5671e1d3d5ee + - bcaa0d571ce2 - cb903c9dc33d + - 5d6ed46cc101 + - 8858fa037a15 + - d37ede8589b2 + - a250929be21b - e3bb03cf207a - - 5671e1d3d5ee - 364f4ffec275 - - a250929be21b + - c092052ed673 + - 9f978da6528a + - 86a20ae274fc tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - abbc8041e8ec - - 230b05597996 - - 38b91a3190cd - 584beffa972b - f95f403841ad + - c5c9f02b6167 + - 38b91a3190cd + - 49236b03e4fd + - 230b05597996 + - 194e3ceee923 - e1a015876aa9 - - 3b6a16d82c1b - ed28dd32141c - - 49236b03e4fd + - abbc8041e8ec + - 3b6a16d82c1b - 12d66d0d05ac - - 194e3ceee923 - - c5c9f02b6167 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 51c23fd7f..f98b3b127 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,8 +2,8 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 0f1724dd59d2 - f198773344e4 + - 0f1724dd59d2 - 17e3b698dd52 - b8a457820315 tool_panel_section_label: Join, Subtract and Group @@ -11,10 +11,10 @@ tools: - name: datamash_transpose owner: iuc revisions: - - ac092723240d - - a513e3fbb4c5 - - 22c2a1ac7ae3 - 374cb875d38a - ba0c40780ecf + - ac092723240d + - 22c2a1ac7ae3 + - a513e3fbb4c5 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index ebd81c4f3..ffd474ac2 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,16 +2,16 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - 522137aaa9c4 + - 66d7efc06000 - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - 8a794e6d3388 + - f22a9297440f - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -19,39 +19,39 @@ tools: owner: bgruening revisions: - b6ef6d0cb6b7 + - 2af1346e68c9 - e1317b5502fa - 818f9b69d8a0 - f1b9a42d6809 - - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 05143043ca13 + - 8334dc98c48e - 1588f9076e32 - - c80db5d6fd8c + - 05143043ca13 - 947c2eacccb8 - - 8334dc98c48e + - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 83228baae3c5 - 29e4122c90de - - 9991c4ddde14 - 1552b8cb4a94 + - 83228baae3c5 - 25b46af53232 + - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 53616c8b0865 - a07ab242b0b5 - f3dfa4bdf87e - 060ca94ac049 + - 53616c8b0865 - 1a53edc4b438 - 841a6cc5fc58 tool_panel_section_label: Machine Learning @@ -59,42 +59,42 @@ tools: - name: sklearn_generalized_linear owner: bgruening revisions: - - 40f4447733b2 - - 2fc89dcd41c8 - - 927586a18553 - - 91c4e3331208 - d4808d5b83da + - 927586a18553 - dc4b5fd604a6 + - 91c4e3331208 + - 2fc89dcd41c8 + - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - e5a5ad882f1f - 7626ea9c2e1b + - 301e07345c93 - 36e8d6d5d01b - 25ab6b4e376e - c6ae57f774c6 - - 301e07345c93 + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 02d2be90dedb - f9639b488779 - - 80852884053f + - 02d2be90dedb - b7c3e9a3b954 - 4ed102b922cb - 0630258dcf35 + - 80852884053f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - ec69cbe34b73 - - caeb57858702 - 14180f9c831e + - caeb57858702 - 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 695ebd60e..26f138daa 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: + - f6877ad76b00 + - a6d65b0c67af - d5ceb9f3c25b - - 017aba02828d - - cd659e8cc5fa - 17062a0decb7 - - 937aa69e715f - - 3ba8d4563129 - - 0d4acadabb04 - - a6d65b0c67af - - f6877ad76b00 - - 03e9b2fbc005 - 749c918495f7 + - 03e9b2fbc005 + - 0d4acadabb04 + - 3ba8d4563129 + - 017aba02828d + - 937aa69e715f + - cd659e8cc5fa tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: - - dfd8b7f78c37 - - 3fe632431b68 - - 64f11cf59c6e - 2477830927ec - - e188dc7a68e6 + - 3fe632431b68 - 53646aaaafef + - e188dc7a68e6 + - dfd8b7f78c37 + - 64f11cf59c6e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -50,44 +50,44 @@ tools: revisions: - 60afcc2c1d05 - e7f19d6a9af8 - - 3e1ea2facca6 - 2ff111fac1d7 - 37b497aa133f + - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - 09b53c1d4ab1 + - f54f5baedfdd + - be1d967337e4 - b3eab4b67562 - c0c2d0941de8 - - 53c0b7a1a0c3 + - 3f4d6399997b + - 037c6e54df11 - 5cc34c3f440d - - be1d967337e4 - - 8c6cd2650d1f - 77b2770508f6 - - 11a0d50a54e6 - - 3f4d6399997b + - 53c0b7a1a0c3 - 6b1e195506a3 - - 037c6e54df11 - - f54f5baedfdd + - 8c6cd2650d1f + - 11a0d50a54e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 45795f582ae9 - - b8f5f6e87f5c - - 42ce70172b72 - - ec9cbd6b9a49 - - 5ef7ec16b04f - - 9ee34ba73ebf - 79b885ce78d7 + - ec9cbd6b9a49 + - e403d27e8f24 - 1cd2511a396e + - 9ee34ba73ebf + - 5ef7ec16b04f - 00fbfac99d39 - - e403d27e8f24 - - 178bdbdb6d24 + - b8f5f6e87f5c + - 42ce70172b72 - 13022c3d3076 + - 178bdbdb6d24 + - 45795f582ae9 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 fadca8ff4..847f59a10 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -82,8 +82,8 @@ tools: - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - 00e66c401366 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -96,8 +96,8 @@ tools: - name: matchms_formatter owner: recetox revisions: - - 9e3c83d2afc3 - 1b09315a3f87 + - 9e3c83d2afc3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -110,8 +110,8 @@ 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 @@ -148,15 +148,15 @@ 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 owner: recetox revisions: - - 0cf68b536cd1 - 500f473df7e4 + - 0cf68b536cd1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -168,8 +168,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - b5467dead5b1 - 90745ecc5e9f + - b5467dead5b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -231,65 +231,65 @@ tools: - 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: - - 149b9cc7499b - - 18ec7635bac6 - f3a18e020cdd + - 18ec7635bac6 + - 149b9cc7499b tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - 481d769e2f7a - dfebc82ba1f0 - 134be5abb208 + - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - 02c772a49998 - - 9064aecc78a7 - 51332c2520c7 + - 9064aecc78a7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - e7305ba0dd38 - - b341cfd4baf8 - b3413f335327 + - b341cfd4baf8 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: - - 99d118321d5f - 24278c6b6d1c - d7f5878a98c3 + - 99d118321d5f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: + - ea0758b41473 - ffbabefbd2e2 - d90187b0f247 - - ea0758b41473 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 3887e5021..b4371517f 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,16 +2,16 @@ tools: - name: bracken owner: iuc revisions: - - 0c7b6eb7e752 - 1d4bd12f01cf + - 0c7b6eb7e752 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_bins owner: iuc revisions: - - 0e63d03c8790 - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a + - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -90,121 +90,121 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 63f86089423e - - 5b5a7af9fbb4 - - 76d3d2b10738 - 65db807336bc + - 5b5a7af9fbb4 - 7c2100246a2f + - 76d3d2b10738 + - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 1c35dadbe76f - - 84fd33a60b35 - - 00f5005840fa - 96336c6a2bb7 - 18a502a9d287 + - 1c35dadbe76f + - 00f5005840fa + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - 34e55239e68b + - e8fba04706d3 - addaf9d22850 + - 34e55239e68b - a9f4a217dcd6 - f732237754fc - - e8fba04706d3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 8c202e741d68 - 5fe3edf19b9c + - 