Mercurial > repos > chrisd > workflow_test
changeset 0:1f4509af191a draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 6fb8bfb033905a37bb6a02a5bc8029c87fa524b0
author | chrisd |
---|---|
date | Mon, 14 Mar 2016 18:15:23 -0400 |
parents | |
children | 41749f206e86 |
files | Workflow-AmrPlusPlus_PE.ga readme.rst repository_dependencies.xml |
diffstat | 3 files changed, 583 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Workflow-AmrPlusPlus_PE.ga Mon Mar 14 18:15:23 2016 -0400 @@ -0,0 +1,575 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "AmrPlusPlus_PE", + "steps": { + "0": { + "annotation": "The genome to align non-host reads to", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "The genome to align non-host reads to", + "name": "AMR Database" + } + ], + "label": "AMR Database", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 199.99998474121094, + "top": 199.99998092651367 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"AMR Database\"}", + "tool_version": null, + "type": "data_input", + "uuid": "7d2f1389-60a2-4e2f-b879-3d089d399123", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "995b7bc5-5f82-4450-b7e3-8e44b3d9eaa8" + } + ] + }, + "1": { + "annotation": "Genome used to filter reads on", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Genome used to filter reads on", + "name": "Host Genome" + } + ], + "label": "Host Genome", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 199.99998474121094, + "top": 283.1818046569824 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Host Genome\"}", + "tool_version": null, + "type": "data_input", + "uuid": "828b361f-e9b5-4175-9261-5bc33d38914d", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "5dc19bbb-b456-4a0d-b4c0-6c0bdfc8b967" + } + ] + }, + "2": { + "annotation": "Forward reads", + "content_id": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Forward reads", + "name": "FastQ Forward" + } + ], + "label": "FastQ Forward", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 199.99998474121094, + "top": 366.3636283874512 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"FastQ Forward\"}", + "tool_version": null, + "type": "data_input", + "uuid": "c42b1fdc-e54c-422f-8c82-12d494a429ac", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f82d5e1c-12e6-4685-a368-496923b41016" + } + ] + }, + "3": { + "annotation": "Reverse reads", + "content_id": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "Reverse reads", + "name": "FastQ Reverse" + } + ], + "label": "FastQ Reverse", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 199.99998474121094, + "top": 449.5454521179199 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"FastQ Reverse\"}", + "tool_version": null, + "type": "data_input", + "uuid": "39a7b4e2-134a-4f45-ae88-82c43b30d7c9", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "113db9c4-3cf2-4fc0-99eb-ab5d971fd35f" + } + ] + }, + "4": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "id": 4, + "input_connections": { + "paired_end|paired_input_type_conditional|fastq_r1_in": { + "id": 2, + "output_name": "output" + }, + "paired_end|paired_input_type_conditional|fastq_r2_in": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Trimmomatic", + "outputs": [ + { + "name": "fastq_out_paired", + "type": "input" + }, + { + "name": "fastq_out_unpaired", + "type": "input" + }, + { + "name": "fastq_out_r1_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r1_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out", + "type": "fastqsanger" + } + ], + "position": { + "left": 428.1818389892578, + "top": 199.99998092651367 + }, + "post_job_actions": { + "DeleteIntermediatesActionfastq_out_paired": { + "action_arguments": {}, + "action_type": "DeleteIntermediatesAction", + "output_name": "fastq_out_paired" + }, + "HideDatasetActionfastq_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "fastq_out" + }, + "HideDatasetActionfastq_out_paired": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "fastq_out_paired" + }, + "HideDatasetActionfastq_out_r1_unpaired": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "fastq_out_r1_unpaired" + }, + "HideDatasetActionfastq_out_r2_unpaired": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "fastq_out_r2_unpaired" + }, + "HideDatasetActionfastq_out_unpaired": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "fastq_out_unpaired" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"True\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": null}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}", + "tool_version": "0.32.3", + "type": "tool", + "uuid": "48c74cd7-a7ca-4b2e-aed8-83ce9fda1de0", + "workflow_outputs": [ + { + "label": null, + "output_name": "fastq_out_r1_paired", + "uuid": "b646d123-7b6e-4850-a1c1-fa67e4b97b2a" + }, + { + "label": null, + "output_name": "fastq_out_r2_paired", + "uuid": "b4795869-e4c5-4144-b070-0259ae2dea53" + } + ] + }, + "5": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.2", + "id": 5, + "input_connections": { + "input_type|fastq_input1": { + "id": 4, + "output_name": "fastq_out_r1_paired" + }, + "input_type|fastq_input2": { + "id": 4, + "output_name": "fastq_out_r2_paired" + }, + "reference_source|ref_file": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map with BWA", + "outputs": [ + { + "name": "bam_output", + "type": "bam" + } + ], + "position": { + "left": 730.3408966064453, + "top": 199.99998092651367 + }, + "post_job_actions": { + "DeleteIntermediatesActionbam_output": { + "action_arguments": {}, + "action_type": "DeleteIntermediatesAction", + "output_name": "bam_output" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.2", + "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": null, \\\"input_type_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\"}", + "tool_version": "0.4.2", + "type": "tool", + "uuid": "eaea0a44-3a05-434a-b2ce-5bcd20c1569c", + "workflow_outputs": [ + { + "label": null, + "output_name": "bam_output", + "uuid": "fff4aa69-6fa4-472d-9d35-33f729ca38ce" + } + ] + }, + "6": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0", + "id": 6, + "input_connections": { + "inputFile": { + "id": 