diff --git a/workflows/VGP-assembly-v2/post-curation-processing/CHANGELOG.md b/workflows/VGP-assembly-v2/post-curation-processing/CHANGELOG.md index eaedd6c7c9..4a25bc3639 100644 --- a/workflows/VGP-assembly-v2/post-curation-processing/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/post-curation-processing/CHANGELOG.md @@ -1,5 +1,21 @@ # Changelog +## [0.2] - 2026-07-20 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.8+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3` +- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.22+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.22+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.7+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy1` + ## [0.1] - 2026-03-18 ### Added diff --git a/workflows/VGP-assembly-v2/post-curation-processing/Post_Curation.ga b/workflows/VGP-assembly-v2/post-curation-processing/Post_Curation.ga index 42085a102c..da7fcd70eb 100644 --- a/workflows/VGP-assembly-v2/post-curation-processing/Post_Curation.ga +++ b/workflows/VGP-assembly-v2/post-curation-processing/Post_Curation.ga @@ -16,7 +16,6 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", "name": "Post-curation assembly processing and evaluation", "readme": "# Post-curation assembly processing and evaluation\n\nThis workflow performs post-curation processing and evaluation for VGP assemblies. It takes a curated AGP file and combined haplotype FASTA, splits by haplotype, applies curation, assigns chromosome names, renames and reorients hap2 to match hap1, and generates QC outputs including Compleasm results, Pretext maps, telomere analysis, and coverage tracks.\n\n## Inputs\n\n### Required Inputs\n\n1. **Species Name** [text] - Species identifier\n2. **Assembly Name** [text] - Assembly identifier\n3. **Curated AGP file** [tabular] - Generated by PretextView after manual curation (PretextView AGP v2.1 format with haplotype labels)\n4. **Fasta file with both haplotypes** [fasta] - Generated by the pre-curation workflow, containing both haplotypes in a single file\n5. **Database For Compleasm Lineages** [text] - OrthoDB database version used by Compleasm (e.g., v5). Default: v5\n6. **Lineage for Compleasm Genes** [text] - Compleasm lineage dataset (e.g., vertebrata_odb10, primates_odb10). Default: vertebrata_odb10\n7. **Hi-C reads** [list:paired] - Paired collection of Hi-C sequencing data\n8. **PacBio reads** [list] - Collection of PacBio HiFi reads\n\n### Processing Options\n\n9. **Genome larger than 10GB** [boolean] - Use BWA-MEM instead of BWA-MEM2 for read alignment. Recommended for genomes larger than 10GB. Default: false\n10. **Expected Genome Size** [integer, optional] - Expected genome size in bp. Required for NG* statistics in the Assembly statistics output.\n11. **Generate Gene tracks with Compleasm?** [boolean] - Enable/disable Compleasm gene annotation tracks\n12. **Trim the Hi-C data?** [boolean] - Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks \"noisy\"\n13. **Remove duplicated Hi-C reads?** [boolean] - Remove PCR duplicates from Hi-C data\n14. **Remove adapters from HiFi reads?** [boolean] - Select no if using HiFi reads trimmed in a previous workflow\n15. **Generate high resolution Hi-C maps?** [boolean] - Generate high resolution Pretext maps\n\n### Analysis Parameters\n\n16. **Canonical telomeric pattern** [text] - Default: TTAGGG (for vertebrate genomes)\n17. **Telomere patterns to explore** [text] - Telomere repeat patterns to search for (comma-separated, IUPAC allowed)\n18. **Minimum Mapping Quality** [integer] - Minimum mapping score for Hi-C alignments. Default: 10\n19. **Bin Size for BigWig files** [integer] - Bin size for coverage tracks. Default: 100\n\n### Haplotype Naming\n\n20. **Name Haplotype 1** [text] - Label for haplotype 1 (used to prefix output names)\n21. **Name Haplotype 2** [text] - Label for haplotype 2 (used to prefix output names)\n\n## Outputs\n\n### Assembly Summary\n\n- **Assembly information** - Assembly summary