75403243703a - 0776d824d896 - 04c15826a0b8 - - 8c202e741d68 - - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - e96bbb9e24ea - - 75c8945b0da2 - 43c99742158b - 1c9b3bcd4261 + - 75c8945b0da2 - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 84743da21318 + - 35176674168c - 5c865a382933 - 306a40d4bb8f - 1d75bd0595e2 - - 84743da21318 - - 35176674168c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 32c9ea835770 - 555ccac8a4c5 + - 8daf4564ccda + - 32c9ea835770 - 78faebd0879c - ac72310b038a - - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 + - f947b4bb5107 + - a58e4a43f49c - 7b8cb2b02978 - cae017b76acb - - a58e4a43f49c - - f947b4bb5107 + - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 073608a50ac3 - 1bc3657cd694 - 04144473e59e - - 7f3b59dee073 + - 073608a50ac3 - 7136e9ab70db + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 0a1224c4b781 - 19299bb1c6af - - 9058d8943303 + - 0a1224c4b781 - d943081510da + - 9058d8943303 - a7817705348e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - e005e659ae21 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: + - f8f56dd6449f - dbf1798c0dcc - - 4d9445dff47b - - c4db8c4de66f + - a68b985913ab - 5c7ba3d85a01 + - 4d9445dff47b - 65d52c693b8e - b907a3c0434f - - f8f56dd6449f - - a68b985913ab + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -217,9 +217,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6d364c65c946 - 6c84982ee6f7 - 654548ae1357 + - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -231,25 +231,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - 6aad8ca3918b - - e66ab198ec15 - bd7a9c6efb10 + - e66ab198ec15 + - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - b084117133af - - d77397f09da1 - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - - 9704f1a3b32d - 7f208f1eb64f + - 9704f1a3b32d + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -288,31 +288,31 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - c409a495841f - - e88b731dad59 - 31c6d107e7a5 + - e88b731dad59 + - c409a495841f - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 172920f67a84 - 094ad9c068af - - 71ea608ddfa3 - 714d5a28cc5c - d24841f5c3d2 + - 172920f67a84 + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a293a742194f + - a4d7148ccee4 - 4137b492233e - 2bdd84912a2b - 12fb63b5f63f - - a4d7148ccee4 - d7e9a3c41657 + - a293a742194f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -324,13 +324,13 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - cf87759761eb - - 6fcb8ac37a3e - - 75bedfb2078b - e2c71b852aba - - 64bc7acc22a9 - 97f7bb0851e7 + - 64bc7acc22a9 + - 6fcb8ac37a3e - a92c06a3afa7 + - 75bedfb2078b + - cf87759761eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -349,57 +349,62 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 2d35528d2141 - - 4e5e73d03f0d - c82508e76ad1 + - 2d35528d2141 + - 5e5a999ffaa9 - 4033827c76b8 + - 4e5e73d03f0d - 080ea153677c - - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - 6b7622dda516 - - 95bf7479d53c - 2cd76b089570 + - 95bf7479d53c - fc6c328c292f 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 owner: iuc revisions: - 385a965c6f87 + - 65b382bf9b7c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution owner: iuc revisions: - 7624945cacd3 + - e699e2747356 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median owner: iuc revisions: - b3d513c7093e + - 570505540a7b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions owner: iuc revisions: - adb3dd5a899f + - 1061711538c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance owner: iuc revisions: + - 29a4d6e2ae9c - b86562b4f3fd tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -407,17 +412,20 @@ tools: owner: iuc revisions: - 19607c740d19 + - 00f7064c564b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median owner: iuc revisions: - b1fe2ef3d244 + - 4d23ab83ea29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition owner: iuc revisions: + - 8388fe31d604 - 5a0fa29951ae tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -430,10 +438,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 20e2f64aa1fe - cdee7158adf3 - - 328c607150ff - 4a9da2b6c2e3 + - 20e2f64aa1fe + - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -466,8 +474,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - 27d65c78863c - bfae8da6082c + - 27d65c78863c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -498,8 +506,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 4960abe31b4d + - 073c867c5244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -511,8 +519,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 88d274322340 - 2deaada69b14 + - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -548,22 +556,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 7f5d7b0e9884 + - 0270541aaf46 - 327d9f4cc95f - - 3cc4a60615c0 - - 27250f92a01a - - 2cff76cf35c6 - e073891b2afc - 4fd3b5d8706b - - 7f5d7b0e9884 - - 0270541aaf46 + - 3cc4a60615c0 + - 2cff76cf35c6 + - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 76bc4efa1aeb - - 708abf08a626 - eb50e7eca3dc + - 708abf08a626 + - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -636,17 +644,17 @@ tools: - name: metaphlan owner: iuc revisions: - - ec368db926f4 - - b89b0765695d + - 1a6cdf55390f + - fd69c607b43f - ef65b083bd0c - 6dee4abadccb - - fd69c607b43f + - 740fd2d16a28 - 2131d7dca455 - - ff8f55893e7d - - a92a632c4d9b - a16313517e55 - - 740fd2d16a28 - - 1a6cdf55390f + - a92a632c4d9b + - ec368db926f4 + - ff8f55893e7d + - b89b0765695d - 289b3807e80c - 1a037928504c tool_panel_section_label: Metagenomic Analysis @@ -654,8 +662,8 @@ tools: - name: metawrapmg_binning owner: galaxy-australia revisions: - - 2a8bc1d26d06 - e3a64a1d2a6e + - 2a8bc1d26d06 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -679,15 +687,15 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 6034c3f3ecf0 - 2f47a294ef49 + - 6034c3f3ecf0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: - - 6eafc1e01a8c - 3b133b8d578a + - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline @@ -700,22 +708,22 @@ tools: - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 680fb3eb574c - 73b56418e7f4 + - 680fb3eb574c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -734,8 +742,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 8e2ac1b8f70a + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -784,20 +792,20 @@ tools: - name: staramr owner: nml revisions: - - 4b9a8031ab74 - 141afacabcfa + - 3b22de20bd4b - aeaa20b96ef2 + - 4d83eccf5f81 + - 4b9a8031ab74 - 2fd4d4c9c5c2 - be818ae858e4 - - 3b22de20bd4b - - 4d83eccf5f81 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - b3c7199d8786 - 9495df9dd6ef + - b3c7199d8786 - 576963db5f1b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index 601b12a7f..193493f23 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 @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 71893ebbf..cc878ad1b 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -3,38 +3,38 @@ tools: owner: galaxy-australia revisions: - 80f03df2e2ce + - 6ae5a7b5a0a2 + - 2263989660f5 - a74dbfee5a86 - - bdfbaf0c10aa + - 48c13389050d - 9baa871cb1d1 - - 2263989660f5 - - 