5, + "output_name": "bam_output" + } + }, + "inputs": [], + "label": null, + "name": "FilterSamReads", + "outputs": [ + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 1058.536880493164, + "top": 199.99998092651367 + }, + "post_job_actions": { + "DeleteIntermediatesActionoutFile": { + "action_arguments": {}, + "action_type": "DeleteIntermediatesAction", + "output_name": "outFile" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"null\", \"filter_type\": \"{\\\"filter\\\": \\\"excludeAligned\\\", \\\"__current_case__\\\": 1}\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", + "tool_version": "1.136.0", + "type": "tool", + "uuid": "65d5c6a4-cbe4-4649-be02-c4292807ee7a", + "workflow_outputs": [ + { + "label": null, + "output_name": "outFile", + "uuid": "e64ed103-3e36-43aa-bf68-a5fff478c23f" + } + ] + }, + "7": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.2", + "id": 7, + "input_connections": { + "input_type|bam_input": { + "id": 6, + "output_name": "outFile" + }, + "reference_source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map with BWA", + "outputs": [ + { + "name": "bam_output", + "type": "bam" + } + ], + "position": { + "left": 1386.718765258789, + "top": 199.99998092651367 + }, + "post_job_actions": { + "DeleteIntermediatesActionbam_output": { + "action_arguments": {}, + "action_type": "DeleteIntermediatesAction", + "output_name": "bam_output" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.2", + "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": null, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"__current_case__\\\": 3, \\\"adv_bam_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\"}", + "tool_version": "0.4.2", + "type": "tool", + "uuid": "247ceef2-d557-458a-a747-8e237df453fa", + "workflow_outputs": [ + { + "label": null, + "output_name": "bam_output", + "uuid": "e6b1c8f7-1f31-4cf3-8a4e-30aa85f51405" + } + ] + }, + "8": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1", + "id": 8, + "input_connections": { + "inputFile": { + "id": 7, + "output_name": "bam_output" + } + }, + "inputs": [], + "label": null, + "name": "SortSam", + "outputs": [ + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 1714.9005279541016, + "top": 199.99998092651367 + }, + "post_job_actions": { + "DeleteIntermediatesActionoutFile": { + "action_arguments": {}, + "action_type": "DeleteIntermediatesAction", + "output_name": "outFile" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1", + "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"queryname\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", + "tool_version": "1.136.1", + "type": "tool", + "uuid": "3fe9acee-3144-4aac-9ad8-6d11205b9ea1", + "workflow_outputs": [ + { + "label": null, + "output_name": "outFile", + "uuid": "b71efaa4-fca9-4060-82ee-deb88042e2c1" + } + ] + }, + "9": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", + "id": 9, + "input_connections": { + "input1": { + "id": 8, + "output_name": "outFile" + } + }, + "inputs": [], + "label": null, + "name": "BAM-to-SAM", + "outputs": [ + { + "name": "output1", + "type": "sam" + } + ], + "position": { + "left": 2043.082290649414, + "top": 199.99998092651367 + }, + "post_job_actions": { + "DeleteIntermediatesActionoutput1": { + "action_arguments": {}, + "action_type": "DeleteIntermediatesAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", + "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}", + "tool_version": "2.0", + "type": "tool", + "uuid": "64102260-42a8-4c58-aad5-48bab5304c10", + "workflow_outputs": [ + { + "label": null, + "output_name": "output1", + "uuid": "472d0a97-2929-4eba-bd8f-d3dc15bd75b9" + } + ] + }, + "10": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", + "id": 10, + "input_connections": { + "input2": { + "id": 9, + "output_name": "output1" + } + }, + "inputs": [], + "label": null, + "name": "Coverage Sampler", + "outputs": [ + { + "name": "output1", + "type": "tabular" + } + ], + "position": { + "left": 2271.264175415039, + "top": 199.99998092651367 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput1": { + "action_arguments": { + "newtype": "csv" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output1" + }, + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + }, + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "Gene Fraction Results" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", + "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "0d245bfb-d95b-4868-ac44-8e4ca0ba8f9b", + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", + "id": 11, + "input_connections": { + "sam_type|sampe_input2": { + "id": 9, + "output_name": "output1" + } + }, + "inputs": [], + "label": null, + "name": "Snip Finder", + "outputs": [ + { + "name": "output1", + "type": "tabular" + } + ], + "position": { + "left": 2271.264175415039, + "top": 337.17329025268555 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput1": { + "action_arguments": { + "newtype": "csv" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output1" + }, + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + }, + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "Snip Results" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", + "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"False\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": null}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "a16bf95a-c26a-4aac-8431-844f676c1dd3", + "workflow_outputs": [] + } + }, + "uuid": "e7a44935-9e5c-46ae-988e-01f0905d885c" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Mon Mar 14 18:15:23 2016 -0400 @@ -0,0 +1,4 @@ +This is a Galaxy workflow that can be used to analyze metagenomic sequence data from diverse microbial populations. + +Availability +============
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Mar 14 18:15:23 2016 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="A meta-package of tools needed to run the workflow"> + <repository changeset_revision="79d448be6111" name="suite_test" owner="chrisd" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +</repositories>