information\n- **Assembly statistics** - Combined gfastats assembly statistics (includes NG* if Expected Genome Size is provided)\n\n### Curation Results\n\n- **Corrected AGP** - AGP file with corrections applied\n- **Curated Hap1** - Curated haplotype 1 FASTA\n- **Curated Hap2** - Curated haplotype 2 FASTA\n- **Compressed Curated Hap1** - Curated haplotype 1 FASTA (gzip-compressed)\n- **Compressed Curated Hap2** - Curated haplotype 2 FASTA (gzip-compressed)\n- **Hap1 AGP** - Haplotype 1 AGP\n- **Hap2 Unlocs no hap dups AGP** - Haplotype 2 AGP without haplotypic duplicates in unlocalized scaffolds\n- **Hap1 Unlocs no hap dups AGP** - Haplotype 1 AGP without haplotypic duplicates in unlocalized scaffolds\n- **Hap1 Unlocs** - Haplotype 1 unlocalized scaffolds\n- **Hap2 Unlocs** - Haplotype 2 unlocalized scaffolds\n- **Hap1 Haplotigs** - Haplotype 1 haplotigs\n- **Hap2 AGP** - Haplotype 2 AGP (primary AGP for haplotype 2)\n\n### Chromosome Assignment\n\n- **Chromosome mapping Hap1** - Scaffold to chromosome mapping for haplotype 1 (SUPER_N naming)\n- **Chromosome mapping Hap2** - Scaffold to chromosome mapping for haplotype 2\n- **Chromosome level Hap2** - Chromosome-level haplotype 2 FASTA\n- **Chromosome File Hap1** - List of scaffolds assigned as chromosomes in haplotype 1\n- **Chromosome File Hap2** - List of scaffolds assigned as chromosomes in haplotype 2\n- **Chromosome Hap1 Csv** - Haplotype 1 chromosome assignment table (CSV)\n- **Chromosome Hap2 Csv** - Haplotype 2 chromosome assignment table (CSV)\n- **Percentage of Sequence Assigned to Chromosomes Hap1** - Fraction of haplotype 1 sequence assigned to chromosomes (relative to total assembly length)\n- **Percentage of Sequence Assigned to Chromosomes Hap2** - Fraction of haplotype 2 sequence assigned to chromosomes (relative to total assembly length)\n- **Sequence Assignment Stats** - Combined chromosome assignment statistics for both haplotypes\n\n### Rename and Reorient\n\n- **Mashmap for Hap2 sync** - Mashmap alignment between haplotypes at chromosome level (from curation subworkflow)\n- **Mashmap Chromosome level** - Mashmap alignment between curated haplotypes\n- **Hap1 Hap2 orientation mapping** - Orientation mapping between haplotypes\n- **Reorientation and renaming instructions** - Instructions for renaming and reorienting hap2\n- **Sequences missing in mashmap** - Sequences not aligned by mashmap\n\n### Visualization\n\n- **JBrowse2 without Gene tracks** - JBrowse2 visualization without gene annotation tracks\n- **JBrowse2 with Gene tracks** - JBrowse2 visualization with Compleasm gene annotation tracks\n- **Hi-C maps for each haplotype** - Combined Hi-C contact maps (MAPQ filtered)\n- **Hi-C maps for each haplotype - Multimapping** - Combined Hi-C contact maps (multimapping)\n\n### Haplotype 1 QC\n\n- **Hap1 Telomere Report** - Telomere analysis report\n- **Hap1 terminal telomeres** - Terminal telomere positions\n- **Hap1 P telomeres BED** - P-arm telomere positions\n- **Hap1 Q telomeres BED** - Q-arm telomere positions\n- **Hap1 Gaps BED** - Assembly gaps BED file\n- **Hap1 Gaps BEDgraph** - Assembly gaps bedgraph\n- **Hap1 Genes track** - Compleasm gene annotation track\n- **Hap1 Compleasm Summary** - Compleasm completeness summary\n- **Hap1 miniprot** - Miniprot protein-to-genome alignments\n- **Hap1 BigWig Coverage** - PacBio read coverage track\n- **Hap1 Coverage Gaps Track** - Coverage gaps track\n- **Hap1 Coverage gap BED for JBrowse2** - Coverage gaps BED for JBrowse2\n- **Hap1 Merged HiFi Alignments** - Merged PacBio HiFi alignments\n- **Hap1 Merged Hi-C Alignments on Curated Assembly** - Merged Hi-C alignments\n- **Hap1 Hi-C alignments on Curated Assembly** - Hi-C alignments\n- **Hap1 Hi-C duplication stats on Curated Assembly** - Hi-C duplication statistics\n- **Hap1 Hi-C duplication stats on Curated Assembly: Raw** - Raw duplication statistics\n- **Hap1 Hi-C duplication stats on Curated Assembly: MultiQC** - MultiQC duplication report\n- **Hap1 