Mercurial > repos > ulfschaefer > phephenix
changeset 7:6ee955e652e0 draft
Uploaded
| author | ulfschaefer |
|---|---|
| date | Wed, 27 Apr 2016 10:06:16 -0400 |
| parents | e713aacaad05 |
| children | 2802f44628ad |
| files | Galaxy-Workflow-Phenix_workflow.ga |
| diffstat | 1 files changed, 195 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-Phenix_workflow.ga Wed Apr 27 10:06:16 2016 -0400 @@ -0,0 +1,195 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Phenix workflow", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "ref fa" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 136.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"ref fa\"}", + "tool_version": null, + "type": "data_input", + "uuid": "b7ff9ad4-b07e-4c50-a38e-de10113b7314", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "r1" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 205, + "top": 273.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"r1\"}", + "tool_version": null, + "type": "data_input", + "uuid": "730623b2-2780-4de8-aa64-20949d734754", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "r2" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 209, + "top": 406.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"r2\"}", + "tool_version": null, + "type": "data_input", + "uuid": "f7d572ac-c3fc-4bb1-97fc-641460c32139", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2", + "id": 3, + "input_connections": { + "fastq_input|fastq_input1": { + "id": 1, + "output_name": "output" + }, + "fastq_input|fastq_input2": { + "id": 2, + "output_name": "output" + }, + "reference_source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map with BWA-MEM", + "outputs": [ + { + "name": "bam_output", + "type": "bam" + } + ], + "position": { + "left": 443, + "top": 203.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"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": "1896896c-a5c5-408b-8f43-54fb3d466e59", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", + "id": 4, + "input_connections": { + "input_bam": { + "id": 3, + "output_name": "bam_output" + }, + "ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "PHE MPileup", + "outputs": [ + { + "name": "outvcf", + "type": "vcf" + } + ], + "position": { + "left": 456, + "top": 425.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", + "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", + "tool_version": "1.0", + "type": "tool", + "uuid": "dd975120-5a22-467b-a8f7-cc801faccfd6", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "outvcf" + } + }, + "inputs": [], + "label": null, + "name": "Filter VCF", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 666, + "top": 379.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", + "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"gq_score\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"snp_filter_type_selector\\\": \\\"gq_score_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\", \"__page__\": 0}", + "tool_version": "1.0", + "type": "tool", + "uuid": "36480e46-74dd-4bb7-b350-c3e75f4f2354", + "workflow_outputs": [] + } + }, + "uuid": "15c9a48b-931d-4ff6-b12f-4c9a1affea2e" +} \ No newline at end of file
