# HG changeset patch # User ulfschaefer # Date 1468331793 14400 # Node ID 55bfe9d1888ed682d32423c1652e6e190752b22e # Parent 48c41c6ad84e7377c526709d0f78e42c9efe344b Uploaded diff -r 48c41c6ad84e -r 55bfe9d1888e Galaxy-Workflow-Phenix_workflow.ga --- a/Galaxy-Workflow-Phenix_workflow.ga Mon Jul 11 10:50:16 2016 -0400 +++ b/Galaxy-Workflow-Phenix_workflow.ga Tue Jul 12 09:56:33 2016 -0400 @@ -20,14 +20,14 @@ "outputs": [], "position": { "left": 200, - "top": 128 + "top": 141 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Reference fasta\"}", "tool_version": null, "type": "data_input", - "uuid": "2f18889e-5448-460b-8167-e04125fd51cf", + "uuid": "108478ac-5f4a-4244-b9db-f6c0ae9674fb", "workflow_outputs": [] }, "1": { @@ -46,14 +46,14 @@ "outputs": [], "position": { "left": 189, - "top": 296 + "top": 309 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"R1 fastq\"}", "tool_version": null, "type": "data_input", - "uuid": "5c634897-4a61-4a99-87c6-d4e23404af6c", + "uuid": "b00e3b0f-c7b6-4704-840b-76ec70d1cb75", "workflow_outputs": [] }, "2": { @@ -72,14 +72,14 @@ "outputs": [], "position": { "left": 211, - "top": 474 + "top": 487 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"R2 fastqs\"}", "tool_version": null, "type": "data_input", - "uuid": "59c1e55a-eda7-4570-be94-d2d3dca0eb25", + "uuid": "5e82d35b-0ce9-4295-a9af-0a5e35283404", "workflow_outputs": [] }, "3": { @@ -100,7 +100,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with BWA-MEM", + "name": "reference_source" + }, + { + "description": "runtime parameter for tool Map with BWA-MEM", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with BWA-MEM", + "name": "fastq_input" + } + ], "label": null, "name": "Map with BWA-MEM", "outputs": [ @@ -111,7 +124,7 @@ ], "position": { "left": 423.5, - "top": 300 + "top": 313 }, "post_job_actions": { "RenameDatasetActionbam_output": { @@ -124,10 +137,16 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", - "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, \\\"index_a\\\": \\\"auto\\\"}\"}", + "tool_shed_repository": { + "changeset_revision": "546ada4a9f43", + "name": "bwa", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", "tool_version": "0.7.12.1", "type": "tool", - "uuid": "104fb0fa-de5b-4202-a8c3-2e8f0fa1321d", + "uuid": "f74219f9-2d53-4eca-9bb7-079a2a8aa65e", "workflow_outputs": [] }, "4": { @@ -144,7 +163,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool PHE MPileup", + "name": "ref_file" + }, + { + "description": "runtime parameter for tool PHE MPileup", + "name": "input_bam" + } + ], "label": null, "name": "PHE MPileup", "outputs": [ @@ -155,7 +183,7 @@ ], "position": { "left": 634, - "top": 138 + "top": 151 }, "post_job_actions": { "RenameDatasetActionoutvcf": { @@ -168,10 +196,16 @@ }, "tool_errors": null, "tool_id": "toolshed.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_shed_repository": { + "changeset_revision": "b13db9e677b4", + "name": "phe_samtools_mpileup", + "owner": "ulfschaefer", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"ref_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "1.0", "type": "tool", - "uuid": "c44a1cad-8e62-4506-84bb-1c4a15f049ca", + "uuid": "83294062-5c05-4a09-938a-96a409216477", "workflow_outputs": [] }, "5": { @@ -188,7 +222,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Filter VCF", + "name": "input" + }, + { + "description": "runtime parameter for tool Filter VCF", + "name": "ref_fa" + } + ], "label": null, "name": "Filter VCF", "outputs": [ @@ -199,7 +242,7 @@ ], "position": { "left": 747, - "top": 326 + "top": 339 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -212,12 +255,18 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", - "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"null\", \"input\": \"null\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"25\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\"}", + "tool_shed_repository": { + "changeset_revision": "48c41c6ad84e", + "name": "phephenix", + "owner": "ulfschaefer", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"5\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 4, \\\"snp_filter_type\\\": {\\\"mq0f_ratio\\\": \\\"0.05\\\", \\\"__current_case__\\\": 8, \\\"snp_filter_type_selector\\\": \\\"mq0f_ratio_option\\\"}}]\"}", "tool_version": "1.0", "type": "tool", - "uuid": "51251f05-75d4-4d89-b757-2248b934d630", + "uuid": "9e3a724f-63e2-45c8-9d61-19643583f4bb", "workflow_outputs": [] } }, - "uuid": "878b2c0c-3b8a-4800-85fe-2c4f6d47adcf" + "uuid": "3392477d-d5ec-402e-b4a9-d25f79403fe9" } \ No newline at end of file