Pairtools MultiQC Stats on Curated Assembly** - Pairtools MultiQC statistics\n- **Hap1 Pairtools MultiQC on Curated Assembly: Plots** - Pairtools MultiQC plots\n- **Hap1 Pretext All tracks** - Pretext map with all tracks (MAPQ filtered)\n- **Hap1 Pretext All tracks - Multimapping** - Pretext map with all tracks (multimapping)\n- **Hap1 Pretext Snapshot** - Pretext snapshot for haplotype 1\n- **Hap1 Pretext Snapshot - Multimapping** - Pretext snapshot with tracks (multimapping)\n\n### Haplotype 2 QC\n\n- **Hap2 Telomere Report** - Telomere analysis report\n- **Hap2 terminal telomeres** - Terminal telomere positions\n- **Hap2 P telomeres BED** - P-arm telomere positions\n- **Hap2 Q telomeres BED** - Q-arm telomere positions\n- **Hap2 Gaps BED** - Assembly gaps BED file\n- **Hap2 Gaps BEDgraph** - Assembly gaps bedgraph\n- **Hap2 Genes track** - Compleasm gene annotation track\n- **Hap2 Compleasm Summary** - Compleasm completeness summary\n- **Hap2 miniprot** - Miniprot protein-to-genome alignments\n- **Hap2 BigWig Coverage** - PacBio read coverage track\n- **Hap2 Coverage Gaps Track** - Coverage gaps track\n- **Hap2 Coverage gap BED for JBrowse2** - Coverage gaps BED for JBrowse2\n- **Hap2 Merged HiFi Alignments** - Merged PacBio HiFi alignments\n- **Hap2 Merged Hi-C Alignments on Curated Assembly** - Merged Hi-C alignments\n- **Hap2 Hi-C alignments on Curated Assembly** - Hi-C alignments\n- **Hap2 Hi-C duplication stats on Curated Assembly** - Hi-C duplication statistics\n- **Hap2 Hi-C duplication stats on Curated Assembly: Raw** - Raw duplication statistics\n- **Hap2 Hi-C duplication stats on Curated Assembly: MultiQC** - MultiQC duplication report\n- **Hap2 Pairtools MultiQC Stats on Curated Assembly** - Pairtools MultiQC statistics\n- **Hap2 Pairtools MultiQC on Curated Assembly: Plots** - Pairtools MultiQC plots\n- **Hap2 Pretext All tracks** - Pretext map with all tracks (MAPQ filtered)\n- **Hap2 Pretext All tracks - Multimapping** - Pretext map with all tracks (multimapping)\n- **Hap2 Pretext Snapshot** - Pretext snapshot for haplotype 2\n- **Hap2 Pretext Snapshot - Multimapping** - Pretext snapshot with tracks (multimapping)\n", "report": { @@ -1078,7 +1077,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "Curated Fasta Hap1", "name": "gfastats", "outputs": [ @@ -1128,7 +1132,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "Curated Fasta Hap2", "name": "gfastats", "outputs": [ @@ -1174,7 +1183,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfa to fasta Hap1", "name": "gfastats", "outputs": [ @@ -1220,7 +1234,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfa to fasta Hap2", "name": "gfastats", "outputs": [ @@ -1470,7 +1489,12 @@ "output_name": "chr_level_fasta" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute sequence length", + "name": "ref" + } + ], "label": null, "name": "Compute sequence length", "outputs": [ @@ -1869,7 +1893,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": "If sak empty", "name": "Map parameter value", "outputs": [ @@ -2056,7 +2085,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -2159,7 +2193,7 @@ } }, "tags": [], - "uuid": "8e47b024-66fd-4814-9039-17c162aaf7c9" + "uuid": "c117a655-f3d1-432b-b5ed-602dbe727651" }, "tool_id": null, "type": "subworkflow", @@ -2241,7 +2275,7 @@ } }, "tags": [], - "uuid": "841705b3-7a8d-4173-92f1-3fe9b8e801de" + "uuid": "1fabb6b7-d2ca-4545-9aac-264bf34ca048" }, "tool_id": null, "type": "subworkflow", @@ -2346,7 +2380,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": "True when no gene track generated", "name": "Map parameter value", "outputs": [ @@ -2396,7 +2435,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": "Trim Hi-C reads 2", "name": "Cutadapt", "outputs": [ @@ -2490,7 +2534,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": "Remove adapters from Hifi reads", "name": "Cutadapt", "outputs": [ @@ -3121,7 +3170,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute sequence