diff --git a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md index e2d6e83a23..9a0150635f 100644 --- a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [2.5] - 2026-06-22 + +### Automatic update +- `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/multiqc/multiqc/1.33+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1` +- `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/iuc/minimap2/minimap2/2.30+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy1` +- `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/0.2.6+galaxy4` +- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1` + ## [2.4] - 2026-04-29 ### Automatic update diff --git a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga index e198200916..1c21c6d998 100644 --- a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga +++ b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga @@ -92,9 +92,9 @@ }, { "child_steps": [ - 44, 34, 43, + 44, 50, 55, 67, @@ -218,9 +218,8 @@ ], "format-version": "0.1", "license": "MIT", - "release": "2.4", "name": "PretextMap Generation from 1 or 2 haplotypes", - "readme": "# Hi-C Contact Map Generation for Manual Curation of Genome Assemblies\n\nThis workflow generates Hi-C contact maps for diploid genome assemblies in the Pretext format. It includes tracks for:\n- **Gene annotations** (Compleasm)\n- **PacBio read coverage** and coverage gaps\n- **Telomeres** (with flexible pattern detection)\n- **Assembly gaps**\n\nThe Pretext files can be opened in PretextView for manual curation of genome assemblies.\n\n## Inputs\n\n### Required Inputs\n\n1. **Haplotype 1** [fasta] - Primary haplotype assembly\n2. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies\n3. **Haplotype 2** [fasta] - Secondary haplotype assembly (required if using two haplotypes)\n4. **Hi-C reads** [fastq] - Paired collection containing Hi-C data\n5. **PacBio reads** [fastq] - Collection of PacBio HiFi reads\n\n### Assembly Annotation Parameters\n\n6. **Generate gene annotations** [boolean] - Enable/disable Compleasm gene annotation tracks (disable for large genomes to avoid memory issues)\n7. **Species Name** [text] - Species identifier for gene annotation\n8. **Assembly Name** [text] - Assembly identifier (e.g., toLid)\n9. **Lineage for Compleasm** [text] - BUSCO lineage dataset (e.g., vertebrata_odb10, primates_odb10)\n10. **Database for Compleasm** [text] - Compleasm database version (default: v5)\n\n### Scaffold Naming Options\n\n11. **Do you want to add suffixes to the scaffold names?** [boolean] - Select yes if scaffold names do not contain haplotype information\n12. **First Haplotype suffix** [text] - Suffix for haplotype 1 scaffolds (default: H1)\n13. **Second Haplotype suffix** [text] - Suffix for haplotype 2 scaffolds (default: H2)\n\n### Hi-C Processing Options\n\n14. **Do you want to trim the Hi-C data?** [boolean] - If yes, removes 5bp at the end of Hi-C reads (recommended for Arima Hi-C data if the map looks \"noisy\")\n15. **Remove duplicated Hi-C reads?** [boolean] - Remove PCR duplicates from Hi-C alignments using Samtools markdup\n16. **Minimum Mapping Quality** [integer] - Minimum MAPQ score for filtered PretextMap (default: 10; set to 0 to keep all mapped reads)\n\n### PacBio Processing Options\n\n17. **Remove adapters from HiFi reads?