From 673730b9bc9cc498ca20ede89f4521f1cdd420ae Mon Sep 17 00:00:00 2001 From: M Bernt Date: Wed, 6 Nov 2019 08:41:10 +0100 Subject: [PATCH] dada2: update workflow --- .../Galaxy-Workflow-dada2_for_paired_data.ga | 593 +++++++++++++----- 1 file changed, 419 insertions(+), 174 deletions(-) diff --git a/tools/dada2/Galaxy-Workflow-dada2_for_paired_data.ga b/tools/dada2/Galaxy-Workflow-dada2_for_paired_data.ga index 3a78a889c4d..892291d372b 100644 --- a/tools/dada2/Galaxy-Workflow-dada2_for_paired_data.ga +++ b/tools/dada2/Galaxy-Workflow-dada2_for_paired_data.ga @@ -2,7 +2,7 @@ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", - "name": "dada2 for paired data", + "name": "dada2 for paired data (imported from uploaded file)", "steps": { "0": { "annotation": "", @@ -20,8 +20,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 100, - "top": 591 + "left": 200, + "top": 613 }, "tool_id": null, "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"Input Dataset Collection\"}", @@ -32,206 +32,295 @@ }, "1": { "annotation": "", - 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"tool_version": "1.10.0+galaxy0", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"err\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "1.12+galaxy0", "type": "tool", - "uuid": "c9045469-5cd6-44f1-bffd-b61290d23145", - "workflow_outputs": [] + "uuid": "188c4ee7-3fb7-4dc7-8efd-30fb38c0d679", + "workflow_outputs": [ + { + "label": null, + "output_name": "data_collection", + "uuid": "7dfc0db1-2376-440c-ac0b-3f9932f063db" + } + ] }, - "10": { + "11": { "annotation": "", "content_id": "dada2_mergePairs", "errors": null, - "id": 10, + "id": 11, "input_connections": { - "dadaf": { - "id": 8, + "dadaF": { + "id": 9, "output_name": "data_collection" }, - "dadar": { - "id": 9, + "dadaR": { + "id": 10, "output_name": "data_collection" }, - "derepf": { - "id": 4, - "output_name": "derep" + "derepF": { + "id": 6, + "output_name": "forward" }, - "derepr": { + "derepR": { "id": 6, - "output_name": "derep" + "output_name": "reverse" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool dada2: mergePairs", + "name": "dadaR" + }, + { + "description": "runtime parameter for tool dada2: mergePairs", + "name": "derepR" + }, + { + "description": "runtime parameter for tool dada2: mergePairs", + "name": "dadaF" + }, + { + "description": "runtime parameter for tool dada2: mergePairs", + "name": "derepF" + } + ], "label": null, "name": "dada2: mergePairs", "outputs": [ @@ -375,25 +579,31 @@ } ], "position": { - "left": 1520, - "top": 704 + "left": 1691, + "top": 652.5 }, "post_job_actions": {}, "tool_id": "dada2_mergePairs", - "tool_state": "{\"__page__\": null, \"minOverlap\": \"\\\"12\\\"\", \"dadaf\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"dadaf|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"derepr\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"derepr|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"maxMismatch\": \"\\\"0\\\"\", \"trimOverhang\": \"\\\"false\\\"\", \"dadar\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"derepf|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"justConcatenate\": \"\\\"false\\\"\", \"dadar|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"derepf\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", - "tool_version": "1.10.0+galaxy0", + "tool_state": "{\"__page__\": null, \"dadaF\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"derepR\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"maxMismatch\": \"\\\"0\\\"\", \"trimOverhang\": \"\\\"false\\\"\", \"minOverlap\": \"\\\"12\\\"\", \"justConcatenate\": \"\\\"false\\\"\", \"dadaR\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"derepF\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "1.12+galaxy0", "type": "tool", - "uuid": "ca8f7d96-9c9c-40f8-ab23-7cb4fb49ab47", - "workflow_outputs": [] + "uuid": "8a74535a-c7a2-4c24-a907-8cb791b779bf", + "workflow_outputs": [ + { + "label": null, + "output_name": "merged", + "uuid": "887453f1-44ea-4882-8b94-91a3b02eaa0d" + } + ] }, - "11": { + "12": { "annotation": "", "content_id": "dada2_makeSequenceTable", "errors": null, - "id": 11, + "id": 12, "input_connections": { "samples": { - "id": 10, + "id": 11, "output_name": "merged" } }, @@ -411,25 +621,36 @@ } ], "position": { - "left": 1829, - "top": 707 + "left": 1999, + "top": 694 + }, + "post_job_actions": { + "HideDatasetActionplot_output": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "plot_output" + }, + "HideDatasetActionstable": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "stable" + } }, - "post_job_actions": {}, "tool_id": "dada2_makeSequenceTable", "tool_state": "{\"orderBy\": \"\\\"abundance\\\"\", \"plot\": \"\\\"true\\\"\", \"__page__\": null, \"filter_cond\": \"{\\\"__current_case__\\\": 0, \\\"filter_select\\\": \\\"no\\\"}\", \"samples\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", - "tool_version": "1.10.0+galaxy0", + "tool_version": "1.12+galaxy0", "type": "tool", "uuid": "3cd64745-bb03-4bfa-b425-a16db0888967", "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "dada2_removeBimeraDenovo", "errors": null, - "id": 