length", + "name": "ref" + } + ], "label": null, "name": "Compute sequence length", "outputs": [ @@ -3647,7 +3701,7 @@ } }, "tags": [], - "uuid": "0a7f943d-cb29-495d-98a4-32168f1bcbf7" + "uuid": "f553df31-8990-4e1c-b802-1c86e178fb8f" }, "tool_id": null, "type": "subworkflow", @@ -3777,7 +3831,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute sequence length", + "name": "ref" + } + ], "label": null, "name": "Compute sequence 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"toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3", "tool_shed_repository": { - "changeset_revision": "d3c07d270a50", + "changeset_revision": "3e27acfa4830", "name": "collection_element_identifiers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.0.2", + "tool_version": "0.0.3", "type": "tool", "uuid": "50f53cad-f20d-4497-bcfd-98085c5a86ee", "when": null, @@ -6878,7 +6961,12 @@ "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": [ @@ -6930,7 +7018,12 @@ "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": [ @@ -6982,7 +7075,12 @@ "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": [ @@ -7025,7 +7123,7 @@ } }, "tags": [], - "uuid": "f3cd0c6f-9666-4d4c-b6b0-d7e107fba5b0" + "uuid": "0d6e2374-6a40-4464-9208-07549043cab1" }, "tool_id": null, "type": "subworkflow", @@ -7044,7 +7142,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": "False when removal is true", "name": "Map parameter value", "outputs": [ @@ -7222,7 +7325,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": "When genome smaller than 10gb", "name": "Map parameter value", "outputs": [ @@ -7259,7 +7367,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1", "errors": null, "id": 4, "input_connections": { @@ -7276,7 +7384,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with BWA-MEM", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with BWA-MEM", + "name": "reference_source" + } + ], "label": null, "name": "Map with BWA-MEM", "outputs": [ @@ -7296,16 +7413,16 @@ "output_name": "bam_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19", + "tool_id": 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\"__rerun_remap_job_id__\": null}", + "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", @@ -7424,7 +7541,16 @@ "output_name": "output_param_boolean" } }, - "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": [ @@ -7524,7 +7650,7 @@ } }, "tags": [], - "uuid": "15e3fe39-e1ff-4016-9850-5d744c9aaed4" + "uuid": "45ec4595-8622-4901-87d5-83594b043acf" }, "tool_id": null, "type": "subworkflow", @@ -7534,7 +7660,7 @@ }, "8": { 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"changeset_revision": "37c8eb55315d", "name": "samtools_merge", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"bamfiles\": {\"__class__\": \"ConnectedValue\"}, \"bed_file\": {\"__class__\": \"RuntimeValue\"}, \"headerbam\": {\"__class__\": \"RuntimeValue\"}, \"idpg\": false, \"idrg\": false, \"region\": null, \"seed\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy1", + "tool_version": "1.22+galaxy2", "type": "tool", "uuid": "03cf4998-54d1-43b4-9005-828e8e1da14c", "when": "$(inputs.when)", @@ -7960,7 +8095,7 @@ }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2", "errors": null, "id": 16, "input_connections": { @@ -7969,7 +8104,12 @@ "output_name": "dedup_pairs_stats" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MultiQC", + "name": "image_content_input" + } + ], "label": "Pairtools MultiQC", "name": "MultiQC", "outputs": [ @@ -8043,16 +8183,16 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2", "tool_shed_repository": { - "changeset_revision": "26ee5e11ecbe", + "changeset_revision": "0559e0711094", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": true, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"pairtools\", \"__current_case__\": 39, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"Hi-C alignements to Scaffold stats\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": true, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"pairtools\", \"__current_case__\": 40, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"Hi-C alignements to Scaffold stats\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.33+galaxy0", + "tool_version": "1.35+galaxy2", "type": "tool", "uuid": "66905684-e6a1-4d2a-91ad-4809ca5e864a", "when": null, @@ -8076,7 +8216,7 @@ }, "17": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy3", "errors": null, "id": 17, "input_connections": { @@ -8125,16 +8265,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy2", + "tool_id": 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\"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy2", + "tool_version": "1.22+galaxy3", "type": "tool", "uuid": "294a749f-e96a-45d7-9e2b-fd71d0afe5b2", "when": "$(inputs.when)", @@ -8142,7 +8282,7 @@ }, "18": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy3", "errors": null, "id": 18, "input_connections": { @@ -8184,16 +8324,16 @@ "output_name": "stats_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy3", "tool_shed_repository": { - "changeset_revision": "ef678e1f70a2", + "changeset_revision": "a50321bc1a90", "name": "samtools_markdup", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"bamfile\": {\"__class__\": 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"description": "runtime parameter for tool Samtools merge", + "name": "headerbam" + } + ], "label": null, "name": "Samtools merge", "outputs": [ @@ -8478,16 +8627,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy2", "tool_shed_repository": { - "changeset_revision": "c8bc9d08b0e3", + "changeset_revision": "37c8eb55315d", "name": "samtools_merge", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"bamfiles\": {\"__class__\": \"ConnectedValue\"}, \"bed_file\": {\"__class__\": \"RuntimeValue\"}, \"headerbam\": {\"__class__\": \"RuntimeValue\"}, \"idpg\": false, \"idrg\": false, \"region\": null, \"seed\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy1", + "tool_version": "1.22+galaxy2", "type": "tool", "uuid": 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"inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": null, "name": "Map parameter value", "outputs": [ @@ -12493,7 +12657,12 @@ "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": [ @@ -12545,7 +12714,12 @@ "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": [ @@ -12588,7 +12762,7 @@ } }, "tags": [], - "uuid": "f3cd0c6f-9666-4d4c-b6b0-d7e107fba5b0" + "uuid": "54adcb90-24b6-4f74-9ebf-cbb6297f7fd5" }, "tool_id": null, "type": "subworkflow", @@ -12598,7 +12772,7 @@ }, "17": { "annotation": "", - "content_id": 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"tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"RuntimeValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", @@ -13727,7 +13944,16 @@ "output_name": "output_param_boolean" } }, - "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": [ @@ -13827,7 +14053,7 @@ } }, "tags": [], - "uuid": "e274f56b-fbf1-4815-8c11-8e8f5461bee0" + "uuid": "32a01e1e-0421-4581-a4fd-8ecfe30a2750" }, "tool_id": null, "type": "subworkflow", @@ -13837,7 +14063,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.22+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.22+galaxy3", "errors": null, "id": 8, "input_connections": { @@ -13873,16 +14099,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.22+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.22+galaxy3", "tool_shed_repository": { - "changeset_revision": "84819580b8a5", + "changeset_revision": "2f395ebff85f", "name": "samtools_fixmate", "owner": "iuc", 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"name": "Samtools merge", "outputs": [ @@ -14072,16 +14307,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy2", "tool_shed_repository": { - "changeset_revision": "c8bc9d08b0e3", + "changeset_revision": "37c8eb55315d", "name": "samtools_merge", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"bamfiles\": {\"__class__\": \"ConnectedValue\"}, \"bed_file\": {\"__class__\": \"RuntimeValue\"}, \"headerbam\": {\"__class__\": \"RuntimeValue\"}, \"idpg\": false, \"idrg\": false, \"region\": null, \"seed\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy1", + "tool_version": "1.22+galaxy2", "type": "tool", "uuid": "03cf4998-54d1-43b4-9005-828e8e1da14c", "when": "$(inputs.when)", @@ -14263,7 +14498,7 @@ }, "16": { "annotation": "", - "content_id": 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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy3", "errors": null, "id": 17, "input_connections": { @@ -14428,16 +14668,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy3", "tool_shed_repository": { - "changeset_revision": "ef678e1f70a2", + "changeset_revision": "a50321bc1a90", "name": "samtools_markdup", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"bamfile\": {\"__class__\": \"ConnectedValue\"}, \"existing_tags\": false, \"include_fails\": false, \"maxlen\": null, \"mode\": \"s\", \"odist\": \"2500\", \"output_options\": {\"stats\": \"yes\", \"output_format\": {\"select_oformat\": \"BAM\", \"__current_case__\": 1}}, \"remove\": true, \"supp\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": 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false, \"maxlen\": null, \"mode\": \"s\", \"odist\": \"2500\", \"output_options\": {\"stats\": \"yes\", \"output_format\": {\"select_oformat\": \"BAM\", \"__current_case__\": 1}}, \"remove\": false, \"supp\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy2", + "tool_version": "1.22+galaxy3", "type": "tool", "uuid": "9172e934-6ce0-4bc6-a526-e3d3fe539e58", "when": "$(inputs.when)", @@ -14634,7 +14874,7 @@ } }, "tags": [], - "uuid": "87b0f03c-8e91-4341-b599-f0d3da3b4c4f" + "uuid": "a2e3e20f-74ac-49a8-882d-a9015c691da1" }, "tool_id": null, "type": "subworkflow", @@ -14680,7 +14920,7 @@ }, "20": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0", "errors": null, "id": 20, "input_connections": { @@ -14725,16 +14965,16 @@ "output_name": "out_file1" } }, - "tool_id": 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+ "changeset_revision": "37c8eb55315d", "name": "samtools_merge", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"bamfiles\": {\"__class__\": \"ConnectedValue\"}, \"bed_file\": {\"__class__\": \"RuntimeValue\"}, \"headerbam\": {\"__class__\": \"RuntimeValue\"}, \"idpg\": false, \"idrg\": false, \"region\": null, \"seed\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy1", + "tool_version": "1.22+galaxy2", "type": "tool", "uuid": "7e687459-5bf3-4f11-8b91-2094c0fc2c59", "when": "$(inputs.when)", @@ -14936,7 +15185,7 @@ }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "errors": null, "id": 25, "input_connections": { @@ -14976,16 +15225,16 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "056f86469460", + "changeset_revision": "7087d9a23185", "name": "pretext_map", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"highRes\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": \"0\", \"sorting\": {\"sortby\": \"length\", \"__current_case__\": 1, \"sortorder\": \"descend\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"highRes\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": \"0\", \"sorting\": {\"sortby\": \"length\", \"__current_case__\": 1, \"sortorder\": \"descend\"}, \"ultraRes\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.2.3+galaxy0", + "tool_version": "0.2.4+galaxy1", "type": "tool", "uuid": "fd264ee1-352d-40fa-91bc-8b20f1d2bcda", "when": null, @@ -14993,7 +15242,7 @@ }, "26": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "errors": null, "id": 26, "input_connections": { @@ -15026,16 +15275,16 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "056f86469460", + "changeset_revision": "7087d9a23185", "name": "pretext_map", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter\": {\"filter_type\": \"\", 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"toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "errors": null, "id": 27, "input_connections": { @@ -15087,16 +15336,16 