Mercurial > repos > matthias > dada2_removebimeradenovo
diff Galaxy-Workflow-dada2_for_paired_data.ga @ 3:d1e2dd10e64c draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
author | matthias |
---|---|
date | Mon, 29 Apr 2019 08:58:43 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-dada2_for_paired_data.ga Mon Apr 29 08:58:43 2019 -0400 @@ -0,0 +1,553 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "dada2 for paired data", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset Collection" + } + ], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 100, + "top": 591 + }, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"Input Dataset Collection\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "b1f16224-49d2-4b7a-a37d-3d93c54f679f", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": "dada2_plotQualityProfile", + "errors": null, + "id": 1, + "input_connections": { + "paired_cond|reads": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "dada2: plotQualityProfile", + "outputs": [ + { + "name": "output", + "type": "pdf" + } + ], + "position": { + "left": 406, + "top": 473 + }, + "post_job_actions": {}, + "tool_id": "dada2_plotQualityProfile", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"n\": \"\\\"500000\\\"\", \"aggregate\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.10.0+galaxy0", + "type": "tool", + "uuid": "f6e0a2ea-a639-48d9-ae3c-c1ec2bab93e5", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "dada2_filterAndTrim", + "errors": null, + "id": 2, + "input_connections": { + "paired_cond|reads": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "dada2: filterAndTrim", + "outputs": [ + { + "name": "paired_output", + "type": "input" + }, + { + "name": "outtab", + "type": "tabular" + } + ], + "position": { + "left": 384, + "top": 612 + }, + "post_job_actions": {}, + "tool_id": "dada2_filterAndTrim", + "tool_state": "{\"trim\": \"{\\\"trimLeft\\\": \\\"0\\\", \\\"trimRight\\\": \\\"0\\\", \\\"truncLen\\\": \\\"0\\\", \\\"truncQ\\\": \\\"2\\\"}\", \"__page__\": null, \"rmPhiX\": \"\\\"true\\\"\", \"seprev_cond\": \"{\\\"__current_case__\\\": 0, \\\"seprev_select\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"TRUE\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"filter\": \"{\\\"maxEE\\\": \\\"\\\", \\\"maxLen\\\": \\\"\\\", \\\"maxN\\\": \\\"0\\\", \\\"minLen\\\": \\\"20\\\", \\\"minQ\\\": \\\"0\\\"}\", \"output_statistics\": \"\\\"true\\\"\", \"orientFwd\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.10.0+galaxy0", + "type": "tool", + "uuid": "353103fd-afc3-4fe0-a4a3-8dca75b59107", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "__UNZIP_COLLECTION__", + "errors": null, + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "paired_output" + } + }, + "inputs": [], + "label": null, + "name": "Unzip Collection", + "outputs": [ + { + "name": "forward", + "type": "data" + }, + { + "name": "reverse", + "type": "data" + } + ], + "position": { + "left": 718, + "top": 609 + }, + "post_job_actions": {}, + "tool_id": "__UNZIP_COLLECTION__", + "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "41ab27fe-f07d-4653-b4b5-e77408957a9a", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "dada2_derepFastq", + "errors": null, + "id": 4, + "input_connections": { + "reads": { + "id": 3, + "output_name": "forward" + } + }, + "inputs": [], + "label": null, + "name": "dada2: derepFastq", + "outputs": [ + { + "name": "derep", + "type": "dada2_derep" + } + ], + "position": { + "left": 987, + "top": 466 + }, + "post_job_actions": {}, + "tool_id": "dada2_derepFastq", + "tool_state": "{\"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"reads|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", + "tool_version": "1.10.0+galaxy0", + "type": "tool", + "uuid": "ad42a0b6-c3f1-4152-ba24-61f7905d896d", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "dada2_learnErrors", + "errors": null, + "id": 