12, + "id": 13, "input_connections": { "unqs": { - "id": 11, + "id": 12, "output_name": "stable" } }, @@ -451,45 +672,57 @@ } ], "position": { - "left": 2137, - "top": 710 + "left": 2299, + "top": 640 + }, + "post_job_actions": { + "HideDatasetActionstable_mergepairs": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "stable_mergepairs" + }, + "HideDatasetActionstable_sequencetable": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "stable_sequencetable" + }, + "HideDatasetActionstable_uniques": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "stable_uniques" + } }, - "post_job_actions": {}, "tool_id": "dada2_removeBimeraDenovo", "tool_state": "{\"unqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"method\": \"\\\"consensus\\\"\", \"__page__\": null}", - "tool_version": "1.10.0+galaxy0", + "tool_version": "1.12+galaxy0", "type": "tool", "uuid": "4c001b98-d20d-4255-96ee-2b9829aa815b", "workflow_outputs": [] }, - "13": { + "14": { "annotation": "", "content_id": "dada2_seqCounts", "errors": null, - "id": 13, + "id": 14, "input_connections": { "inrep_0|input": { - "id": 2, + "id": 3, "output_name": "outtab" }, "inrep_1|input": { - "id": 8, - "output_name": "data_collection" - }, - "inrep_2|input": { "id": 9, "output_name": "data_collection" }, - "inrep_3|input": { + "inrep_2|input": { "id": 10, - "output_name": "merged" + "output_name": "data_collection" }, "inrep_4|input": { - "id": 11, + "id": 12, "output_name": "stable" }, "inrep_5|input": { - "id": 12, + "id": 13, "output_name": "stable_sequencetable" } }, @@ -503,25 +736,31 @@ } ], "position": { - "left": 1870, - "top": 277 + "left": 2616, + "top": 320 + }, + "post_job_actions": { + "HideDatasetActioncounts": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "counts" + } }, - "post_job_actions": {}, "tool_id": "dada2_seqCounts", "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"inrep\": \"[{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"filt\\\"}, {\\\"__index__\\\": 1, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"denoised fwd\\\"}, {\\\"__index__\\\": 2, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"denoised rev\\\"}, {\\\"__index__\\\": 3, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"merged\\\"}, {\\\"__index__\\\": 4, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"tabled\\\"}, {\\\"__index__\\\": 5, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"nochim\\\"}]\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.10.0+galaxy0", + "tool_version": "1.12+galaxy0", "type": "tool", "uuid": "cbdb7105-6e81-418e-98fb-7f36df117fb5", "workflow_outputs": [] }, - "14": { + "15": { "annotation": "", "content_id": "dada2_assignTaxonomyAddspecies", "errors": null, - "id": 14, + "id": 15, "input_connections": { "seqs": { - "id": 12, + "id": 13, "output_name": "stable_sequencetable" } }, @@ -535,19 +774,25 @@ } ], "position": { - "left": 2444, - "top": 710 + "left": 2623, + "top": 688 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } }, - "post_job_actions": {}, "tool_id": "dada2_assignTaxonomyAddspecies", - "tool_state": "{\"__page__\": null, \"tryRC\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"addSpecies_cond\": \"{\\\"__current_case__\\\": 1, \\\"addSpecies_select\\\": \\\"TRUE\\\", \\\"allowMultiple_cond\\\": {\\\"__current_case__\\\": 0, \\\"allowMultiple\\\": \\\"FALSE\\\"}, \\\"speciesreference_cond\\\": {\\\"__current_case__\\\": 0, \\\"speciesrefFasta\\\": \\\"rdp16\\\", \\\"speciesreference_select\\\": \\\"builtin\\\"}, \\\"tryRC\\\": \\\"false\\\"}\", \"reference_cond\": \"{\\\"__current_case__\\\": 0, \\\"refFasta\\\": \\\"rdp16\\\", \\\"reference_select\\\": \\\"builtin\\\"}\", \"outputBootstraps\": \"\\\"false\\\"\", \"minBoot\": \"\\\"50\\\"\", \"seqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.10.0+galaxy0", + "tool_state": "{\"__page__\": null, \"tryRC\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"addSpecies_cond\": \"{\\\"__current_case__\\\": 1, \\\"addSpecies_select\\\": \\\"TRUE\\\", \\\"allowMultiple_cond\\\": {\\\"__current_case__\\\": 0, \\\"allowMultiple\\\": \\\"FALSE\\\"}, \\\"speciesreference_cond\\\": {\\\"__current_case__\\\": 0, \\\"speciesrefFasta\\\": \\\"test_buildid\\\", \\\"speciesreference_select\\\": \\\"builtin\\\"}, \\\"tryRC\\\": \\\"false\\\"}\", \"reference_cond\": \"{\\\"__current_case__\\\": 0, \\\"refFasta\\\": \\\"test_buildid\\\", \\\"reference_select\\\": \\\"builtin\\\"}\", \"outputBootstraps\": \"\\\"false\\\"\", \"minBoot\": \"\\\"50\\\"\", \"seqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.12+galaxy0", "type": "tool", "uuid": "babc7594-ae73-4818-919f-561836c45c17", "workflow_outputs": [] } }, "tags": [], - "uuid": "48912525-da2b-44b4-b225-f3e3adecad96", + "uuid": "a4ba74bb-5a8a-403d-885c-822bbe9d6e03", "version": 1 } \ No newline at end of file