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "056f86469460", + "changeset_revision": "7087d9a23185", "name": "pretext_map", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"highRes\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": {\"__class__\": \"ConnectedValue\"}, \"sorting\": {\"sortby\": \"length\", \"__current_case__\": 1, \"sortorder\": \"descend\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"highRes\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": {\"__class__\": \"ConnectedValue\"}, \"sorting\": {\"sortby\": \"length\", \"__current_case__\": 1, \"sortorder\": \"descend\"}, \"ultraRes\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.2.3+galaxy0", + "tool_version": "0.2.4+galaxy1", "type": "tool", "uuid": "4d50046f-bcad-487a-8c73-8c41b0ceab05", "when": null, @@ -15104,7 +15353,7 @@ }, "28": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "errors": null, "id": 28, "input_connections": { @@ -15144,16 +15393,16 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "056f86469460", + "changeset_revision": "7087d9a23185", "name": "pretext_map", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"highRes\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": {\"__class__\": \"ConnectedValue\"}, \"sorting\": {\"sortby\": \"length\", \"__current_case__\": 1, \"sortorder\": \"descend\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"highRes\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": {\"__class__\": \"ConnectedValue\"}, \"sorting\": {\"sortby\": \"length\", \"__current_case__\": 1, \"sortorder\": \"descend\"}, \"ultraRes\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.2.3+galaxy0", + "tool_version": "0.2.4+galaxy1", "type": "tool", "uuid": "a19293a8-6347-4ef6-93fc-d640c5fb6a13", "when": null, @@ -15691,7 +15940,7 @@ }, "39": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.7+galaxy0", "errors": null, "id": 39, "input_connections": { @@ -15720,16 +15969,16 @@ "output_name": "pretext_snap_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.7+galaxy0", "tool_shed_repository": { - "changeset_revision": "ff02cf8f66f0", + "changeset_revision": "c4fb391275a0", "name": "pretext_snapshot", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"colormap\": \"8\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, 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"toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.7+galaxy0", "tool_shed_repository": { - "changeset_revision": "ff02cf8f66f0", + "changeset_revision": "c4fb391275a0", "name": "pretext_snapshot", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"colormap\": \"8\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": \"yes\", \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"2000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.0.5+galaxy1", + "tool_version": "0.0.7+galaxy0", "type": "tool", "uuid": "01b0af42-60b9-4422-8f0d-e7bc202242ea", "when": null, @@ -15932,7 +16181,12 @@ "output_name": "text_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": "False if Q telomere track is empty", "name": "Map parameter value", "outputs": [ @@ -15978,7 +16232,12 @@ "output_name": "text_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": "False if P telomere track is empty", "name": "Map parameter value", "outputs": [ @@ -16139,7 +16398,7 @@ }, "48": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0", "errors": null, "id": 48, "input_connections": { @@ -16168,16 +16427,16 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "aff5135563c6", + "changeset_revision": "61f9ddbc63ca", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"c2-1\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "2.1", + "tool_version": "2.1+galaxy0", "type": "tool", "uuid": "7ae87113-f9b8-4be3-bb11-68af03f58b29", "when": null, @@ -17207,7 +17466,7 @@ } }, "tags": [], - "uuid": "0eeb0b61-e256-4457-b5bc-9af658cc5248" + "uuid": "ae02907d-d05d-47cc-ad5e-04c2978d03af" }, 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