** [boolean] - Trim adapters from PacBio HiFi reads using Cutadapt\n\n### Telomere Detection\n\n18. **Canonical telomeric pattern** [text] - Expected telomere repeat sequence (default: TTAGGG for vertebrates; use CCCTAA for reverse complement)\n19. **Telomeric Patterns to explore (comma-separated), IUPAC allowed** [text] - Additional telomeric patterns to search for (e.g., TTAGGG,CCCTAA)\n\n### Hi-C Map Resolution\n\n20. **Generate high resolution Hi-C maps** [boolean] - Generate high resolution Pretext maps (slower, requires more resources)\n\n### Visualization Options\n\n21. **Bin Size for Bigwig files** [integer] - Resolution for coverage tracks (default: 100; larger values = smaller files but lower resolution)\n\n## Outputs\n\n### Assembly Outputs\n\n1. **Assembly for curation** [fasta] - Merged assembly (if two haplotypes used) or single haplotype with optional suffix\n2. **Assembly Info** [tabular] - Summary statistics from gfastats\n3. **Both Haplotypes merged** [fasta] - Concatenated assembly file\n\n### Gene Annotation Outputs\n\n4. **Compleasm Genes track** [GFF] - Combined gene annotations for Pretext track (if gene annotations enabled)\n\n### Hi-C Alignment Outputs\n\n5. **Merged Hi-C Alignments on Scaffolds** [BAM] - Combined Hi-C read alignments\n6. **Precuration Hi-C alignments** [BAM] - Hi-C alignments before filtering\n7. **Trimmed Hi-C data** [fastq] - Hi-C reads after adapter trimming (if trimming enabled)\n8. **Hi-C duplication stats on Scaffolds** [tabular] - Samtools markdup statistics (if duplicate removal enabled)\n9. **Hi-C duplication stats on Scaffolds: MultiQc** [HTML] - MultiQC report of duplicate statistics (if duplicate removal enabled)\n10. **Hi-C duplication stats on Scaffolds: Raw** [tabular] - Raw Samtools markdup metrics (if duplicate removal enabled)\n11. **Pairtools Multiqc Stats on Scaffolds** [tabular] - Pairtools statistics\n12. **Pairtools MultiQc on Scaffolds: Plots** [HTML] - Pairtools MultiQC plots\n\n### PacBio Processing Outputs\n\n13. **HiFi reads without adapters** [fastq] - Adapter-trimmed PacBio reads (if adapter removal enabled)\n14. **HiFi reads adapters trimming report** [tabular] - Cutadapt trimming statistics (if adapter removal enabled)\n\n### PacBio Coverage Outputs\n\n15. **BigWig Coverage** [bigwig] - PacBio read coverage track\n16. **Coverage Gaps Track** [bedgraph] - Regions with low or no PacBio coverage\n17. **Merged HiFi Alignments** [BAM] - Combined PacBio alignments\n\n### Telomere Outputs\n\n18. **Telomere Report** [tabular] - Comprehensive telomere analysis from Teloscope\n19. **terminal telomeres** [bedgraph] - All detected telomeric regions\n20. **P telomeres bed** [BED] - P-arm (5') telomeres only\n21. **Q telomeres Bed** [BED] - Q-arm (3') telomeres only\n\n### Gap Outputs\n\n22. **Gaps Bed** [BED] - Assembly gap coordinates\n23. **Gaps Bedgraph** [bedgraph] - Assembly gap track for Pretext\n\n### Assembly Haplotype Outputs\n\n24. **Decontaminated Hap1 with Suffix** [fasta] - Haplotype 1 with suffix applied\n25. **Decontaminated Hap2 with Suffix** [fasta] - Haplotype 2 with suffix applied\n\n### Pretext Map Outputs\n\nAll Pretext outputs are generated in two versions:\n- **With MAPQ filtering** (default MAPQ \u2265 10): Cleaner maps with high-confidence contacts\n- **Without filtering (Multimapping)**: Shows all mapped contacts including low-quality alignments\n\n26. **Pretext All tracks** [pretext] - Contact map with all annotation tracks (MAPQ filtered)\n27. **Pretext All tracks - Multimapping** [pretext] - Contact map with all tracks (unfiltered)\n28. **Pretext Snapshot With tracks** [PNG] - Image of contact map with tracks (MAPQ filtered)\n29. **Pretext Snapshot With tracks - Multimapping** [PNG] - Image of contact map with tracks (unfiltered)\n\n## Usage Notes\n\n### When to trim Hi-C data\nEnable trimming if you're using Arima Hi-C kits and notice a \"noisy\" contact map pattern.\n\n### MAPQ filtering\nThe default MAPQ threshold of 10 removes ambiguously mapped Hi-C contacts, resulting in cleaner contact maps. Compare both filtered and unfiltered outputs to assess mapping quality.