5, + "input_connections": { + "reads": { + "id": 3, + "output_name": "forward" + } + }, + "inputs": [], + "label": null, + "name": "dada2: learnErrors", + "outputs": [ + { + "name": "errors", + "type": "dada2_errorrates" + }, + { + "name": "plot", + "type": "pdf" + } + ], + "position": { + "left": 984, + "top": 592 + }, + "post_job_actions": {}, + "tool_id": "dada2_learnErrors", + "tool_state": "{\"__page__\": null, \"plotopt\": \"{\\\"errin\\\": \\\"false\\\", \\\"errout\\\": \\\"true\\\", \\\"nominalQ\\\": \\\"true\\\", \\\"obs\\\": \\\"true\\\"}\", \"__rerun_remap_job_id__\": null, \"nbases\": \"\\\"8\\\"\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"advanced\": \"{\\\"errfoo\\\": \\\"loessErrfun\\\", \\\"maxconsist\\\": \\\"10\\\", \\\"omegac\\\": \\\"0\\\", \\\"randomize\\\": \\\"false\\\"}\"}", + "tool_version": "1.10.0+galaxy0", + "type": "tool", + "uuid": "e8c86ffd-118c-44f6-a58d-5c1704bb6ed6", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "dada2_derepFastq", + "errors": null, + "id": 6, + "input_connections": { + "reads": { + "id": 3, + "output_name": "reverse" + } + }, + "inputs": [], + "label": null, + "name": "dada2: derepFastq", + "outputs": [ + { + "name": "derep", + "type": "dada2_derep" + } + ], + "position": { + "left": 979, + "top": 794 + }, + "post_job_actions": {}, + "tool_id": "dada2_derepFastq", + "tool_state": "{\"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"reads|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", + "tool_version": "1.10.0+galaxy0", + "type": "tool", + "uuid": "19c7747c-a3c3-498f-8a0a-a351aa2e408d", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "dada2_learnErrors", + "errors": null, + "id": 7, + "input_connections": { + "reads": { + "id": 3, + "output_name": "reverse" + } + }, + "inputs": [], + "label": null, + "name": "dada2: learnErrors", + "outputs": [ + { + "name": "errors", + "type": "dada2_errorrates" + }, + { + "name": "plot", + "type": "pdf" + } + ], + "position": { + "left": 970, + "top": 922 + }, + "post_job_actions": {}, + "tool_id": "dada2_learnErrors", + "tool_state": "{\"__page__\": null, \"plotopt\": \"{\\\"errin\\\": \\\"false\\\", \\\"errout\\\": \\\"true\\\", \\\"nominalQ\\\": \\\"true\\\", \\\"obs\\\": \\\"true\\\"}\", \"__rerun_remap_job_id__\": null, \"nbases\": \"\\\"8\\\"\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"advanced\": \"{\\\"errfoo\\\": \\\"loessErrfun\\\", \\\"maxconsist\\\": \\\"10\\\", \\\"omegac\\\": \\\"0\\\", \\\"randomize\\\": \\\"false\\\"}\"}", + "tool_version": "1.10.0+galaxy0", + "type": "tool", + "uuid": "2cbc5056-7cc7-4e3e-a283-959a261ca4c5", + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "dada2_dada", + "errors": null, + "id": 8, + "input_connections": { + "batch_cond|derep": { + "id": 4, + "output_name": "derep" + }, + "errorrates": { + "id": 5, + "output_name": "errors" + } + }, + "inputs": [], + "label": null, + "name": "dada2: dada", + "outputs": [ + { + "name": "data_collection", + "type": "input" + } + ], + "position": { + "left": 1294, + "top": 562 + }, + "post_job_actions": {}, + "tool_id": "dada2_dada", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"errorrates\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", + "tool_version": "1.10.0+galaxy0", + "type": "tool", + "uuid": "44bab152-645c-43f1-8356-8ef3f45de057", + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "dada2_dada", + "errors": null, + "id": 9, + "input_connections": { + "batch_cond|derep": { + "id": 6, + "output_name": "derep" + }, + "errorrates": { + "id": 7, + "output_name": "errors" + } + }, + "inputs": [], + "label": null, + "name": "dada2: dada", + "outputs": [ + { + "name": "data_collection", + "type": "input" + } + ], + "position": { + "left": 1280, + "top": 881 + }, + "post_job_actions": {}, + "tool_id": "dada2_dada", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"errorrates\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", + "tool_version": "1.10.0+galaxy0", + "type": "tool", + "uuid": "c9045469-5cd6-44f1-bffd-b61290d23145", + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "dada2_mergePairs", + "errors": null, + "id": 10, + "input_connections": { + "dadaf": { + "id": 8, + "output_name": "data_collection" + }, + "dadar": { + "id": 9, + "output_name": "data_collection" + }, + "derepf": { + "id": 4, + "output_name": "derep" + }, + "derepr": { + "id": 6, + "output_name": "derep" + } + }, + "inputs": [], + "label": null, + "name": "dada2: mergePairs", + "outputs": [ + { + "name": "merged", + "type": "dada2_mergepairs" + } + ], + "position": { + "left": 1520, + "top": 704 + }, + "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", + "type": "tool", + "uuid": "ca8f7d96-9c9c-40f8-ab23-7cb4fb49ab47", + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "dada2_makeSequenceTable", + "errors": null, + "id": 11, + "input_connections": { + "samples": { + "id": 10, + "output_name": "merged" + } + }, + "inputs": [], + "label": null, + "name": "dada2: makeSequenceTable", + "outputs": [ + { + "name": "stable", + "type": "dada2_sequencetable" + }, + { + "name": "plot_output", + "type": "pdf" + } + ], + "position": { + "left": 1829, + "top": 707 + }, + "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", + "type": "tool", + "uuid": "3cd64745-bb03-4bfa-b425-a16db0888967", + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "dada2_removeBimeraDenovo", + "errors": null, + "id": 12, + "input_connections": { + "unqs": { + "id": 11, + "output_name": "stable" + } + }, + "inputs": [], + "label": null, + "name": "dada2: removeBimeraDenovo", + "outputs": [ + { + "name": "stable_uniques", + "type": "dada2_uniques" + }, + { + "name": "stable_mergepairs", + "type": "dada2_mergepairs" + }, + { + "name": "stable_sequencetable", + "type": "dada2_sequencetable" + } + ], + "position": { + "left": 2137, + "top": 710 + }, + "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", + "type": "tool", + "uuid": "4c001b98-d20d-4255-96ee-2b9829aa815b", + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "dada2_seqCounts", + "errors": null, + "id": 13, + "input_connections": { + "inrep_0|input": { + "id": 2, + "output_name": "outtab" + }, + "inrep_1|input": { + "id": 8, + "output_name": "data_collection" + }, + "inrep_2|input": { + "id": 9, + "output_name": "data_collection" + }, + "inrep_3|input": { + "id": 10, + "output_name": "merged" + }, + "inrep_4|input": { + "id": 11, + "output_name": "stable" + }, + "inrep_5|input": { + "id": 12, + "output_name": "stable_sequencetable" + } + }, + "inputs": [], + "label": null, + "name": "dada2: sequence counts", + "outputs": [ + { + "name": "counts", + "type": "tabular" + } + ], + "position": { + "left": 1870, + "top": 277 + }, + "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", + "type": "tool", + "uuid": "cbdb7105-6e81-418e-98fb-7f36df117fb5", + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "dada2_assignTaxonomyAddspecies", + "errors": null, + "id": 14, + "input_connections": { + "seqs": { + "id": 12, + "output_name": "stable_sequencetable" + } + }, + "inputs": [], + "label": null, + "name": "dada2: assignTaxonomy and addSpecies", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 2444, + "top": 710 + }, + "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", + "type": "tool", + "uuid": "babc7594-ae73-4818-919f-561836c45c17", + "workflow_outputs": [] + } + }, + "tags": [], + "uuid": "48912525-da2b-44b4-b225-f3e3adecad96", + "version": 1 +} \ No newline at end of file