From c2a75dd591dc5bca5af25470d8a33ffa8139a8bb Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 27 Mar 2024 08:42:20 -0400 Subject: [PATCH] add Busco gff output --- .../Purge-duplicate-contigs-VGP6/CHANGELOG.md | 4 ++ .../Purge-duplicate-contigs-VGP6.ga | 56 +++++++++++++++---- 2 files changed, 48 insertions(+), 12 deletions(-) diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md index b04c4e621..a335e4842 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## [0.3.7] 2024-03-27 + +- Add Gff output to Busco + ## [0.3.6] 2024-03-25 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga index d562a7dd8..9f69032c0 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.3.6", + "release": "0.3.7", "name": "Purge-duplicate-contigs-VGP6", "steps": { "0": { @@ -1082,6 +1082,10 @@ } }, "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "input" + }, { "description": "runtime parameter for tool Busco", "name": "lineage" @@ -1105,6 +1109,10 @@ { "name": "summary_image", "type": "png" + }, + { + "name": "busco_gff", + "type": "gff3" } ], "position": { @@ -1112,6 +1120,13 @@ "top": 1520.5883525119295 }, "post_job_actions": { + "TagDatasetActionbusco_gff": { + "action_arguments": { + "tags": "name:p1,busco_p1_gff" + }, + "action_type": "TagDatasetAction", + "output_name": "busco_gff" + }, "TagDatasetActionbusco_missing": { "action_arguments": { "tags": "busco_p1_missing, #p1" @@ -1148,12 +1163,17 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "88073363-2f5c-4486-a23a-1cfdc4f5e6a6", "when": null, "workflow_outputs": [ + { + "label": "Busco Gff Purged Primary Assembly", + "output_name": "busco_gff", + "uuid": "82fb18a1-ff3a-401c-8c85-910ed255168d" + }, { "label": "Busco on Purged Primary assembly: short summary", "output_name": "busco_sum", @@ -1993,15 +2013,15 @@ "uuid": "0496de4b-ec62-48d5-8c36-e2f946ca728d", "when": null, "workflow_outputs": [ - { - "label": "Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot", - "output_name": "hist", - "uuid": "f12c1cc7-a12a-4314-ae16-2738b80afe70" - }, { "label": "Cutoffs for alternate assembly", "output_name": "calcuts_cutoff", "uuid": "49bf0c95-0290-4f8b-a9d7-2f17f53e9d26" + }, + { + "label": "Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot", + "output_name": "hist", + "uuid": "f12c1cc7-a12a-4314-ae16-2738b80afe70" } ] }, @@ -2399,6 +2419,13 @@ "action_type": "TagDatasetAction", "output_name": "bed_files" }, + "TagDatasetActionhist_files": { + "action_arguments": { + "tags": "name:p,merqury_p_gff" + }, + "action_type": "TagDatasetAction", + "output_name": "hist_files" + }, "TagDatasetActionpng_files": { "action_arguments": { "tags": "merqury_p_png, #p" @@ -2449,14 +2476,19 @@ "when": null, "workflow_outputs": [ { - "label": "Merqury on Phased assemblies: stats", - "output_name": "stats_files", - "uuid": "70f44477-6a3b-4ac4-b01a-f812ea880bae" + "label": "Merqury on Phased assemblies: Gff", + "output_name": "hist_files", + "uuid": "bc07fbdf-b57c-4e11-a03b-5693741b3b4b" }, { "label": "Merqury on Phased assemblies: Images", "output_name": "png_files", "uuid": "ff9cfc96-449e-41d8-9c10-7f586ab6f479" + }, + { + "label": "Merqury on Phased assemblies: stats", + "output_name": "stats_files", + "uuid": "70f44477-6a3b-4ac4-b01a-f812ea880bae" } ] }, @@ -3543,6 +3575,6 @@ "tags": [ "VGP_curated" ], - "uuid": "6b1b52f2-833c-4532-95c0-c85bc238fc76", - "version": 1 + "uuid": "3b1b0946-90db-441b-9d76-5b9b123e5ef6", + "version": 2 } \ No newline at end of file