\n\n### Choosing Compleasm lineage\nSelect the most specific lineage available for your species:\n- Vertebrates: `vertebrata_odb10`\n- Mammals: `mammalia_odb10`\n- Primates: `primates_odb10`\n- Birds: `aves_odb10`\n- See [BUSCO datasets](https://busco-data.ezlab.org/v5/data/lineages/) for complete list\n\n### Telomere patterns\n- Vertebrates typically use TTAGGG\n- Some species have variant patterns - check the literature\n- IUPAC codes are supported (e.g., TTAGGK for TTAGGG/TTAGGC)\n\n## Citation\n\nIf you use this workflow, please cite:\n- PretextMap and PretextView tools\n- Compleasm for gene completeness assessment\n- Teloscope for telomere detection\n- Other tools as listed in the workflow\n", + "readme": "# Hi-C Contact Map Generation for Manual Curation of Genome Assemblies\n\nThis workflow generates Hi-C contact maps for diploid genome assemblies in the Pretext format. It includes tracks for:\n- **Gene annotations** (Compleasm)\n- **PacBio read coverage** and coverage gaps\n- **Telomeres** (with flexible pattern detection)\n- **Assembly gaps**\n\nThe Pretext files can be opened in PretextView for manual curation of genome assemblies.\n\n## Inputs\n\n### Required Inputs\n\n1. **Haplotype 1** [fasta] - Primary haplotype assembly\n2. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies\n3. **Haplotype 2** [fasta] - Secondary haplotype assembly (required if using two haplotypes)\n4. **Hi-C reads** [fastq] - Paired collection containing Hi-C data\n5. **PacBio reads** [fastq] - Collection of PacBio HiFi reads\n\n### Assembly Annotation Parameters\n\n6. **Generate gene annotations** [boolean] - Enable/disable Compleasm gene annotation tracks (disable for large genomes to avoid memory issues)\n7. **Species Name** [text] - Species identifier for gene annotation\n8. **Assembly Name** [text] - Assembly identifier (e.g., toLid)\n9. **Lineage for Compleasm** [text] - BUSCO lineage dataset (e.g., vertebrata_odb10, primates_odb10)\n10. **Database for Compleasm** [text] - Compleasm database version (default: v5)\n\n### Scaffold Naming Options\n\n11. **Do you want to add suffixes to the scaffold names?** [boolean] - Select yes if scaffold names do not contain haplotype information\n12. **First Haplotype suffix** [text] - Suffix for haplotype 1 scaffolds (default: H1)\n13. **Second Haplotype suffix** [text] - Suffix for haplotype 2 scaffolds (default: H2)\n\n### Hi-C Processing Options\n\n14. **Do you want to trim the Hi-C data?** [boolean] - If yes, removes 5bp at the end of Hi-C reads (recommended for Arima Hi-C data if the map looks \"noisy\")\n15. **Remove duplicated Hi-C reads?** [boolean] - Remove PCR duplicates from Hi-C alignments using Samtools markdup\n16. **Minimum Mapping Quality** [integer] - Minimum MAPQ score for filtered PretextMap (default: 10; set to 0 to keep all mapped reads)\n\n### PacBio Processing Options\n\n17. **Remove adapters from HiFi reads?** [boolean] - Trim adapters from PacBio HiFi reads using Cutadapt\n\n### Telomere Detection\n\n18. **Canonical telomeric pattern** [text] - Expected telomere repeat sequence (default: TTAGGG for vertebrates; use CCCTAA for reverse complement)\n19. **Telomeric Patterns to explore (comma-separated), IUPAC allowed** [text] - Additional telomeric patterns to search for (e.g., TTAGGG,CCCTAA)\n\n### Hi-C Map Resolution\n\n20. **Generate high resolution Hi-C maps** [boolean] - Generate high resolution Pretext maps (slower, requires more resources)\n\n### Visualization Options\n\n21. **Bin Size for Bigwig files** [integer] - Resolution for coverage tracks (default: 100; larger values = smaller files but lower resolution)\n\n## Outputs\n\n### Assembly Outputs\n\n1. **Assembly for curation** [fasta] - Merged assembly (if two haplotypes used) or single haplotype with optional suffix\n2. **Assembly Info** [tabular] - Summary statistics from gfastats\n3. **Both Haplotypes merged** [fasta] - Concatenated assembly file\n\n### Gene Annotation Outputs\n\n4. **Compleasm Genes track** [GFF] - Combined