9eeb13a92d79 - - 8b67dd48fec1 - 9422c5a87ee2 - - cd07731e4434 - - 098506c54016 - - 6ae5a7b5a0a2 - 94b8c6013083 - - 48c13389050d + - 098506c54016 + - bdfbaf0c10aa + - 9eeb13a92d79 + - cd07731e4434 + - 8b67dd48fec1 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f14193ec1f50 - - 2e093badc689 + - fc2e49f91e52 + - 5abf2c2249aa + - d390fe1567dc + - be78f13134e2 - '764845535798' + - 2e093badc689 + - f14193ec1f50 + - aaa0d6a8b808 - 4a60927aaca5 - c18157c68134 - - d7ce0ec78e51 + - 3ff17bad4006 - c44f824c051a - - aaa0d6a8b808 - - d390fe1567dc - - be78f13134e2 - - 5abf2c2249aa - - fc2e49f91e52 - - bc3831dd65c1 - f0af8936ed41 - - 3ff17bad4006 + - bc3831dd65c1 + - d7ce0ec78e51 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -53,66 +53,67 @@ tools: - name: clustalw owner: devteam revisions: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: - 5efbd15675ca + - 1de657a3198d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - - f0d493f8f84f - - f1a5908ea2cb - bf28a8cff401 - c5908940967d - - 15974dd17515 - - a65296ffb4a0 - 8e649f27aa0d + - a65296ffb4a0 - 6f28e90db932 + - 15974dd17515 + - f1a5908ea2cb + - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - e8fdceffea4c - fbca557a4847 + - e8fdceffea4c - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 5561a1193611 - - c9685bc0407c - 60698466facd + - c9685bc0407c + - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - bcd65de9725b - 57f042937ba7 + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - fb43e8887350 - ebe3b0f84de9 + - fb43e8887350 - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 7cd7a55a678d + - e18267f90096 - 636b049e6141 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 627566ea1..47cffb622 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -8,37 +8,37 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 28928576e1ea - - 7c47b3c9e493 - 18a8d140ec6f + - 7c47b3c9e493 + - 28928576e1ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado owner: galaxy-australia revisions: + - 63d8ecfcfab1 - 99c9427219d3 - fc5b6491cf78 - - 63d8ecfcfab1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - fc8804320156 - cb34f00cc10f - - 0e9e7fcdd543 - - 72b5e9dda577 - a7228a7ea146 + - fc8804320156 - 79e9a869f40e + - 72b5e9dda577 + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - fa11aa8103b2 + - db25ec99c3ea - 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: - - 222669c4afb6 - - edf6d4003fad - - eb746fa6f514 - - 19f3b583a9b3 - 43815fa60f3a - - 0f5f4a208660 - - 2bf63b38ee9b - cc36773a3681 + - 2bf63b38ee9b - ec699520444c + - eb746fa6f514 + - 19f3b583a9b3 + - 222669c4afb6 + - 0f5f4a208660 + - edf6d4003fad 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 @@ -77,53 +77,53 @@ tools: - name: nanoplot owner: iuc revisions: + - a02b8b3f5a0c + - 7b379e98b9a9 - a3c4fe6f49ab - - 645159bcee2d - - a38bdcec9e4c - edbb6c5028f5 + - 645159bcee2d - 0f1c34698076 - - a02b8b3f5a0c - - 7b379e98b9a9 + - a38bdcec9e4c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 3b6f94fc7e1d - d219b6d8158a - 85a394edc247 + - 3b6f94fc7e1d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - - a8d4be409446 - be95355fef8d + - a8d4be409446 + - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: + - 4857d5bcce52 - 449e9aeded2d - d376944466bf - - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - a3afc5f0a96c - de5b3d8f5b90 + - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - 93d623d9979c - 5f76b20953e5 + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -168,15 +168,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 626b6c2be5c2 - 2e22ebec211a + - 626b6c2be5c2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - 26e6c9362b7b - ce8af9373061 + - 26e6c9362b7b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index ca07c8bab..3e9f7e5fa 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - a5921c09b7b7 - 592ef3959907 + - a5921c09b7b7 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -27,11 +27,11 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - baceff842902 + - 97b1b5ad1cda - 3e73c97f025d - d74850cf4e42 + - baceff842902 - adfd6bf710bd - - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder @@ -51,12 +51,12 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 2f27f3b86827 - ed1518ce2237 - 13851aefa67a - - 19b6a2f0dbe2 + - 2f27f3b86827 - e4b4837f06f5 - 1e34d2e3d285 + - 19b6a2f0dbe2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -75,8 +75,8 @@ 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 @@ -90,8 +90,8 @@ tools: - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -104,8 +104,8 @@ 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 @@ -131,10 +131,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - b4b2b284230a - - 172815da3d41 - 27a6a256cd23 + - 172815da3d41 - 52b6a4d98009 + - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -159,9 +159,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: + - 87febc68b45b - 19bbd19b74b3 - fea85c467896 - - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -193,34 +193,34 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 2c61c30a57e7 - - 5fe20c915fa6 + - 0cb27ea69dc1 + - 4ba60cb14cb0 - d8dc037e3c13 + - 2c61c30a57e7 - 9c43baa60906 - - 4ba60cb14cb0 - - 0cb27ea69dc1 + - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 0db22932bc39 - aec831b54a5b + - 0db22932bc39 - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - ed7a967cb11b - df30a2f1db55 + - ed7a967cb11b - 6e24e79d3d69 - 29c738066906 tool_panel_section_label: None @@ -240,8 +240,8 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - 3e4d45aca422 - 1865e693d8b2 + - 3e4d45aca422 - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -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: - - 94a50db37d1a - 625fd9476402 - 9946bc39c834 + - 94a50db37d1a 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 - - 9a22227bb6d0 - ab5b7f6b7198 - - 58a870ef434c + - 9a22227bb6d0 - f77f7a7f3b83 + - ba7b0f11e470 + - 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 e7e5fdce9..025fbc10c 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,64 +33,64 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - a6619171428e - - 107d3ba7024a - - d7c7ef3353fe - - 3b8b5bde0bd9 - - f04a1264e2a2 - - '841557158611' - c78f3d7dd1db - - d033ffc1c161 + - f04a1264e2a2 + - 3f59ebfbfe3d - 26de3a7b1cb9 + - '841557158611' + - 6a457678efcb - 81e66674859e - - 8834daeb9892 + - d033ffc1c161 + - 3b8b5bde0bd9 + - 107d3ba7024a + - cce7b18495e4 - f73435dc282b - - 3f59ebfbfe3d - - 6a457678efcb - b89cac5156ec - - cce7b18495e4 + - 8834daeb9892 - 5a7c56a5cc08 + - d7c7ef3353fe + - a6619171428e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - aa8cc71438cf - - 02b8758214b0 + - 5b777002c2de - 659517798cc4 + - 4755f52427c4 - 6a726db04d4b - - 7a2092844346 + - 6283babe736e + - 88c4aa435ded - 6223845127ea - - df47d4845b62 + - 7a2092844346 + - 02b8758214b0 + - e75442c7f4da - 5fcd1ece3a6e - - 6283babe736e - - 5b777002c2de - b0af57c1a968 + - df47d4845b62 + - aa8cc71438cf - 3b96e92e8ec3 - - 4755f52427c4 - - e75442c7f4da - - 88c4aa435ded - a185b079b095 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: + - 0878b7fd5260 - 111bd54f6bc4 - - 70acec670c30 - - 24d024316465 - b8476e82ac20 - f97743d52b87 - - d1c340a5664b - - 0878b7fd5260 - c1d53e95327f + - d1c340a5664b + - 70acec670c30 + - 24d024316465 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 9e10ba792be2 - feb40665d7cd + - 9e10ba792be2 - daddf188c13f - 4f6349228462 tool_panel_section_label: Phylogenetics @@ -104,33 +104,33 @@ tools: - name: pangolin owner: iuc revisions: - - 83a69484cb87 - - 42a174224817 + - abf6dbe8c9d7 - ca0d8cf80567 - - 81804a978fc0 - - 8ad84c5753ea - ca337cce3888 - - 3a43c3982401 - - b6abccb1f25b + - 7bb8726be37c + - b7e297c2ede6 + - 03ed9524dcd1 - 437e28791761 + - 3a43c3982401 - 9d61d3fa046c + - 2fa9d4f1b48f + - 8ad84c5753ea - 2f1019071464 - - 14ae456b8cc5 - - b7e297c2ede6 - - 03ed9524dcd1 + - 5f8727ff21e7 - a2099fb98cdb - - abf6dbe8c9d7 - - 7bb8726be37c - - 2fa9d4f1b48f + - 83a69484cb87 + - 81804a978fc0 + - 42a174224817 + - b6abccb1f25b + - 14ae456b8cc5 - 36912871ccdc - - 5f8727ff21e7 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -143,22 +143,22 @@ tools: owner: iuc revisions: - b1e68bbe4cef - - a4b71be30c3c - - ea30d3089354 - 29ff6a849eac - - ba29b5e2a4be - 73a469f7dc96 + - a4b71be30c3c + - ba29b5e2a4be + - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 15ac71df11a0 - 9b2b122d0415 - - e88a7de55d6e - f1ccc8a6eb05 - 91887494eb97 - - dbe2b2204555 + - e88a7de55d6e - 809e42326fc2 + - 15ac71df11a0 + - dbe2b2204555 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 0594cfbbe..48f392836 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: + - f9242e01365a + - 7d34178f2812 - 881d7645d1bf - 3f254c5ced1d - b502c227b5e6 - - 1aac2a13842a - - f6ced08779c4 - - 7d34178f2812 - fc288950c3b7 - - f9242e01365a + - 1aac2a13842a - a1f0b3f4b781 + - f6ced08779c4 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 1e3098252..b81b146b0 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 - - eb085b3dbaf8 + - 2f7702fd0a4c - 6ab1a261520a - - 3bd420ec162d - - c0e71cb2bd1b + - 7fbec959cf2b - d00e15139065 + - a58f7eb0df2c + - c0e71cb2bd1b - ca90d17ff51b - - 5b85006245f3 + - eb085b3dbaf8 - e4a053d67e24 - - 2f7702fd0a4c - - 7fbec959cf2b + - 3bd420ec162d + - 5b85006245f3 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 a5ca3c648..dde3cd029 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -4,70 +4,70 @@ tools: revisions: - b18329a8ac14 - 4c177985028a - - b574b84afc4d - 0a18ac48ac53 - - ece627528a78 + - b574b84afc4d - f28ad96b76dc - 277dc652246e + - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - a9a28e46d54a - b41107d8fe89 - - e215f71d7983 - e988563cc6e5 - 525f201b86c1 + - e215f71d7983 - bf06d196e23d - - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 - bb6397b94018 - - 56da27be956a - 4fbffddde8cd + - 8da3511c9467 + - 56da27be956a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - 890845926d4b + - a8157342d9a3 + - 528fb09022be - b8c79e70516d - f23d67e28cc8 - - 528fb09022be - - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a69865da6f80 - 59e85306eae5 - - 80600735685d - a95a82eb4d50 - ae304a72db7b + - a69865da6f80 - 25b83cbd596a + - 80600735685d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d - - 83aac7741200 - - f1897eb07081 - - e0669b1854b1 - ed9ed1e6cca2 + - f1897eb07081 - 798da6bdff3d + - e0669b1854b1 + - 611d80c0e29d + - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - d426a9107a6c - 74b61bf5bc4b + - d426a9107a6c - 5a35e3a8d013 - a7fb9b395ddf tool_panel_section_label: Proteomics @@ -75,21 +75,21 @@ tools: - name: cardinal_segmentations owner: galaxyp revisions: - - df2187f9013b - - cc430977c8ff - 82f6c2f4332d - 91f0f5922011 + - cc430977c8ff + - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: + - 043f9c91f686 - 1693b2126f30 - - d2483487e077 - c5aa9fca18c6 - - 043f9c91f686 - - 10566783d718 - ba92b59cd529 + - d2483487e077 + - 10566783d718 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - ff8c9e0e8a7b - 9fa3dbf06f17 - - bf0728e000cd + - ff8c9e0e8a7b - ae4dc0c041f9 + - bf0728e000cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,17 +122,17 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - - d0ea7589e95f - eac99effe86f + - d0ea7589e95f + - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 0fa397f4f40b - 4081e4faa4ab - 1c5cbf8f79ce + - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -145,9 +145,9 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - 0d2e93e01e68 - - ce1a157a41bd - d6a4dfdad269 + - ce1a157a41bd + - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -159,16 +159,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: + - e66f552a3c47 - 160538a890a6 - d286ff4600dd - - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 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: - - 97a7f34fcb6a - - e42225f8a659 - - 7f432d87c82c - - 837224ad1694 - - 2133b0be850a - - 4d17fcdeb8ff - - f522c08e900c - 1f39c833f65f - 37d669de2828 + - 7f432d87c82c - 9c52362ae7bb + - 837224ad1694 + - 97a7f34fcb6a + - f522c08e900c + - e42225f8a659 + - 4d17fcdeb8ff + - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,54 +202,54 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - 85b8866f06d7 - - 0ed07016d668 - e63db1aa82ee - a72ac2c7cc5b + - 0ed07016d668 + - 85b8866f06d7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 1974224d63c2 + - 352b37c66d97 - 990b4560ead7 - 767c1d761aaf - - 352b37c66d97 + - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: + - 4f359549383c + - 99450519d727 - 35cc7ca0bdc7 - deaf035bbe9f - - 99450519d727 - - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - c7745841de24 - - c1343e3389ca - e79958768a2c + - c1343e3389ca - 06f6826d380c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 - - d2eac53666f0 - - da986f83631b - d46d64e7964d + - da986f83631b + - d2eac53666f0 + - b9d453dca8d3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - 9bf325045235 - - 1199751329b0 - 8bd7734309f6 + - 1199751329b0 - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -270,196 +270,196 @@ tools: - name: msstats owner: galaxyp revisions: - - 593839e1f2c3 - - 8212e342e482 - de7593c29499 - 28434abe6c5c + - 8212e342e482 + - 593839e1f2c3 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: - 01dbaf6a57e0 - - f4be248c3d47 - - 4e77b8f12cd3 - 8960fb791701 + - 4e77b8f12cd3 + - f4be248c3d47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - - 25529df60a81 - 06cca574e337 + - 25529df60a81 + - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - c9eff69a7c62 - - 9cdf15d3cfc8 - 6ccbf9a2072c - - f7fef900f5b2 + - 9cdf15d3cfc8 - 518b1730cf2a + - f7fef900f5b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - - 9876bda3ec53 - - ca88bd28f116 - 5e948629bc73 + - ca88bd28f116 + - 9876bda3ec53 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - 41859bbdc16e - - 890025d6e426 - - 1595601708ec - 658494a2cb00 + - 1595601708ec + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - 9b7977080f6d - 5ad0b5bf1deb - 2a93a25f0599 + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - 05d5e1ddc985 - - fe4e4587d265 - - 0bb5056cb775 - d6878d27f051 + - 0bb5056cb775 + - fe4e4587d265 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 4af67edd5aef - - 52ba9695e752 - febd569ad26f - 