diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md index cf97a9cbf..62d72d42f 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.2.2] 2024-02-05 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2` + ## [0.2.1] 2023-11-20 - Fix author in dockstore diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index ada438fe8..c9cb04593 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -14,7 +14,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.1", + "release": "0.2.2", "name": "Scaffolding-HiC-VGP8", "steps": { "0": { @@ -268,7 +268,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": null, "name": "Parse parameter value", "outputs": [ @@ -311,7 +316,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + }, + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -447,7 +461,7 @@ "name": "bwa_mem2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" - }, + }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"output_sort\": \"name\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1+galaxy1", "type": "tool", @@ -470,7 +484,16 @@ "output_name": "bam_output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Filter and merge", + "name": "forward" + }, + { + "description": "runtime parameter for tool Filter and merge", + "name": "reverse" + } + ], "label": null, "name": "Filter and merge", "outputs": [ @@ -508,7 +531,7 @@ }, "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1", "errors": null, "id": 13, "input_connections": { @@ -517,7 +540,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool PretextMap", + "name": "input" + } + ], "label": null, "name": "PretextMap", "outputs": [ @@ -539,15 +567,15 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "dfb8a4497339", + "changeset_revision": "511e5e3cd55e", "name": "pretext_map", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": null, \"sorting\": {\"sortby\": \"nosort\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.9+galaxy0", + "tool_version": "0.1.9+galaxy1", "type": "tool", "uuid": "6d280ad6-6803-44c3-8afe-5b5ff424c98d", "when": null, @@ -576,7 +604,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool YAHS", + "name": "function" + }, + { + "description": "runtime parameter for tool YAHS", + "name": "function" + }, + { + "description": "runtime parameter for tool YAHS", + "name": "function" + } + ], "label": null, "name": "YAHS", "outputs": [ @@ -654,7 +695,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2", "errors": null, "id": 15, "input_connections": { @@ -663,7 +704,12 @@ "output_name": "pretext_map_out" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Pretext Snapshot", + "name": "input" + } + ], "label": null, "name": "Pretext Snapshot", "outputs": [ @@ -690,15 +736,15 @@ "output_name": "pretext_snap_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "44c66e8d21e6", + "changeset_revision": "0a10fddd97d2", "name": "pretext_snapshot", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.0.3+galaxy1", + "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": \"no\", \"__current_case__\": 1}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.0.3+galaxy2", "type": "tool", "uuid": "ad7305d0-d613-4203-8ae8-d8ca469eddd5", "when": null, @@ -719,7 +765,16 @@ "output_name": "final_agp_out" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + }, + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -779,7 +834,12 @@ "output_name": "pretext_snap_out" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Extract dataset", + "name": "input" + } + ], "label": null, "name": "Extract dataset", "outputs": [ @@ -830,7 +890,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + }, + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -887,7 +956,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -940,7 +1014,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -997,7 +1076,16 @@ "output_name": "output" } }, - "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": [ @@ -1046,7 +1134,16 @@ "output_name": "output" } }, - "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": [ @@ -1095,7 +1192,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "input" + }, + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1196,6 +1302,7 @@ "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", + "comments": [], "format-version": "0.1", "name": "gfastats_data_prep", "steps": { @@ -1237,7 +1344,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort", + "name": "input" + } + ], "label": null, "name": "Sort", "outputs": [ @@ -1276,7 +1388,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Text reformatting", + "name": "infile" + } + ], "label": null, "name": "Text reformatting", "outputs": [ @@ -1321,7 +1438,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -1366,7 +1488,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Add column", + "name": "input" + } + ], "label": null, "name": "Add column", "outputs": [ @@ -1405,7 +1532,12 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": null, "name": "Parse parameter value", "outputs": [ @@ -1493,7 +1625,12 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute", + "name": "input" + } + ], "label": null, "name": "Compute", "outputs": [ @@ -1537,7 +1674,7 @@ } }, "tags": "", - "uuid": "1302e300-2959-4af9-8532-e42bbba8aea4" + "uuid": "6ae05cd1-bf71-439a-aaba-c4beb22a6d21" }, "tool_id": null, "type": "subworkflow", @@ -1560,7 +1697,16 @@ "output_name": "bam_output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Filter and merge", + "name": "forward" + }, + { + "description": "runtime parameter for tool Filter and merge", + "name": "reverse" + } + ], "label": null, "name": "Filter and merge", "outputs": [ @@ -1607,7 +1753,12 @@ "output_name": "gfastats data for plotting" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -1640,7 +1791,12 @@ "output_name": "gfastats data for plotting" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -1670,7 +1826,7 @@ }, "28": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1", "errors": null, "id": 28, "input_connections": { @@ -1679,7 +1835,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool PretextMap", + "name": "input" + } + ], "label": null, "name": "PretextMap", "outputs": [ @@ -1701,15 +1862,15 @@ "output_name": "pretext_map_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "dfb8a4497339", + "changeset_revision": "511e5e3cd55e", "name": "pretext_map", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": null, \"sorting\": {\"sortby\": \"nosort\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.9+galaxy0", + "tool_version": "0.1.9+galaxy1", "type": "tool", "uuid": "2eebc19f-da4f-4ec2-8030-81f81cc38fdf", "when": null, @@ -1726,7 +1887,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool bedtools BAM to BED", + "name": "input" + } + ], "label": null, "name": "bedtools BAM to BED", "outputs": [ @@ -1771,7 +1937,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Scatterplot with ggplot2", + "name": "input1" + } + ], "label": "Nx Plot", "name": "Scatterplot with ggplot2", "outputs": [ @@ -1831,7 +2002,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Scatterplot with ggplot2", + "name": "input1" + } + ], "label": "Size Plot", "name": "Scatterplot with ggplot2", "outputs": [ @@ -1882,7 +2058,7 @@ }, "32": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2", "errors": null, "id": 32, "input_connections": { @@ -1891,7 +2067,12 @@ "output_name": "pretext_map_out" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Pretext Snapshot", + "name": "input" + } + ], "label": null, "name": "Pretext Snapshot", "outputs": [ @@ -1918,15 +2099,15 @@ "output_name": "pretext_snap_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "44c66e8d21e6", + "changeset_revision": "0a10fddd97d2", "name": "pretext_snapshot", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.0.3+galaxy1", + "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": \"no\", \"__current_case__\": 1}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.0.3+galaxy2", "type": "tool", "uuid": "6e14e43c-ac36-499c-bf33-c513edd7445d", "when": null, @@ -1943,7 +2124,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort", + "name": "infile" + } + ], "label": null, "name": "Sort", "outputs": [ @@ -1990,7 +2176,12 @@ "output_name": "pretext_snap_out" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Extract dataset", + "name": "input" + } + ], "label": null, "name": "Extract dataset", "outputs": [