| Previous changeset 15:48c41c6ad84e (2016-07-11) Next changeset 17:f7494340ae7f (2016-07-14) |
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Commit message:
Uploaded |
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modified:
Galaxy-Workflow-Phenix_workflow.ga |
| b |
| 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 |
| [ |
| b'@@ -20,14 +20,14 @@\n "outputs": [], \n "position": {\n "left": 200, \n- "top": 128\n+ "top": 141\n }, \n "tool_errors": null, \n "tool_id": null, \n "tool_state": "{\\"name\\": \\"Reference fasta\\"}", \n "tool_version": null, \n "type": "data_input", \n- "uuid": "2f18889e-5448-460b-8167-e04125fd51cf", \n+ "uuid": "108478ac-5f4a-4244-b9db-f6c0ae9674fb", \n "workflow_outputs": []\n }, \n "1": {\n@@ -46,14 +46,14 @@\n "outputs": [], \n "position": {\n "left": 189, \n- "top": 296\n+ "top": 309\n }, \n "tool_errors": null, \n "tool_id": null, \n "tool_state": "{\\"name\\": \\"R1 fastq\\"}", \n "tool_version": null, \n "type": "data_input", \n- "uuid": "5c634897-4a61-4a99-87c6-d4e23404af6c", \n+ "uuid": "b00e3b0f-c7b6-4704-840b-76ec70d1cb75", \n "workflow_outputs": []\n }, \n "2": {\n@@ -72,14 +72,14 @@\n "outputs": [], \n "position": {\n "left": 211, \n- "top": 474\n+ "top": 487\n }, \n "tool_errors": null, \n "tool_id": null, \n "tool_state": "{\\"name\\": \\"R2 fastqs\\"}", \n "tool_version": null, \n "type": "data_input", \n- "uuid": "59c1e55a-eda7-4570-be94-d2d3dca0eb25", \n+ "uuid": "5e82d35b-0ce9-4295-a9af-0a5e35283404", \n "workflow_outputs": []\n }, \n "3": {\n@@ -100,7 +100,20 @@\n "output_name": "output"\n }\n }, \n- "inputs": [], \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool Map with BWA-MEM", \n+ "name": "reference_source"\n+ }, \n+ {\n+ "description": "runtime parameter for tool Map with BWA-MEM", \n+ "name": "fastq_input"\n+ }, \n+ {\n+ "description": "runtime parameter for tool Map with BWA-MEM", \n+ "name": "fastq_input"\n+ }\n+ ], \n "label": null, \n "name": "Map with BWA-MEM", \n "outputs": [\n@@ -111,7 +124,7 @@\n ], \n "position": {\n "left": 423.5, \n- "top": 300\n+ "top": 313\n }, \n "post_job_actions": {\n "RenameDatasetActionbam_output": {\n@@ -124,10 +137,16 @@\n }, \n "tool_errors": null, \n "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", \n- "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\\\\\\"}\\"}", \n+ "tool_shed_repository": {\n+ '..b'": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input_bam\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n "tool_version": "1.0", \n "type": "tool", \n- "uuid": "c44a1cad-8e62-4506-84bb-1c4a15f049ca", \n+ "uuid": "83294062-5c05-4a09-938a-96a409216477", \n "workflow_outputs": []\n }, \n "5": {\n@@ -188,7 +222,16 @@\n "output_name": "output"\n }\n }, \n- "inputs": [], \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool Filter VCF", \n+ "name": "input"\n+ }, \n+ {\n+ "description": "runtime parameter for tool Filter VCF", \n+ "name": "ref_fa"\n+ }\n+ ], \n "label": null, \n "name": "Filter VCF", \n "outputs": [\n@@ -199,7 +242,7 @@\n ], \n "position": {\n "left": 747, \n- "top": 326\n+ "top": 339\n }, \n "post_job_actions": {\n "RenameDatasetActionoutput": {\n@@ -212,12 +255,18 @@\n }, \n "tool_errors": null, \n "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", \n- "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\\\\\\"}}]\\"}", \n+ "tool_shed_repository": {\n+ "changeset_revision": "48c41c6ad84e", \n+ "name": "phephenix", \n+ "owner": "ulfschaefer", \n+ "tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "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\\\\\\"}}]\\"}", \n "tool_version": "1.0", \n "type": "tool", \n- "uuid": "51251f05-75d4-4d89-b757-2248b934d630", \n+ "uuid": "9e3a724f-63e2-45c8-9d61-19643583f4bb", \n "workflow_outputs": []\n }\n }, \n- "uuid": "878b2c0c-3b8a-4800-85fe-2c4f6d47adcf"\n+ "uuid": "3392477d-d5ec-402e-b4a9-d25f79403fe9"\n }\n\\ No newline at end of file\n' |