5ad830edc021 + - 4af67edd5aef + - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - 27cba4c5fc42 + - b2fc8da99bcc - 39e8fde08881 - 92352a475eed - - b2fc8da99bcc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: + - 9e26f5c770f8 - d3546bb9fd8e - 0efbc235f314 - - 9e26f5c770f8 - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - ca1740533b59 - 3720e349ba2a - - 8a04ed1c1d1b - c28f13cab67a + - ca1740533b59 + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c427a8628cbe + - c55dddc5844a + - ca799a7246e7 - a5d785af0ad8 + - c427a8628cbe - 382cde407f81 - - ca799a7246e7 - - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: + - 8ddb7bab1138 - b5d0905419da - - 39caaa778d2e - adca857b4884 - - 8ddb7bab1138 + - 39caaa778d2e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: + - 18f93351f8b6 - 34e7afee141d - - f817513840a9 - 1c5f31b8d632 - 8d4db262964c - - 18f93351f8b6 + - f817513840a9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - 5d9f175dff81 - - 986e03d3201e - - 111c3a00136d - c69f69d7867a + - 111c3a00136d + - 986e03d3201e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 4204882495f2 - - 0e52c85f3b15 - - be74a8cd7d66 - 476b5e296979 + - be74a8cd7d66 + - 0e52c85f3b15 + - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - a407b6790342 - - 2b2a7551a857 - - f5ec766d80cf - c18d8efa4474 + - f5ec766d80cf + - 2b2a7551a857 + - a407b6790342 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 4e66c4e73909 - - 021fdb80f204 - d0304fb829c0 + - 021fdb80f204 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - bf32e0bcf554 - - ee860980edc6 - 2735db4dd8d9 - 8098330f6d91 + - ee860980edc6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - 08488066d588 - a2a6e9551046 + - 08488066d588 - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -474,9 +474,9 @@ tools: - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - 1bf940c18d93 - - c1809c05ae8c - e8f64a7dc470 + - c1809c05ae8c + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator @@ -490,25 +490,25 @@ tools: - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - 0bddef8d144e - c99d5004b74f - d4396637b9f5 + - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 4bb198c0bd3e - 8b814eafce2c - 89254095cbf6 - - 4bb198c0bd3e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - f9ed7e074900 - - f82b320ceb90 - 05ec9fb05ed1 + - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer @@ -522,16 +522,16 @@ tools: - name: openms_openswathworkflow owner: galaxyp revisions: - - bc63b4d12779 - 2aebe58de46e + - bc63b4d12779 - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 5ae104d0da6e - decc397c3b7e + - 5ae104d0da6e - 6b01678ec2fc - 3d8d4ada5405 tool_panel_section_label: Proteomics @@ -539,34 +539,34 @@ tools: - name: openms_peptideindexer owner: galaxyp revisions: + - 539a3a4dcc9e - e039cc5c7aed - - d6aca689dd48 - 5182338d5e7c + - d6aca689dd48 - dd173849c3d8 - - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - d426affe977c - 8a45fd5a608a + - 16026cdb1330 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: - - 9020199dba0a - d063e2fe4ba4 + - 9020199dba0a - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -574,17 +574,17 @@ tools: owner: galaxyp revisions: - 78c080d36945 - - f036e8cf1a55 - ad2ba3a95a02 + - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - c8b225c69a7f - - 7f6a1f27553e - fb52e95a370c - 5c2a97a234d6 + - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -603,21 +603,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - a72c48001f7c - 7fdd9119cc4f + - 07ff622ec007 + - 943a34df6047 + - 1beff3ddce58 + - 3634c90301af - 3ec27b4cee7c + - a72c48001f7c - da885ca16cb2 - - 3634c90301af - - 1beff3ddce58 - - 943a34df6047 - - 07ff622ec007 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -678,9 +678,9 @@ tools: owner: galaxyp revisions: - 265c35540faa - - a371252a2cf6 - 1a5690a5eedc - 12692567c7f9 + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 3540cf884..e403c664a 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,131 +2,131 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 110a346daf36 - - 2f1d464ebfd2 - - e345aadf914f - 42201b90e3f4 - 289b7d6b69a4 + - e345aadf914f - cd5f98911089 + - 110a346daf36 + - 2f1d464ebfd2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 8501601a118d - c207119ba5f6 - - 0345dbaaa79b - - 0cd2df8af811 - fcce77c09289 + - 8501601a118d + - 0345dbaaa79b - 42d9087b4789 + - 0cd2df8af811 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 04db7fd6b238 - - 89eb29319bf4 - - 33486216eec0 - 421c33b8bf17 - 405a212b32ab - ad5ab22ffe24 + - 04db7fd6b238 + - 89eb29319bf4 + - 33486216eec0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - 7370bb65bad4 + - 7b72fde3d27e + - 1d839ead7ad3 - f6e91108b7b1 - eb784fa07f80 - - 1d839ead7ad3 - fa51dc5e8386 - - 7b72fde3d27e + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - c9b77ced9a78 - 3d70c2996730 - - a3e86cd9cac7 - - 8a55d29c8fcf - d30e36c48c93 + - 8a55d29c8fcf + - a3e86cd9cac7 - 1544278c272e + - c9b77ced9a78 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - 7b881f5f5ad5 - - b242deb58952 - - e2db212d64ad - a5969aa9347e - 564c33e5c3e3 + - b242deb58952 + - e2db212d64ad - 887cf585cafc tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - b4bab607eb05 - 9a171f9a450b - - bd5ff77e2036 - - e897c74a48bb - 8cff84759bf6 + - b4bab607eb05 + - e897c74a48bb + - bd5ff77e2036 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - adc7a7610d4f - 33f0793edf93 - 887e0991eb24 - - 5e10f396979e - - 4f65e343ecdf - 6dafad990086 + - 4f65e343ecdf + - adc7a7610d4f + - 5e10f396979e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 4e280b27a831 + - 97575d01f06b - c5d7050e4ad7 - 17d39bf0a63a - - 97575d01f06b - - 43e3eeb2e0ec - c287418eb288 + - 4e280b27a831 + - 43e3eeb2e0ec tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - a819ec3b362d - - 0b8c84a7fdb5 - - d9bf483266a1 - 09b8edb56d80 + - 0b8c84a7fdb5 + - a819ec3b362d - 9586f08634c0 + - d9bf483266a1 - cd034465d4a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: + - 95351dd0fd3f - a4b4bd84f69e + - a9c34a289493 + - 69842dd5aa48 - 2645575d1bf2 - bf0e43ab0416 - - 69842dd5aa48 - - 95351dd0fd3f - - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - d1fda11e602f - - 912f904a6e1e - - d033e1ccb386 - cfb504394ae1 - 8a35a3bc6752 + - d033e1ccb386 + - 912f904a6e1e + - d1fda11e602f - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -163,8 +163,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - d504d945a655 - 95286af4139b + - d504d945a655 - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -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 d3e2e9727..107c3e5bb 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,18 +2,18 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - cf01dd6c6b1f - 2d4e3aff9dc7 - 31f8063eedea - 7acb00fc980a - - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - 125d20cb23d7 - - 7a5a2d28c539 - 703a2cb3fb38 + - 7a5a2d28c539 - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -33,8 +33,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: chira_collapse @@ -84,18 +84,21 @@ tools: revisions: - f648e5180e40 - e66b9b5b8580 + - ad5d061fbdf2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 + - 6926716bbfb5 - d080005cffe1 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: + - 22cf48ad7b16 - 6a6717a5f421 - 86285ddd4512 - cf747d1bd79a @@ -104,6 +107,7 @@ tools: - name: cuffnorm owner: devteam revisions: + - 28b94cfbfdb9 - 9a854107dbb2 - 6cbfede05833 tool_panel_section_label: RNA-seq @@ -112,6 +116,7 @@ tools: owner: devteam revisions: - 679d93c99757 + - 93148c05136f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cummerbund @@ -129,49 +134,49 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - - e3b16fd7dd08 - - 3b36efd62b3e - 8f0181aacb7a + - 3b36efd62b3e + - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - d027d1f4984e - cd9874cb9019 - - 9a882d108833 - 0696db066a5b + - 24a09ca67621 - 6a3a025714d3 + - 9a882d108833 + - d027d1f4984e - 8fe98f7094de - - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - df929f257179 - b47c006d90c5 - 9a7c5b6d8f1e - 62adf13b86ea - 2872c633f07e + - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 0cb907a2a810 + - 555659de7321 + - a8305cf0c951 + - 334ce9b1bac5 + - f2843df56434 + - ae2aad0a6d50 + - 6e53e565fc6a - 070900306913 + - 9bdff28ae1b1 + - 0cb907a2a810 + - df0c8d0a5992 - 3d89af8a44f0 - - 6e53e565fc6a - 5bf899c13979 - - f2843df56434 - - df0c8d0a5992 - - 334ce9b1bac5 - - 9bdff28ae1b1 - - a8305cf0c951 - - 555659de7321 - - ae2aad0a6d50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -190,17 +195,17 @@ tools: - name: featurecounts owner: iuc revisions: + - a56fbe2d6ba7 + - 38b6d12edc68 - 7db9d3ea71c9 - - f9d49f5cb597 + - af814359d244 - 90d16db017d7 - - ea04b737afa0 - - f3a5f075498f + - a37612abf7f9 + - f9d49f5cb597 - e6a2a912677a + - f3a5f075498f - 6f66ae7c5f7a - - a56fbe2d6ba7 - - a37612abf7f9 - - af814359d244 - - 38b6d12edc68 + - ea04b737afa0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -224,9 +229,10 @@ tools: - name: gffcompare owner: iuc revisions: - - f99dd58de04f - - 3c97c841a443 + - 3c5e024a18cf - 0f710191a66d + - 3c97c841a443 + - f99dd58de04f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -238,21 +244,21 @@ tools: - name: hisat2 owner: iuc revisions: - - 6c19daec423d - - f4af63aaf57a - - a86e80d3c09c - d4b55e2beb12 + - 26371a1df031 + - a86e80d3c09c - 3fb01a8c902d - 6ab42baa56e9 - - 26371a1df031 + - 6c19daec423d + - f4af63aaf57a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: + - 4418229c501e - 67b0b160903a - 916cb26bd9d3 - - 4418229c501e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -265,31 +271,31 @@ tools: owner: iuc revisions: - 5ae5c312d718 - - 87c11c05d238 - 01247aaf0a10 - - 1c75aa5de15e - ce5d418183c5 + - 87c11c05d238 + - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 10c98fab6c5a - - 40985510cd98 - 4f9c4e6566e5 + - 40985510cd98 + - 10c98fab6c5a - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - e827f9aae031 - 58c35179ebf0 + - 119b069fc845 - 0921444c832d - 32511f586472 - 708348a17fa1 + - e827f9aae031 - d6f5fa4ee473 - - 119b069fc845 - 97e06a4c7c75 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -327,8 +333,8 @@ 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 @@ -346,21 +352,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - b0f2be869d6d - - 4074fc1940e2 - - 5ec75f5dae3c - - 4df95e2d7f61 - 980d2a2e1180 - - 7ed2edc1337f - - e132e7d02a3e - b9e04854e2bb + - 5ec75f5dae3c + - e132e7d02a3e + - 3ea5a2a63fa2 + - 4df95e2d7f61 + - 79de45b5069b + - 4074fc1940e2 + - c772497b2c32 + - b0f2be869d6d - 99b17b74a8cd - c7c55b694974 - - c772497b2c32 - - 3ea5a2a63fa2 - 0a563fd2f22e + - 7ed2edc1337f - 4014de1b6daf - - 79de45b5069b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -373,34 +379,34 @@ tools: owner: bgruening revisions: - e3d32471da11 - - ebab418107f5 - 2c0ca397d302 - - 15cd64d7c58b - cc05793bb896 - 49121db48873 - - f4d5237a84f6 + - ebab418107f5 - 53e9709776a0 + - 15cd64d7c58b + - f4d5237a84f6 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - 56242ff81c84 - - c0fd285eb553 - 8c28affc7c48 + - c0fd285eb553 - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 76d290331481 - - 258d696dbd7e - - cef79931dda5 - - dd4df992d93d - 914cfcba0ec8 - ae618321f34a + - 258d696dbd7e - 1ebd14235b92 + - cef79931dda5 + - 76d290331481 + - dd4df992d93d - cbf488da3b2c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -431,19 +437,19 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 - - ffd1300599a1 - c6334cb383ff - 0db979fead3a + - ffd1300599a1 + - d0d4cef4f967 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 + - 74217fbfba4d - d6a479fd4281 - ba3720d7e68b - - 74217fbfba4d + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -451,15 +457,15 @@ tools: revisions: - 478f36effca1 - 2fb4ee002432 - - 56162e446004 - c2b82a94493e + - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - 9ff3765e7172 - 3f4094b6a565 + - 9ff3765e7172 - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -467,45 +473,45 @@ tools: owner: iuc revisions: - 870ac06dff8e + - 4687ecf0eb2d - be3f26533209 - 34a018cbee9c - - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - 5192f657f305 - - 33406f5a445c - - c5fbddcac63a - 65e7dea767ea - 05ab8d5e04a2 + - c5fbddcac63a + - 33406f5a445c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - - a35cba31d904 - 6f0fb35b799c + - a35cba31d904 - e406ac71165d + - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - c2c039e421af - - 964b7efe2639 - 7c7fbf13aadd + - 964b7efe2639 + - c2c039e421af - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: + - eafea3083352 - 1d689e4e1caf - 047c22569787 - - eafea3083352 - 24e94d84adc9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -513,8 +519,8 @@ tools: owner: iuc revisions: - 3a4ac03d1266 - - 1812dbc5bb7b - 04bb8bb7c198 + - 1812dbc5bb7b - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -533,15 +539,15 @@ tools: - name: trinity owner: iuc revisions: - - 48636f857c4b - - d2bc35f3d1c5 - - cee61b3fcf78 - - 32b86cd8eb50 - 8f1c3df4dd49 + - d2bc35f3d1c5 + - c9cfec002f71 - 9fa24d5aac68 - d84caa5a98ad + - 32b86cd8eb50 + - 48636f857c4b + - cee61b3fcf78 - db1f362cca3e - - c9cfec002f71 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 5c8b52871..0693de33b 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -3,8 +3,8 @@ tools: owner: nilesh revisions: - 473382134e56 - - 1a052c827e88 - 080fd5739bb4 - 27e16a30667a + - 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 2f2989d3a..e13a82f94 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,17 +2,17 @@ tools: - name: bam_to_sam owner: devteam revisions: + - 88eedb4abea0 - 10184eaa85fc - 3c661e57a88f - - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 993b19f20c76 - - cb20f99fd45b - 1dfd95ee241e + - cb20f99fd45b + - 993b19f20c76 - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -32,8 +32,8 @@ 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: bamtools @@ -75,17 +75,17 @@ tools: - name: qualimap_bamqc owner: iuc revisions: + - 5f8e69cc4c6e + - e7fd6754d093 - 30a201c9c310 - 19ece8afbaab - - e7fd6754d093 - - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - 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: sam2interval @@ -130,9 +130,9 @@ tools: - name: samtools_bedcov owner: devteam revisions: + - 9149ad20699a - 6856f8a01905 - 46c6639921f1 - - 9149ad20699a - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -140,9 +140,9 @@ tools: owner: devteam revisions: - 26b4f9f98aca - - 06dc50b7b711 - 92ec40abcdcf - 33208952b99d + - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,81 +160,81 @@ tools: - name: samtools_fastx owner: iuc revisions: + - b3d99709fe1a - a8d69aee190e - b906586a6596 - 720217c23995 - 66e23b11feae - - b3d99709fe1a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - cc61ade70eb8 - fe34990e5ce7 - - db17d5321bad - 22970df7a40e + - cc61ade70eb8 + - db17d5321bad - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - - 7def34e6cf4d - 88b8c2916784 - - 811fc2d75ad4 + - 7def34e6cf4d - 7a6034296ae9 + - 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 - - 65a38e8c8e2a - 36677f429310 + - 65a38e8c8e2a + - 740ce0a18f0d + - cae2794d2deb + - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 8da515fbc1bf + - 9da0311ab1dd + - 329deb17a9f7 - b61f5d6a7f25 - 583abf29fc8e - - 329deb17a9f7 - - 9da0311ab1dd + - 8da515fbc1bf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - - 85e38b31e8b3 + - 30388d878f81 - bb8cfc6f6e0c + - 85e38b31e8b3 - db000c6007a0 - - 30388d878f81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -254,46 +254,46 @@ tools: - name: samtools_sort owner: devteam revisions: + - cab3f8d35989 - d54a4df48867 - e613c1ad4c4c - 6c2c1836728b - - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: + - 5d9ae78f34d3 + - 135c85f4cfaf - bd850490c7f1 - bcedabb53ddf - - 135c85f4cfaf - b7f7826ef1cd - - 5d9ae78f34d3 - 818030fa6bbf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 5a08c09b9311 + - 541082d03bef - 1cc79f49b8d5 - 3a0efe14891f - - 541082d03bef - - 145f6d74ff5e + - 5a08c09b9311 - 24c5d43cb545 + - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - b01db2684fa5 - - 6be888be75f9 - b72793637686 - - 0dbf49c414ae + - b01db2684fa5 - 350bbc5c2ffd - - bf328cec6a42 - c370440f901e - - 5826298f6a73 - - 32dc5f781059 + - bf328cec6a42 - 2dce91e11ca7 + - 6be888be75f9 + - 0dbf49c414ae + - 32dc5f781059 + - 5826298f6a73 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/send_data.yml b/usegalaxy.org.au/send_data.yml index 9d74eb127..fbceade24 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: + - d147d6455873 + - 5cb6146337d8 + - 480d9e9d156b - ea5e944f447d - a62c4a11a67d - - d147d6455873 - 6f6537780379 - 4aab5ae907b6 - 59bb6d34fca6 - - 5cb6146337d8 - - 480d9e9d156b 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 0035dea5e..b34887655 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -10,87 +10,87 @@ tools: revisions: - ecb9ea6269ee - e4c01dcece8b + - f2000bc73102 - e32b215b7c04 - c9944a2600f1 - - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - c0b037b12765 - - 707023fa62fe - cfaf5a405371 + - 707023fa62fe - e1c3c2f2a834 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - d330b3082107 - cfc3f5a57dc6 - - 00712416fdaa - - fb9e030ffae4 - - 93dd15e13e6a + - d330b3082107 - 55e35e9203cf - 32e547223c9e + - fb9e030ffae4 + - 00712416fdaa + - 93dd15e13e6a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 0bf7fddf90c7 - 39e945f0b2c1 - - 688357ad5e61 - - 6f0d0c784f09 - ee98d611afc6 - - 038e32885fec - b9fac48532eb + - 6f0d0c784f09 + - 038e32885fec + - 0bf7fddf90c7 + - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 3d748954434b - 7e8c677a7b71 + - 3d748954434b - d4af736e7b83 + - b85871dd69f9 - 9bd945a03d7b - 43cb7b5a6fe7 - ed4996a16f7f - - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - 2e8022f1923c - - a4774b7b2e85 - fe75d2414dc0 + - a4774b7b2e85 + - 2e8022f1923c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 0e70b2dfe4be - 769d815e4b0d - - 4fff5a293013 - 02b1fe7aed76 + - 4fff5a293013 + - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - aa4a6f0916b4 - c29e7bb492bf - - a90f8efe08b4 - 344c2af50552 + - a90f8efe08b4 + - aa4a6f0916b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 050cf43887d3 - b13d3e4c48e1 + - 050cf43887d3 - 5b7c81b35b89 - c32347702e12 tool_panel_section_label: Single-cell @@ -98,9 +98,9 @@ tools: - name: baredsc_combine_2d owner: iuc revisions: - - 1d77986f9ddc - - 02fc39c8610d - 239193b96d72 + - 02fc39c8610d + - 1d77986f9ddc - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,10 +137,10 @@ tools: - name: dropletutils owner: iuc revisions: + - cdf4443d5625 - a9caad671439 - cfe1e6c28d95 - 8855361fcfc5 - - cdf4443d5625 - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -185,36 +185,36 @@ tools: - 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 owner: bgruening revisions: - - f47ac4a0b337 - 013e53ccc7ac + - f47ac4a0b337 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - b892fa1fcaec - a63e9713c39d + - b892fa1fcaec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -269,15 +269,15 @@ tools: - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 62b720dceb56 - ea19190ce5e0 + - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2b4d6a8dab36 - 2786a931cad2 + - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops @@ -297,15 +297,15 @@ 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 owner: bgruening revisions: - - 409396ea5cf0 - 7f7c6ead2d0d + - 409396ea5cf0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo @@ -318,8 +318,8 @@ 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 @@ -339,15 +339,15 @@ tools: - 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 owner: bgruening revisions: - - ea5d67ec94ab - dd9988943f53 + - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts @@ -360,22 +360,22 @@ tools: - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - 337705015ee8 - b4e780e93c91 + - 337705015ee8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - ea8fb5e899e8 - 21d859ad4502 + - ea8fb5e899e8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices @@ -407,18 +407,18 @@ 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: - - 4b0adaa31c95 - - 0f1aaff9b22d - 59be31ac9dc3 - - e98619de2776 - eeab712b0b99 + - 0f1aaff9b22d + - 4b0adaa31c95 + - e98619de2776 - 7784821452ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -431,8 +431,8 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 282819d09a4f - 7ffaa0968da3 + - 282819d09a4f - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -446,8 +446,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -465,46 +465,46 @@ tools: - name: raceid_clustering owner: iuc revisions: - - c4f39bf4a068 - - 0bff0ee0683a + - f911a64454fb - 7e014059a88d + - 0bff0ee0683a - a4b734cd253b - - f911a64454fb + - c4f39bf4a068 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - b83fbc90161e - 7608d5faee41 - - d45f092caf24 - 43c146e25a43 + - d45f092caf24 + - b83fbc90161e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: - - f3eb2291da05 - 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 + - df8e4e54d367 + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - 72979cac22b2 + - 44b935f2271b - e93b008c637a - 2af7c5086a96 - c92d0f9338c5 - - 44b935f2271b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -522,101 +522,106 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - 38db3fef7aad + - 77b91b9bdf52 + - 4d8f983cd751 + - 