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 995e83fa9..d791f7129 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 @@ -23,7 +23,7 @@ "release": "0.1.12", "name": "Assembly-Hifi-HiC-phasing-VGP4", "report": { - "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\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 (Vertebrata database)\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_display(output=\"Assembly statistics for Hap1 and Hap2\")\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" + "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\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 (Vertebrata database)\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" }, "steps": { "0": { @@ -186,13 +186,7 @@ "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a7c8f776-78b1-4caa-b63f-f2cb96c9308b" - } - ] + "workflow_outputs": [] }, "6": { "annotation": "", @@ -219,13 +213,7 @@ "type": "parameter_input", "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "d130c749-1851-491e-83a2-794f3ca263a1" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "", @@ -252,13 +240,7 @@ "type": "parameter_input", "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "63859139-a7ef-4b30-a6a3-6b849b90d650" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", @@ -285,13 +267,7 @@ "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "81580b69-a114-4351-b9ae-b64f2ecc930c" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "", @@ -318,13 +294,7 @@ "type": "data_input", "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "c191eaba-164b-424c-949b-a0582810d785" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", @@ -351,13 +321,7 @@ "type": "parameter_input", "uuid": "b251eddc-49e6-4899-a893-a904c29b9e75", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "fe00ec3a-b6cd-4b28-ac33-98fd7c119b75" - } - ] + "workflow_outputs": [] }, "11": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", @@ -1666,7 +1630,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 189.90056800842285 }, "tool_id": null, @@ -1699,7 +1663,7 @@ ], "position": { "left": 302.6136245727539, - "top": 0.0 + "top": 0 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -2048,7 +2012,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 189.90056800842285 }, "tool_id": null, @@ -2081,7 +2045,7 @@ ], "position": { "left": 302.6136245727539, - "top": 0.0 + "top": 0 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -2540,7 +2504,7 @@ } }, "tool_id": "join1", - "tool_state": "{\"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"fill_empty\", \"__current_case__\": 1, \"fill_columns_by\": \"fill_unjoined_only\", \"do_fill_empty_columns\": {\"column_fill_type\": \"single_fill_value\", \"__current_case__\": 0, \"fill_value\": \".\"}}, \"header\": \"\", \"input1\": {\"__class__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"fill_empty\", \"__current_case__\": 1, \"fill_columns_by\": \"fill_unjoined_only\", \"do_fill_empty_columns\": {\"column_fill_type\": \"single_fill_value\", \"__current_case__\": 0, \"fill_value\": \".\"}}, \"header\": \"\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.1.3", "type": "tool", "uuid": "00e95547-9451-4c37-bc19-b29de3864c6a", @@ -2620,8 +2584,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, - "top": 0.0 + "left": 0, + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -3078,25 +3042,15 @@ "uuid": "1b8e2d4e-3380-4414-bdb0-b356383c0ee2", "when": null, "workflow_outputs": [ - { - "label": "Nx Plot", - "output_name": "Nx Plot", - "uuid": "781f8511-c3fe-4954-afa8-d21c94c996a4" - }, - { - "label": null, - "output_name": "3:output", - "uuid": "58904682-a049-4844-a9a9-fa3a83e67415" - }, - { - "label": null, - "output_name": "2:output", - "uuid": "997a0a2c-a9f4-47b0-b096-be9f4617ec91" - }, { "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" } ] }, @@ -3194,6 +3148,11 @@ "uuid": "08066bc3-0992-4606-844d-16be3c56691a", "when": null, "workflow_outputs": [ + { + "label": "Busco Summary Image Hap2", + "output_name": "summary_image", + "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" + }, { "label": "Busco Summary Hap2", "output_name": "busco_sum", @@ -3203,11 +3162,6 @@ "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" } ] }, @@ -3328,16 +3282,6 @@ "uuid": "9985e575-3113-4c2c-bc2c-78faab3a1291", "when": null, "workflow_outputs": [ - { - "label": "Merqury QV", - "output_name": "qv_files", - "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" - }, - { - "label": "Merqury Stats", - "output_name": "stats_files", - "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" - }, { "label": "Merqury images", "output_name": "png_files", @@ -3347,6 +3291,16 @@ "label": "Merqury Histograms", "output_name": "hist_files", "uuid": "67d9d45d-989d-43c0-9ebd-0da9cc35763a" + }, + { + "label": "Merqury QV", + "output_name": "qv_files", + "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" + }, + { + "label": "Merqury Stats", + "output_name": "stats_files", + "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" } ] }, @@ -3449,15 +3403,15 @@ "output_name": "summary_image", "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" }, - { - "label": "Busco Summary Hap1", - "output_name": "busco_sum", - "uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8" - }, { "label": "Busco Gff File - Hap1", "output_name": "busco_gff", "uuid": "ba26cb24-25d4-4669-982c-abe4816753a6" + }, + { + "label": "Busco Summary Hap1", + "output_name": "busco_sum", + "uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8" } ] }, @@ -3790,12 +3744,63 @@ "uuid": "c10c5102-6b26-4cdc-bc35-50af09e36d9d" } ] + }, + "51": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, + "id": 51, + "input_connections": { + "infile": { + "id": 44, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 2973.2736415223585, + "top": 446.09145245110693 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "fbf99087e067", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "7528118f-3c8c-47a8-86e8-6085145c38d1", + "when": null, + "workflow_outputs": [ + { + "label": "clean_stats", + "output_name": "outfile", + "uuid": "0d69a8ab-29c1-4fef-97d9-af243ca8eb83" + } + ] } }, "tags": [ "VGP", "Reviewed" ], - "uuid": "a128697a-2106-483f-9bbd-67b78c21b832", - "version": 24 + "uuid": "4135d455-ac66-4d86-b4a3-643580ff877f", + "version": 5 } \ No newline at end of file