gene annotations for Pretext track (if gene annotations enabled)\n\n### Hi-C Alignment Outputs\n\n5. **Merged Hi-C Alignments on Scaffolds** [BAM] - Combined Hi-C read alignments\n6. **Precuration Hi-C alignments** [BAM] - Hi-C alignments before filtering\n7. **Trimmed Hi-C data** [fastq] - Hi-C reads after adapter trimming (if trimming enabled)\n8. **Hi-C duplication stats on Scaffolds** [tabular] - Samtools markdup statistics (if duplicate removal enabled)\n9. **Hi-C duplication stats on Scaffolds: MultiQc** [HTML] - MultiQC report of duplicate statistics (if duplicate removal enabled)\n10. **Hi-C duplication stats on Scaffolds: Raw** [tabular] - Raw Samtools markdup metrics (if duplicate removal enabled)\n11. **Pairtools Multiqc Stats on Scaffolds** [tabular] - Pairtools statistics\n12. **Pairtools MultiQc on Scaffolds: Plots** [HTML] - Pairtools MultiQC plots\n\n### PacBio Processing Outputs\n\n13. **HiFi reads without adapters** [fastq] - Adapter-trimmed PacBio reads (if adapter removal enabled)\n14. **HiFi reads adapters trimming report** [tabular] - Cutadapt trimming statistics (if adapter removal enabled)\n\n### PacBio Coverage Outputs\n\n15. **BigWig Coverage** [bigwig] - PacBio read coverage track\n16. **Coverage Gaps Track** [bedgraph] - Regions with low or no PacBio coverage\n17. **Merged HiFi Alignments** [BAM] - Combined PacBio alignments\n\n### Telomere Outputs\n\n18. **Telomere Report** [tabular] - Comprehensive telomere analysis from Teloscope\n19. **terminal telomeres** [bedgraph] - All detected telomeric regions\n20. **P telomeres bed** [BED] - P-arm (5') telomeres only\n21. **Q telomeres Bed** [BED] - Q-arm (3') telomeres only\n\n### Gap Outputs\n\n22. **Gaps Bed** [BED] - Assembly gap coordinates\n23. **Gaps Bedgraph** [bedgraph] - Assembly gap track for Pretext\n\n### Assembly Haplotype Outputs\n\n24. **Decontaminated Hap1 with Suffix** [fasta] - Haplotype 1 with suffix applied\n25. **Decontaminated Hap2 with Suffix** [fasta] - Haplotype 2 with suffix applied\n\n### Pretext Map Outputs\n\nAll Pretext outputs are generated in two versions:\n- **With MAPQ filtering** (default MAPQ ≥ 10): Cleaner maps with high-confidence contacts\n- **Without filtering (Multimapping)**: Shows all mapped contacts including low-quality alignments\n\n26. **Pretext All tracks** [pretext] - Contact map with all annotation tracks (MAPQ filtered)\n27. **Pretext All tracks - Multimapping** [pretext] - Contact map with all tracks (unfiltered)\n28. **Pretext Snapshot With tracks** [PNG] - Image of contact map with tracks (MAPQ filtered)\n29. **Pretext Snapshot With tracks - Multimapping** [PNG] - Image of contact map with tracks (unfiltered)\n\n## Usage Notes\n\n### When to trim Hi-C data\nEnable trimming if you're using Arima Hi-C kits and notice a \"noisy\" contact map pattern.\n\n### MAPQ filtering\nThe default MAPQ threshold of 10 removes ambiguously mapped Hi-C contacts, resulting in cleaner contact maps. Compare both filtered and unfiltered outputs to assess mapping quality.\n\n### Choosing Compleasm lineage\nSelect the most specific lineage available for your species:\n- Vertebrates: `vertebrata_odb10`\n- Mammals: `mammalia_odb10`\n- Primates: `primates_odb10`\n- Birds: `aves_odb10`\n- See [BUSCO datasets](https://busco-data.ezlab.org/v5/data/lineages/) for complete list\n\n### Telomere patterns\n- Vertebrates typically use TTAGGG\n- Some species have variant patterns - check the literature\n- IUPAC codes are supported (e.g., TTAGGK for TTAGGG/TTAGGC)\n\n## Citation\n\nIf you use this workflow, please cite:\n- PretextMap and PretextView tools\n- Compleasm for gene completeness assessment\n- Teloscope for telomere detection\n- Other tools as listed in the workflow\n", "report": { "markdown": "# Precuration workflow