6f83f8fd381f - b2df381a6004 + - cb43c5d3acd3 - f9353ee6a0d4 - 6acb08931836 - - 77b91b9bdf52 - - 38db3fef7aad - - 4d8f983cd751 - aaa5da8e73a9 - - 6f83f8fd381f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - a97abb8cd15b - 277313130da5 + - 3c86f71498bc + - fc0321c000a3 + - 72a6bebab2a5 + - a97abb8cd15b - b409c2486353 - d636ce5cde16 - 8cb783c81905 - a03ff8633507 - - 3c86f71498bc - - 72a6bebab2a5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: + - 4338bf96809e - 18262103fa61 - - 6bd82ed14acd - - d1cd8c147809 - - 5c3ebe2adc77 - 3081ff5c84a3 - - f54f0f0598ad - c5d3684f7c4c - - 6c145a6868cc - - 5e9171dc8244 - c0a80a16560f + - 5e9171dc8244 + - 5c3ebe2adc77 + - 6bd82ed14acd + - 6c145a6868cc + - f54f0f0598ad tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 7b9fafe32c86 - - c9cb76cf8d6c + - 3bcd5445cd7a - 56c0d4acef02 + - 146ae5d70b47 + - 94c19fb1281c + - ab55fe8030b6 + - 7b9fafe32c86 + - a407e7f8bdc1 - d844935c906c + - c9cb76cf8d6c - 9f354c7c8c92 - - a407e7f8bdc1 - - 3bcd5445cd7a - - ab55fe8030b6 - - 94c19fb1281c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 6f5349dd5c49 - - aa0c474463c2 - f7446fd8d5e7 - 1072ce66b426 - 9b0cdb8cf6be - - 95777145cb92 - 6adf98e782f3 + - 95777145cb92 + - dbbe1ea8ecb1 + - aa0c474463c2 + - 6f5349dd5c49 + - 40812a65a78b - 7647e5cd1b8b - 0185bd174ea0 - - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 458e8f43a775 - - a39040ae0a38 - - 9fb627495ec2 - - 215733a383f2 - - c65fce500915 - f2f6c703da06 - 73ab2ac53d06 - d18e7a6e5cd4 + - 458e8f43a775 + - a39040ae0a38 + - c65fce500915 + - 215733a383f2 + - fe8f16c594ec - bf2017df9837 + - 9fb627495ec2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - fd808de478b1 - - b834074a9aff - 8f333f90d8d6 + - b834074a9aff tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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_normalize @@ -867,6 +872,7 @@ tools: owner: iuc revisions: - d1b34ac42b8f + - d0f56ac6bb60 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: sinto_fragments @@ -892,8 +898,8 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 88192fe25375 - 588c811fdd48 + - 88192fe25375 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting @@ -919,8 +925,8 @@ 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 c6eea94a3..790342608 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,25 +32,25 @@ tools: - name: datamash_ops owner: iuc revisions: - - 562f3c677828 - 2f3c6f2dcf39 - - 746e8e4bf929 - 419027d822d6 - 4c07ddedc198 + - 746e8e4bf929 + - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - e01e8a9a82f4 - 8564f6927b87 + - e01e8a9a82f4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - 7a15159140d1 - cb1c59d69557 - 6c29c7e347e8 + - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e + - 4c4ec859c31a - b1eda492f063 + - 7442b94d6a1e - 840f29aad145 - aef56d0e7a61 - - 4c4ec859c31a - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 9fda0b82f419 - - 30d21a6041f6 - 375bbd555f4a - d0352e8b4c10 + - 30d21a6041f6 - 07843f917990 + - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - cd02bf168d23 - 4cc980df6265 - - 7ae443e6217d - - 2c58b83c9bad + - cd02bf168d23 - 8b1b2b91f8d0 + - 2c58b83c9bad + - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - ad7e0b4291ee - - bb9fc9d46ea4 - - e10e776f2109 - - 1dd433d2c92c - 4bbaf77573ef + - 1dd433d2c92c + - e10e776f2109 - 7dd3fb35904f + - bb9fc9d46ea4 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 ff317a5e3..6d44e9766 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -34,14 +34,14 @@ tools: - name: column_maker owner: devteam revisions: - - 464b9305180e - - 6595517c2dd8 + - 9cd341095afd - aff5135563c6 - - 6e8d94597139 - 13b6f0007d9e - - 9cd341095afd - - 02026300aa45 - be25c075ed54 + - 6595517c2dd8 + - 464b9305180e + - 02026300aa45 + - 6e8d94597139 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -53,8 +53,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: + - 557ec8d7087d + - 37cde8134c6a + - 34d29339abab - 90f657745fea - 9cc411a62277 - - 34d29339abab - - 37cde8134c6a - - 557ec8d7087d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -106,29 +106,29 @@ tools: - name: merge_cols owner: devteam revisions: - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: + - 623f3eb7aa48 + - 1ea4e668bf73 + - 3a6b78c39dca + - 33d61c89fb8d - cf4397560712 - 2e8f945f7285 - - 33d61c89fb8d - cf34c344508d - - 623f3eb7aa48 - 83069b38aa85 - - 1ea4e668bf73 - - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 399da6b5ec21 - - ae8c4b2488e7 - 503bcd6ebe4b + - ae8c4b2488e7 + - 399da6b5ec21 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 + - b722161a845a + - 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: - - 12615d397df7 - - ddf54b12c295 - - d698c222f354 - a6f147a050a2 - - 9ff72e942410 + - 12615d397df7 - 74a8bef53a00 + - ddf54b12c295 - fbf99087e067 - - 86755160afbf - f46f0e4f75c4 + - 86755160afbf + - 9ff72e942410 + - d698c222f354 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 6d6bb1c62..b99dbedeb 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 + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -34,9 +34,9 @@ tools: - name: freebayes owner: devteam revisions: + - 57def2d7c093 - a5937157062f - 04fa42777df9 - - 57def2d7c093 - ef2c525bd8cd - 156b60c1530f tool_panel_section_label: Variant Calling @@ -45,20 +45,21 @@ tools: owner: iuc revisions: - 791f73caa0c8 - - 09d6e4693887 - 435b157bed6d - e61c9ac190ad + - 09d6e4693887 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 03627f24605f - - 3b4b2121842f - - 4805fe3d8fda - 65432c3abf6c - e1461b5c52a0 + - 03627f24605f + - 4805fe3d8fda + - 3b4b2121842f - dfadc322b065 + - b11e8e9c23bf - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -73,18 +74,18 @@ tools: - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 - - c27549b9aa1f - - f4473557ffc7 - 971e07ca4456 + - f4473557ffc7 + - c27549b9aa1f + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: + - aa35ee7f3ab2 - dbd9f2db9ed8 - cdaab621d454 - - 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revisions: - - 57a16b310fe8 - a8a4f94aa321 + - 57a16b310fe8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate @@ -421,22 +421,22 @@ tools: - name: vcfannotategenotypes owner: devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect owner: devteam revisions: - - aea8e90ad788 - 9edfe5145ba8 + - aea8e90ad788 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck @@ -449,8 +449,8 @@ tools: - name: vcfcombine owner: devteam revisions: - - 53edb91ed051 - 1f0ba67cc85a + - 53edb91ed051 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples @@ -470,23 +470,23 @@ tools: - name: vcffilter owner: devteam revisions: + - 4bdc111b2470 - 6b935ab36d7b - eae7c08ebb6f - - 4bdc111b2470 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten owner: devteam revisions: - - b24e368ae7b1 - f285aa6bdcfb + - b24e368ae7b1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo @@ -499,8 +499,8 @@ tools: - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -520,8 +520,8 @@ tools: - name: vcfprimers owner: devteam revisions: - - d226a7327946 - 17096387c0e6 + - d226a7327946 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample