From 6f881fb8a49d3b71fe397096b71a2a8388560174 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 19 May 2025 04:23:40 +0000 Subject: [PATCH 1/3] Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.5 to 0.3.6 --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 139 ++++++++++++++---- .../CHANGELOG.md | 5 + 2 files changed, 113 insertions(+), 31 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index eee8bc0793..81828dac7f 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -20,7 +20,6 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.3.5", "name": "Genome Assembly from Hifi reads with HiC phasing - VGP4", "report": { "markdown": "\nSpecies\n\n```galaxy\nhistory_dataset_embedded(output=\"Species Name for workflow report\")\n```\n\nAssembly\n\r\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Name for workflow report\")\n```\r\n\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results \n\nDatabase: \r\n```galaxy\nhistory_dataset_embedded(output=\"Lineage for workflow report\")\n```\r\n\n\n\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -517,7 +516,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -599,7 +603,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -824,7 +833,12 @@ "output_name": "report" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MultiQC", + "name": "image_content_input" + } + ], "label": null, "name": "MultiQC", "outputs": [ @@ -1444,7 +1458,24 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Hifiasm", + "name": "assembly_options" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "hic_partition" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "hic_partition" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + } + ], "label": "Hifiasm", "name": "Hifiasm", "outputs": [ @@ -1785,7 +1816,12 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfastats gfa hap2 no sequences", "name": "gfastats", "outputs": [ @@ -1899,7 +1935,12 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfastats gfa hap1", "name": "gfastats", "outputs": [ @@ -1959,7 +2000,12 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfastats gfa hap2", "name": "gfastats", "outputs": [ @@ -2019,7 +2065,12 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -2064,7 +2115,12 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfastats gfa hap1 no sequences", "name": "gfastats", "outputs": [ @@ -2124,7 +2180,12 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -2622,7 +2683,7 @@ } }, "tags": [], - "uuid": "a3590f70-7886-4096-8d53-28869da840af" + "uuid": "37af071a-7430-4872-9d17-f0b5dbed96d4" }, "tool_id": null, "type": "subworkflow", @@ -3004,7 +3065,7 @@ } }, "tags": [], - "uuid": "ed2b25e0-e661-4e26-ad0b-629284ef607b" + "uuid": "a16e4b3b-e8c0-46dd-96a1-870ecb335664" }, "tool_id": null, "type": "subworkflow", @@ -3579,7 +3640,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2", "errors": null, "id": 9, "input_connections": { @@ -3617,15 +3678,15 @@ "output_name": "output1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2", "tool_shed_repository": { - "changeset_revision": "5298e06f14f9", + "changeset_revision": "f87634b12749", "name": "ggplot2_point", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"x\", \"xplot\": \"2\", \"ylab\": \"Nx (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.4.0+galaxy1", + "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"x\", \"xplot\": \"2\", \"ylab\": \"Nx (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.1+galaxy2", "type": "tool", "uuid": "18c6ac70-f4d3-4d68-93f8-c08afafbc6c5", "when": null, @@ -3639,7 +3700,7 @@ }, "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2", "errors": null, "id": 10, "input_connections": { @@ -3677,15 +3738,15 @@ "output_name": "output1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2", "tool_shed_repository": { - "changeset_revision": "5298e06f14f9", + "changeset_revision": "f87634b12749", "name": "ggplot2_point", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"Scaffold number\", \"xplot\": \"2\", \"ylab\": \"Cumulative Size (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.4.0+galaxy1", + "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"Scaffold number\", \"xplot\": \"2\", \"ylab\": \"Cumulative Size (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.1+galaxy2", "type": "tool", "uuid": "cce1fe43-55c6-4c1a-a957-ac7af9271c46", "when": null, @@ -3699,7 +3760,7 @@ } }, "tags": [], - "uuid": "1e832881-2cb0-4dcf-be0b-5b5075b17cb2" + "uuid": "b7c05272-e413-4781-bd31-7cfc04ca02b6" }, "tool_id": null, "type": "subworkflow", @@ -3737,7 +3798,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": "Busco Hap2", "name": "Busco", "outputs": [ @@ -3852,7 +3918,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": "Busco Hap1", "name": "Busco", "outputs": [ @@ -3967,7 +4038,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": "Merqury", "name": "Merqury", "outputs": [ @@ -4196,7 +4272,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"busco_database\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"miniprot\", \"translated_protein\", \"full_table\"], \"specified_contigs\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"busco_database\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"miniprot\", \"translated_protein\", \"full_table\"], \"specified_contigs\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.6+galaxy2", "type": "tool", "uuid": "8bf3b0a1-fb66-48d3-9fed-ba9d45c11ede", @@ -4333,7 +4409,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"busco_database\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"miniprot\", \"translated_protein\", \"full_table\"], \"specified_contigs\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"busco_database\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"miniprot\", \"translated_protein\", \"full_table\"], \"specified_contigs\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.6+galaxy2", "type": "tool", "uuid": "de8c2331-d858-45d4-9a89-cfc4d1f8d139", @@ -4747,6 +4823,7 @@ "VGP", "Reviewed" ], - "uuid": "4e348b09-dc7e-4dc4-93ed-70ce40e7caf8", - "version": 4 + "uuid": "04b5901a-7f1e-4374-b109-93cec5f1d119", + "version": 1, + "release": "0.3.6" } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index c87a060de0..e9a27890e1 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.3.6] - 2025-05-19 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2` + ## [0.3.5] - 2025-05-14 ### Changes From bfacefa7dc2e80c3ab6fbd51b2fc41b54d88cd78 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 27 May 2025 14:57:43 -0400 Subject: [PATCH 2/3] Correct missing parameters in ggplot --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 226 ++++++------------ 1 file changed, 70 insertions(+), 156 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index 81828dac7f..a6bac90abd 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -20,6 +20,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", + "release": "0.3.6", "name": "Genome Assembly from Hifi reads with HiC phasing - VGP4", "report": { "markdown": "\nSpecies\n\n```galaxy\nhistory_dataset_embedded(output=\"Species Name for workflow report\")\n```\n\nAssembly\n\r\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Name for workflow report\")\n```\r\n\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results \n\nDatabase: \r\n```galaxy\nhistory_dataset_embedded(output=\"Lineage for workflow report\")\n```\r\n\n\n\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -99,7 +100,7 @@ "top": 436.29891808920377 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\", \"fields\": null}", "tool_version": null, "type": "data_collection_input", "uuid": "f7ef62fa-eb54-4489-b444-b6be262a45c0", @@ -153,7 +154,7 @@ "top": 696.2638488357833 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}", + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\", \"fields\": null}", "tool_version": null, "type": "data_collection_input", "uuid": "8638c94b-e32e-4af6-9437-e169d9620b75", @@ -516,12 +517,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - } - ], + "inputs": [], "label": null, "name": "Cutadapt", "outputs": [ @@ -603,12 +599,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - } - ], + "inputs": [], "label": null, "name": "Cutadapt", "outputs": [ @@ -833,12 +824,7 @@ "output_name": "report" } }, - "inputs": [ - { - "description": "runtime parameter for tool MultiQC", - "name": "image_content_input" - } - ], + "inputs": [], "label": null, "name": "MultiQC", "outputs": [ @@ -1458,24 +1444,7 @@ "output_name": "out1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Hifiasm", - "name": "assembly_options" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "hic_partition" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "hic_partition" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "mode" - } - ], + "inputs": [], "label": "Hifiasm", "name": "Hifiasm", "outputs": [ @@ -1603,8 +1572,8 @@ } ], "position": { - "left": 1926.9095153244123, - "top": 353.9506096547913 + "left": 1914.7668021452362, + "top": 335.3975119201031 }, "post_job_actions": { "TagDatasetActionoutfile": { @@ -1816,12 +1785,7 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": "gfastats gfa hap2 no sequences", "name": "gfastats", "outputs": [ @@ -1935,12 +1899,7 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": "gfastats gfa hap1", "name": "gfastats", "outputs": [ @@ -2000,12 +1959,7 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": "gfastats gfa hap2", "name": "gfastats", "outputs": [ @@ -2065,12 +2019,7 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -2115,12 +2064,7 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": "gfastats gfa hap1 no sequences", "name": "gfastats", "outputs": [ @@ -2180,12 +2124,7 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -2329,8 +2268,8 @@ "name": "gfastats_data_prep", "outputs": [], "position": { - "left": 2206.9095153244125, - "top": 977.9506096547914 + "left": 2200.044670170724, + "top": 893.5014994382691 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2711,8 +2650,8 @@ "name": "gfastats_data_prep", "outputs": [], "position": { - "left": 2208.428185457544, - "top": 1138.3529534047914 + "left": 2186.785242502161, + "top": 1071.3190628049088 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -3292,6 +3231,9 @@ "format-version": "0.1", "license": "CC-BY-4.0", "name": "gfastats_plot", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "", @@ -3372,13 +3314,7 @@ "type": "parameter_input", "uuid": "6118c82a-61da-4856-9e25-1f0d93297527", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "894be62c-079d-4209-a098-1858de70948a" - } - ] + "workflow_outputs": [] }, "3": { "annotation": "", @@ -3405,13 +3341,7 @@ "type": "parameter_input", "uuid": "3204b6e0-bd83-4a8d-8ddb-3b0dd89dbd04", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "3d7657f7-0651-43c1-80bb-57c4fa6d3502" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "", @@ -3685,7 +3615,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"x\", \"xplot\": \"2\", \"ylab\": \"Nx (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0, \"xplot\": \"1\", \"yplot\": \"2\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"Nx Plot\", \"xlab\": \"x\", \"ylab\": \"Nx (Mb)\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_version": "3.5.1+galaxy2", "type": "tool", "uuid": "18c6ac70-f4d3-4d68-93f8-c08afafbc6c5", @@ -3745,7 +3675,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"Scaffold number\", \"xplot\": \"2\", \"ylab\": \"Cumulative Size (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0, \"xplot\": \"1\", \"yplot\": \"2\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"Size Plot\", \"xlab\": \"Scaffold number\", \"ylab\": \"Cumulative Size (Mb)\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_version": "3.5.1+galaxy2", "type": "tool", "uuid": "cce1fe43-55c6-4c1a-a957-ac7af9271c46", @@ -3760,22 +3690,22 @@ } }, "tags": [], - "uuid": "b7c05272-e413-4781-bd31-7cfc04ca02b6" + "uuid": "8db0cd5c-5fd6-435e-b0cd-e33073814a70" }, "tool_id": null, "type": "subworkflow", "uuid": "1b8e2d4e-3380-4414-bdb0-b356383c0ee2", "when": null, "workflow_outputs": [ - { - "label": "Size Plot", - "output_name": "Size Plot", - "uuid": "03a0d2a8-c2d5-4ca7-80fe-7d04d1c4894a" - }, { "label": "Nx Plot", "output_name": "Nx Plot", "uuid": "781f8511-c3fe-4954-afa8-d21c94c996a4" + }, + { + "label": "Size Plot", + "output_name": "Size Plot", + "uuid": "03a0d2a8-c2d5-4ca7-80fe-7d04d1c4894a" } ] }, @@ -3798,12 +3728,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - } - ], + "inputs": [], "label": "Busco Hap2", "name": "Busco", "outputs": [ @@ -3887,15 +3812,15 @@ "output_name": "summary_image", "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" }, - { - "label": "Busco Gff File - Hap2", - "output_name": "busco_gff", - "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" - }, { "label": "Busco Summary Hap2", "output_name": "busco_sum", "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" + }, + { + "label": "Busco Gff File - Hap2", + "output_name": "busco_gff", + "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" } ] }, @@ -3918,12 +3843,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - } - ], + "inputs": [], "label": "Busco Hap1", "name": "Busco", "outputs": [ @@ -4002,6 +3922,11 @@ "uuid": "a4957dee-45cc-4f34-ae2e-e07f93b9fcc4", "when": null, "workflow_outputs": [ + { + "label": "Busco Summary Image Hap1", + "output_name": "summary_image", + "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" + }, { "label": "Busco Summary Hap1", "output_name": "busco_sum", @@ -4011,11 +3936,6 @@ "label": "Busco Gff File - Hap1", "output_name": "busco_gff", "uuid": "ba26cb24-25d4-4669-982c-abe4816753a6" - }, - { - "label": "Busco Summary Image Hap1", - "output_name": "summary_image", - "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" } ] }, @@ -4038,12 +3958,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - } - ], + "inputs": [], "label": "Merqury", "name": "Merqury", "outputs": [ @@ -4278,16 +4193,6 @@ "uuid": "8bf3b0a1-fb66-48d3-9fed-ba9d45c11ede", "when": null, "workflow_outputs": [ - { - "label": "Compleasm on Contigs hap1 Full Table", - "output_name": "full_table", - "uuid": "65eb263e-d723-4992-8899-d032f07463b6" - }, - { - "label": "Compleasm on Contigs hap1 Miniprot", - "output_name": "miniprot", - "uuid": "6e760b6b-66c1-4123-a6bd-e8be378cccf4" - }, { "label": "Compleasm on Contigs hap1 Translated Proteins", "output_name": "translated_protein", @@ -4297,6 +4202,16 @@ "label": "Compleasm on Contigs hap1 Full Table Busco", "output_name": "full_table_busco", "uuid": "4503b22b-d2fe-4315-8086-732692a8ebe8" + }, + { + "label": "Compleasm on Contigs hap1 Full Table", + "output_name": "full_table", + "uuid": "65eb263e-d723-4992-8899-d032f07463b6" + }, + { + "label": "Compleasm on Contigs hap1 Miniprot", + "output_name": "miniprot", + "uuid": "6e760b6b-66c1-4123-a6bd-e8be378cccf4" } ] }, @@ -4416,9 +4331,9 @@ "when": null, "workflow_outputs": [ { - "label": "Compleasm hap2 Full Table Busco", - "output_name": "full_table_busco", - "uuid": "0eff5217-577f-483d-8d4a-ca3d04a98f8d" + "label": "Compleasm on Contigs hap2 Full Table", + "output_name": "full_table", + "uuid": "1d6fbe87-d899-4a8a-91c0-75d0d758ac2b" }, { "label": "Compleasm on Contigs hap2 Translated Proteins", @@ -4431,9 +4346,9 @@ "uuid": "5bae72bd-9ba3-429a-9352-ffed843c85ab" }, { - "label": "Compleasm on Contigs hap2 Full Table", - "output_name": "full_table", - "uuid": "1d6fbe87-d899-4a8a-91c0-75d0d758ac2b" + "label": "Compleasm hap2 Full Table Busco", + "output_name": "full_table_busco", + "uuid": "0eff5217-577f-483d-8d4a-ca3d04a98f8d" } ] }, @@ -4530,7 +4445,7 @@ }, "tool_id": "__EXTRACT_DATASET__", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.spectra-cn.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.1", + "tool_version": "1.0.2", "type": "tool", "uuid": "9b56f0a5-6a0c-4280-9338-c08831e89c3c", "when": null, @@ -4575,7 +4490,7 @@ }, "tool_id": "__EXTRACT_DATASET__", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.spectra-asm.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.1", + "tool_version": "1.0.2", "type": "tool", "uuid": "7fc6530d-4701-40c7-8b83-ba94ac3f11b5", "when": null, @@ -4620,7 +4535,7 @@ }, "tool_id": "__EXTRACT_DATASET__", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.1", + "tool_version": "1.0.2", "type": "tool", "uuid": "9e10d9ad-b16c-4904-a61f-6e1ec40fcf23", "when": null, @@ -4665,7 +4580,7 @@ }, "tool_id": "__EXTRACT_DATASET__", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.assembly_01.spectra-cn.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.1", + "tool_version": "1.0.2", "type": "tool", "uuid": "3d96d433-af93-45f1-aaab-907addea2461", "when": null, @@ -4710,7 +4625,7 @@ }, "tool_id": "__EXTRACT_DATASET__", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.completeness\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.1", + "tool_version": "1.0.2", "type": "tool", "uuid": "c7ad672f-341b-4f2a-a5d2-b5ba9771cfef", "when": null, @@ -4755,7 +4670,7 @@ }, "tool_id": "__EXTRACT_DATASET__", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.assembly_02.spectra-cn.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.1", + "tool_version": "1.0.2", "type": "tool", "uuid": "75f49e14-af85-4a07-81f1-3b75f591f965", "when": null, @@ -4823,7 +4738,6 @@ "VGP", "Reviewed" ], - "uuid": "04b5901a-7f1e-4374-b109-93cec5f1d119", - "version": 1, - "release": "0.3.6" -} \ No newline at end of file + "uuid": "5d328e09-f993-416f-a6ac-30c91d14c217", + "version": 5 +} From 91a267d82ea5188aafbb0103f6dc9ca2c983d29a Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 27 May 2025 15:04:53 -0400 Subject: [PATCH 3/3] fix column numbers for plotting --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 52 +++++++++---------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index a6bac90abd..01a0ed6595 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -3615,7 +3615,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0, \"xplot\": \"1\", \"yplot\": \"2\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"Nx Plot\", \"xlab\": \"x\", \"ylab\": \"Nx (Mb)\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0, \"xplot\": \"2\", \"yplot\": \"3\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"Nx Plot\", \"xlab\": \"x\", \"ylab\": \"Nx (Mb)\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_version": "3.5.1+galaxy2", "type": "tool", "uuid": "18c6ac70-f4d3-4d68-93f8-c08afafbc6c5", @@ -3675,7 +3675,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0, \"xplot\": \"1\", \"yplot\": \"2\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"Size Plot\", \"xlab\": \"Scaffold number\", \"ylab\": \"Cumulative Size (Mb)\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"cols\": {\"header\": \"yes\", \"__current_case__\": 0, \"xplot\": \"2\", \"yplot\": \"3\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"Size Plot\", \"xlab\": \"Scaffold number\", \"ylab\": \"Cumulative Size (Mb)\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_version": "3.5.1+galaxy2", "type": "tool", "uuid": "cce1fe43-55c6-4c1a-a957-ac7af9271c46", @@ -3690,7 +3690,7 @@ } }, "tags": [], - "uuid": "8db0cd5c-5fd6-435e-b0cd-e33073814a70" + "uuid": "5cd0bc4e-16c8-4458-9a9f-1a41a0191bc2" }, "tool_id": null, "type": "subworkflow", @@ -3808,9 +3808,9 @@ "when": null, "workflow_outputs": [ { - "label": "Busco Summary Image Hap2", - "output_name": "summary_image", - "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" + "label": "Busco Gff File - Hap2", + "output_name": "busco_gff", + "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" }, { "label": "Busco Summary Hap2", @@ -3818,9 +3818,9 @@ "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" }, { - "label": "Busco Gff File - Hap2", - "output_name": "busco_gff", - "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" + "label": "Busco Summary Image Hap2", + "output_name": "summary_image", + "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" } ] }, @@ -3922,11 +3922,6 @@ "uuid": "a4957dee-45cc-4f34-ae2e-e07f93b9fcc4", "when": null, "workflow_outputs": [ - { - "label": "Busco Summary Image Hap1", - "output_name": "summary_image", - "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" - }, { "label": "Busco Summary Hap1", "output_name": "busco_sum", @@ -3936,6 +3931,11 @@ "label": "Busco Gff File - Hap1", "output_name": "busco_gff", "uuid": "ba26cb24-25d4-4669-982c-abe4816753a6" + }, + { + "label": "Busco Summary Image Hap1", + "output_name": "summary_image", + "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" } ] }, @@ -4193,6 +4193,11 @@ "uuid": "8bf3b0a1-fb66-48d3-9fed-ba9d45c11ede", "when": null, "workflow_outputs": [ + { + "label": "Compleasm on Contigs hap1 Miniprot", + "output_name": "miniprot", + "uuid": "6e760b6b-66c1-4123-a6bd-e8be378cccf4" + }, { "label": "Compleasm on Contigs hap1 Translated Proteins", "output_name": "translated_protein", @@ -4207,11 +4212,6 @@ "label": "Compleasm on Contigs hap1 Full Table", "output_name": "full_table", "uuid": "65eb263e-d723-4992-8899-d032f07463b6" - }, - { - "label": "Compleasm on Contigs hap1 Miniprot", - "output_name": "miniprot", - "uuid": "6e760b6b-66c1-4123-a6bd-e8be378cccf4" } ] }, @@ -4330,16 +4330,16 @@ "uuid": "de8c2331-d858-45d4-9a89-cfc4d1f8d139", "when": null, "workflow_outputs": [ - { - "label": "Compleasm on Contigs hap2 Full Table", - "output_name": "full_table", - "uuid": "1d6fbe87-d899-4a8a-91c0-75d0d758ac2b" - }, { "label": "Compleasm on Contigs hap2 Translated Proteins", "output_name": "translated_protein", "uuid": "484f8887-14a2-4eae-8b41-0bf52491cf5d" }, + { + "label": "Compleasm on Contigs hap2 Full Table", + "output_name": "full_table", + "uuid": "1d6fbe87-d899-4a8a-91c0-75d0d758ac2b" + }, { "label": "Compleasm on Contigs hap2 Miniprot", "output_name": "miniprot", @@ -4738,6 +4738,6 @@ "VGP", "Reviewed" ], - "uuid": "5d328e09-f993-416f-a6ac-30c91d14c217", - "version": 5 + "uuid": "f1111a69-4b38-4f95-9707-f098804899f0", + "version": 6 }