diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md index 092a2da7b6..15156586d3 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md @@ -1,5 +1,20 @@ # Changelog +## [3.4] - 2026-02-16 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3` + ## [3.3] - 2025-12-10 ## Changes diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index 918525844f..596d2c37cd 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -15,7 +15,6 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "3.3", "name": "Scaffolding with Hi-C data VGP8", "readme": "# Scaffolding with HiC data\n\nThis workflow performs genome assembly scaffolding using HiC data with YAHS. It is designed to be run as part of the VGP analysis trajectories, but can be used on any assembly in GFA format with Hi-C data. To generate a GFA from a fasta assembly, you can use the gfastats tool in Galaxy. \n\nExample of VGP trajectory : \n- VGP1: Kmer profiling \n- VGP4: Genome assembly with HiC phasing\n- VGP6: Purge duplicated haplotigs\n- VGP8: Scaffolding with HiC\n\n## Inputs\n\n1. Genome assembly [gfa]\n2. Haplotype being scaffolded (Will be added to scaffold names: e.g. `>scaffold_01_H1`)\n3. HiC reads paired collection [fastq]\n5. Trim Hi-C data? If `yes`, trim five bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks \"noisy\" and the reads haven't been trimmed before. \n6. Minimum Mapping Quality [int] (Default:20). Minimum mapping quality for Hi-C alignments. Set to 0 if you want no filtering. \n6. Database for busco lineage (recommended: latest)\n7. Busco lineage (recommended for VGP data: vertebrata)\n8. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0)\n9. Estimated genome size [txt] (Output from the contigging workflows 3,4, or 5). A simple text file containing the estimated genome size as an integer. E.g. `2288021`\n\n\n### Outputs\n\n1. Scaffolds in [fasta] and [gfa] format with the haplotype in the scaffold names.\n2. If you selected `yes` for Hi-C trimming, the trimmed collections of Hi-C reads.\n3. QC: Assembly statistics.\n4. QC: Nx plot.\n5. QC: Size plot.\n6. QC: BUSCO report.\n7. QC: Compleasm report.\n8. QC: Pretext Maps before and after scaffolding.\n9. QC: Statistics on Hi-C alignements before and after scaffolding\n", "report": { @@ -321,7 +320,7 @@ }, "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", "errors": null, "id": 11, "input_connections": { @@ -330,7 +329,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -350,16 +354,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", "tool_shed_repository": { - "changeset_revision": "59150c883ed5", + "changeset_revision": "0fe699ced54f", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - 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"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "c41d78ae5fee", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"Total Sequences\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "9.5+galaxy2", + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "8cc2544f-5d67-484a-8581-97c09cc40937", "when": null, @@ -1078,7 +1100,7 @@ } }, "tags": [], - "uuid": "0c5c1b32-9be6-47ba-a1ad-f15f92cb6d89" + "uuid": "8f87593d-a509-4437-9c42-0aafa9e3a877" }, "tool_id": null, "type": "subworkflow", @@ -1331,7 +1353,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": "Trim Hi-C reads 2", "name": "Cutadapt", "outputs": [ @@ -1464,7 +1491,16 @@ "output_name": "index" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "reference_source" + } + ], "label": null, "name": "BWA-MEM2", "outputs": [ @@ -1514,7 +1550,7 @@ } }, "tags": [], - "uuid": "2b879822-4978-40b2-bfe0-b325e69df5c4" + "uuid": "45769d0a-721b-456d-9625-d267e8f2b7cb" }, "tool_id": null, "type": "subworkflow", @@ -1806,7 +1842,12 @@ "output_name": "text_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": null, "name": "Map parameter value", "outputs": [ @@ -1858,7 +1899,12 @@ "output_name": "text_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": null, "name": "Map parameter value", "outputs": [ @@ -1910,7 +1956,12 @@ "output_name": "text_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": null, "name": "Map parameter value", "outputs": [ @@ -1953,7 +2004,7 @@ } }, "tags": [], - "uuid": "e474a2bd-8d4b-46fe-b088-33426b37ddca" + "uuid": "b4503d7c-a2ab-4ffa-b790-d0f6774d74a2" }, "tool_id": null, "type": "subworkflow", @@ -1976,7 +2027,16 @@ "output_name": "Has multiple samples" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Samtools merge", + "name": "bed_file" + }, + { + "description": "runtime parameter for tool Samtools merge", + "name": "headerbam" + } + ], "label": null, "name": "Samtools merge", "outputs": [ @@ -2226,7 +2286,12 @@ "output_name": "data_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Samtools stats", + "name": "addref_cond" + } + ], "label": "Hi-C Alignment Stats pre-scaffolding", "name": "Samtools stats", "outputs": [ @@ -2339,7 +2404,12 @@ "output_name": "data_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Samtools stats", + "name": "addref_cond" + } + ], "label": "Hi-C Alignment Stats contigs summary", "name": "Samtools stats", "outputs": [ @@ -2390,7 +2460,7 @@ }, "28": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.3+galaxy0", "errors": null, "id": 28, "input_connections": { @@ -2436,16 +2506,16 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "62e4d6cdbaa7", + "changeset_revision": "47db0f26ca31", "name": "bamtools_filter", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"conditions\": [{\"__index__\": 0, \"filters\": [{\"__index__\": 0, \"bam_property\": {\"bam_property_selector\": \"mapQuality\", \"__current_case__\": 14, \"bam_property_value\": {\"__class__\": \"ConnectedValue\"}}}]}], \"input_bam\": {\"__class__\": \"ConnectedValue\"}, \"rule_configuration\": {\"rules_selector\": \"false\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "2.5.2+galaxy3", + "tool_version": "2.5.3+galaxy0", "type": "tool", "uuid": "d0695b3c-002e-45f7-8bb7-98d3d51b2690", "when": null, @@ -2459,7 +2529,7 @@ }, "29": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", "errors": null, "id": 29, "input_connections": { @@ -2495,16 +2565,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "c41d78ae5fee", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"2\", \"lines_before\": \"0\", \"regex_type\": \"-G\", \"url_paste\": \"## METRICS CLASS\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "9.5+galaxy2", + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "4f792590-575c-4b69-993a-e5aefd4371cf", "when": null, @@ -2642,7 +2712,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool YAHS", + "name": "function" + }, + { + "description": "runtime parameter for tool YAHS", + "name": "function" + }, + { + "description": "runtime parameter for tool YAHS", + "name": "function" + } + ], "label": null, "name": "YAHS", "outputs": [ @@ -2857,7 +2940,7 @@ }, "35": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy3", "errors": null, "id": 35, "input_connections": { @@ -2886,16 +2969,16 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "c41d78ae5fee", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"complement\": \"+\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"2\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "9.5+galaxy2", + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "bafb604a-fbe8-4c7a-8bfb-a06c902aae0f", "when": null, @@ -2903,7 +2986,7 @@ }, "36": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3", "errors": null, "id": 36, "input_connections": { @@ -2936,16 +3019,16 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "c41d78ae5fee", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"scaffold_[0-9]*\", \"replace_pattern\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": true, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "9.5+galaxy2", + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "4d5d4a06-e906-4c73-8159-050d49158dd3", "when": null, @@ -2959,7 +3042,7 @@ }, "37": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "errors": null, "id": 37, "input_connections": { @@ -2988,16 +3071,16 @@ "output_name": "outfile" } }, - 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"inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -3047,16 +3135,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", "tool_shed_repository": { - "changeset_revision": "59150c883ed5", + "changeset_revision": "0fe699ced54f", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"scaffolding\", \"__current_case__\": 2, \"agp_to_path\": {\"__class__\": \"ConnectedValue\"}, \"discover_paths\": false, \"no_sequence\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"scaffolding\", \"__current_case__\": 2, \"agp_to_path\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}, \"no_sequence\": false, \"discover_paths\": false}}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - 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"changeset_revision": "65703c06c1f6", + "changeset_revision": "fc43cdc81408", "name": "imagemagick_image_montage", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -6264,7 +6415,12 @@ "output_name": "output_filtered" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Relabel identifiers", + "name": "how" + } + ], "label": null, "name": "Relabel identifiers", "outputs": [ @@ -6308,7 +6464,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Filter collection", + "name": "how" + } + ], "label": "Filter cnt", "name": "Filter collection", "outputs": [ @@ -6375,7 +6536,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Filter collection", + "name": "how" + } + ], "label": "Filter pct", "name": "Filter collection", "outputs": [ @@ -6462,7 +6628,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1", "tool_shed_repository": { - "changeset_revision": "65703c06c1f6", + "changeset_revision": "fc43cdc81408", "name": "imagemagick_image_montage", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -6623,7 +6789,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3", "errors": null, "id": 3, "input_connections": { @@ -6652,16 +6818,16 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "c41d78ae5fee", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"pair_by_orient_cis_ranges_(.*)-([a-z]{3})\\\\tNA\", \"replace_pattern\": \"pair_by_orient_cis_ranges_\\\\1-\\\\2\\\\t\\\\1\", \"sed_options\": null}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - 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"tool_version": "9.5+galaxy2", + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "038dfd5c-0118-469b-ba42-9f0d9839e9f0", "when": null, @@ -7383,7 +7554,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort collection", + "name": "sort_type" + } + ], "label": null, "name": "Sort collection", "outputs": [ @@ -7427,7 +7603,7 @@ } }, "tags": [], - "uuid": "16c1eebe-f99e-4c1f-a83c-b4b918b8f340" + "uuid": "025be1fb-199f-47ef-a46b-dd2009351523" }, "tool_id": null, "type": "subworkflow", @@ -7470,7 +7646,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1", "tool_shed_repository": { - "changeset_revision": "65703c06c1f6", + "changeset_revision": "fc43cdc81408", "name": "imagemagick_image_montage", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -7524,7 +7700,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1", "tool_shed_repository": { - "changeset_revision": "65703c06c1f6", + "changeset_revision": "fc43cdc81408", "name": "imagemagick_image_montage", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -7545,7 +7721,7 @@ } }, "tags": [], - "uuid": "b4f89c74-9efb-45b0-aeb4-d4378aa2ba76" + "uuid": "ba3b207f-95c6-48bb-b464-cf61295f6c43" }, "tool_id": null, "type": "subworkflow", @@ -7576,7 +7752,7 @@ }, "77": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3", "errors": null, "id": 77, "input_connections": { @@ -7621,16 +7797,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "c41d78ae5fee", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"delimiter\": \"\", \"colnames_option\": {\"header\": \"N\", \"__current_case__\": 1, \"list\": [\"3\"]}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "9.5+galaxy2", + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "c0b8fc81-1da7-4f59-936d-5faf5e7b9fe7", "when": null, @@ -7646,6 +7822,7 @@ "tags": [ "VGP_curated" ], - "uuid": "cb4d4f6f-ab78-4ef6-a09c-410200089d6e", - "version": 1 -} + "uuid": "1d2330be-d17b-4d43-bf1a-5065871c09a3", + "version": 1, + "release": "3.4" +} \ No newline at end of file