on:\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Info\")\n```\n\n## Duplication Stats\n\nSamtools markdup deduplication stats (if applicable)\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats\")\n```\n\n\n\nPairtools stats\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats: MultiQC\")\n```\n\n## Telomere report\n\n```galaxy\nhistory_dataset_embedded(output=\"Telomere Report\")\n```\n\n## Pretext Snapshots\n\nWith Multimapping\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks - Multimapping\")\n```\n\n\nWith MAPQ filtering\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks\")\n```\n\n\n" }, @@ -866,7 +865,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": "Hap2 not provided", "name": "Map parameter value", "outputs": [ @@ -1480,7 +1484,7 @@ } }, "tags": [], - "uuid": "981c39a4-4f6b-47d1-ac30-08ce1d6a9394" + "uuid": "f1854d1b-7b2b-458b-b752-4d357ad42878" }, "tool_id": null, "type": "subworkflow", @@ -1721,7 +1725,12 @@ "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": [ @@ -1773,7 +1782,12 @@ "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": [ @@ -1825,7 +1839,12 @@ "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": [ @@ -1868,7 +1887,7 @@ } }, "tags": [], - "uuid": "dddd606b-1301-4fa4-bde5-0281131c064d" + "uuid": "7abeef23-c38c-4fac-b0ac-d388254da9ab" }, "tool_id": null, "type": "subworkflow", @@ -1891,7 +1910,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -2244,7 +2268,7 @@ } }, "tags": [], - "uuid": "3b32e78f-36dd-4dc9-94c6-2b62613fb166" + "uuid": "fffe1aaf-9d47-417e-bbe5-21e2f20085a2" }, "tool_id": null, "type": "subworkflow", @@ -2980,7 +3004,12 @@ "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": [ @@ -3032,7 +3061,12 @@ "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": [ @@ -3084,7 +3118,12 @@ "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": [ @@ -3127,7 +3166,7 @@ } }, "tags": [], - "uuid": "5f125eb2-c713-4df4-8a71-e49ba9852fc8" + "uuid": "57f8cecb-a284-4165-b2d1-a5254f392d0e" }, "tool_id": null, "type": "subworkflow", @@ -3150,7 +3189,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": "Trim Hi-C reads 2", "name": "Cutadapt", "outputs": [ @@ -3219,7 +3263,12 @@ "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": [ @@ -3334,7 +3383,16 @@ "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": [ @@ -3378,7 +3436,7 @@ }, "11": { "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": 11, "input_connections": { @@ -3414,16 +3472,16 @@ "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", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addms\": true, \"bamfile\": {\"__class__\": \"ConnectedValue\"}, \"noprop\": false, \"remsec\": false, \"tempcigar\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy2", + "tool_version": "1.22+galaxy3", "type": "tool", "uuid": "1db82bd3-3108-4f39-a0f0-f9e5450e1f4f", "when": null, @@ -3593,7 +3651,16 @@ "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": [ @@ -3804,7 +3871,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1", "errors": null, "id": 19, "input_connections": { @@ -3813,7 +3880,12 @@ "output_name": "dedup_pairs_stats" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MultiQC", + "name": "image_content_input" + } + ], "label": "Pairtools Multiqc", "name": "MultiQC", "outputs": [ @@ -3887,16 +3959,16 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1", "tool_shed_repository": { - "changeset_revision": "862943c10425", + "changeset_revision": "fac2260bc88a", "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__\": 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+galaxy3", + "tool_version": "1.35+galaxy1", "type": "tool", "uuid": "66905684-e6a1-4d2a-91ad-4809ca5e864a", "when": null, @@ -3920,7 +3992,7 @@ }, "20": { "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": 20, "input_connections": { @@ -3969,16 +4041,16 @@ "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": "1.22+galaxy2", + "tool_version": "1.22+galaxy3", "type": "tool", "uuid": "294a749f-e96a-45d7-9e2b-fd71d0afe5b2", "when": "$(inputs.when)", @@ -3986,7 +4058,7 @@ }, "21": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy3", "errors": null, "id": 21, "input_connections": { @@ -4028,16 +4100,16 @@ "output_name": "stats_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.22+galaxy3", "tool_shed_repository": { - "changeset_revision": "ef678e1f70a2", + "changeset_revision": "a50321bc1a90", "name": "samtools_markdup", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"bamfile\": {\"__class__\": \"RuntimeValue\"}, \"existing_tags\": false, \"include_fails\": false, \"maxlen\": null, \"mode\": \"s\", \"odist\": \"2500\", \"output_options\": {\"stats\": \"yes\", \"output_format\": {\"select_oformat\": \"BAM\", \"__current_case__\": 1}}, \"remove\": false, \"supp\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"bamfile\": {\"__class__\": \"ConnectedValue\"}, \"existing_tags\": false, \"include_fails\": false, \"maxlen\": null, \"mode\": \"s\", \"odist\": \"2500\", \"output_options\": {\"stats\": \"yes\", \"output_format\": {\"select_oformat\": \"BAM\", \"__current_case__\": 1}}, \"remove\": false, \"supp\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy2", + "tool_version": "1.22+galaxy3", "type": "tool", "uuid": "9172e934-6ce0-4bc6-a526-e3d3fe539e58", "when": "$(inputs.when)", @@ -4175,7 +4247,7 @@ } }, "tags": [], - "uuid": "ffd72082-7eba-4b9b-a8c6-c85c94891a79" + "uuid": "d041796d-061f-4838-a41b-6bddd87c9b26" }, "tool_id": null, "type": "subworkflow", @@ -4386,7 +4458,7 @@ }, "34": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.30+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy1", "errors": null, "id": 34, "input_connections": { @@ -4399,7 +4471,16 @@ "output_name": "data_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -4419,16 +4500,16 @@ "output_name": "alignment_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.30+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy1", "tool_shed_repository": { - "changeset_revision": "3faf9a2bf58d", + "changeset_revision": "7a6382582d76", "name": "minimap2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"b\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"end_bonus\": \"0\", \"score_N\": \"1\", \"no_end_flt\": true, \"jump_min_match\": \"3\", \"end_seed_pen\": \"6\", \"cap_sw_mem\": \"100m\", \"cap_kalloc\": \"500m\"}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"map-hifi\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"BAM\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false, \"copy_comments\": false, \"ds_tag\": false, \"secondary_seq\": false, \"two_io_threads\": false, \"seed\": null}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null, \"rmq_inner\": \"1000\", \"no_hash_name\": false, \"pairing\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"b\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"end_bonus\": \"0\", \"score_N\": \"1\", \"no_end_flt\": true, \"jump_min_match\": \"3\", \"end_seed_pen\": \"6\", \"cap_sw_mem\": \"100m\", \"cap_kalloc\": \"500m\"}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"map-hifi\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"BAM\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false, \"copy_comments\": false, \"ds_tag\": false, \"secondary_seq\": false, \"two_io_threads\": false, \"seed\": null}, \"mapping_options\": {\"N\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null, \"rmq_inner\": \"1000\", \"no_hash_name\": false}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "2.30+galaxy0", + "tool_version": "2.31+galaxy1", "type": "tool", "uuid": "9c9cf464-20c0-457f-9c37-8a7018546bd1", "when": null, @@ -4663,7 +4744,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy4", "errors": null, "id": 5, "input_connections": { @@ -4718,16 +4799,16 @@ "output_name": "miniprot" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy4", "tool_shed_repository": { - "changeset_revision": "fc7334661489", + "changeset_revision": "f421fd0c42ea", "name": "compleasm", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"busco_database\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"miniprot\"], \"specified_contigs\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.2.6+galaxy3", + "tool_version": "0.2.6+galaxy4", "type": "tool", "uuid": "e4ca5b86-c0b2-464a-b382-a4f4e97c40a0", "when": null, @@ -4746,7 +4827,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy4", "errors": null, "id": 6, "input_connections": { @@ -4805,16 +4886,16 @@ "output_name": "miniprot" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy4", "tool_shed_repository": { - "changeset_revision": "fc7334661489", + "changeset_revision": "f421fd0c42ea", "name": "compleasm", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"busco_database\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"miniprot\"], \"specified_contigs\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.2.6+galaxy3", + "tool_version": "0.2.6+galaxy4", "type": "tool", "uuid": "f1c6f5a9-c3a6-42b3-ae7c-8a10068550b3", "when": "$(inputs.when)", @@ -5127,7 +5208,7 @@ } }, "tags": [], - "uuid": "18b64162-46a2-4251-bfa5-961b9be0e794" + "uuid": "54bad220-950d-48ad-8883-38c88f2579e7" }, "tool_id": null, "type": "subworkflow", @@ -5143,7 +5224,7 @@ }, "36": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "errors": null, "id": 36, "input_connections": { @@ -5187,16 +5268,16 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "bd07b0d0f568", + "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": "0.2.4+galaxy0", + "tool_version": "0.2.4+galaxy1", "type": "tool", "uuid": "2bc11d1e-ba89-4a9c-80c9-2b83aa638457", "when": null, @@ -5204,7 +5285,7 @@ }, "37": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "errors": null, "id": 37, "input_connections": { @@ -5244,16 +5325,16 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "bd07b0d0f568", + "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": "0.2.4+galaxy0", + "tool_version": "0.2.4+galaxy1", "type": "tool", "uuid": "b7934163-451f-4cab-9f11-2b88bc88f535", "when": null, @@ -5261,7 +5342,7 @@ }, "38": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "errors": null, "id": 38, "input_connections": { @@ -5290,16 +5371,16 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "bd07b0d0f568", + "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\": \"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\": false, \"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": "0.2.4+galaxy0", + "tool_version": "0.2.4+galaxy1", "type": "tool", "uuid": "5a5244b8-55c5-454f-89a0-34e156f18a98", "when": null, @@ -5307,7 +5388,7 @@ }, "39": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "errors": null, "id": 39, "input_connections": { @@ -5340,16 +5421,16 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "bd07b0d0f568", + "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": "0.2.4+galaxy0", + "tool_version": "0.2.4+galaxy1", "type": "tool", "uuid": "e70fec59-6087-46ec-964c-aece775f69ca", "when": null, @@ -5532,7 +5613,16 @@ "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": [ @@ -6242,7 +6332,12 @@ "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": [ @@ -6288,7 +6383,12 @@ "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": [ @@ -7510,6 +7610,7 @@ } }, "tags": [], - "uuid": "df881079-652c-4da2-ad8f-c3b098f5ce91", - "version": 4 -} + "uuid": "2ffa1785-8f2c-46e3-b87a-aee4640fe09e", + "version": 1, + "release": "2.5" +} \ No newline at end of file