Mercurial > repos > ulfschaefer > phephenix

changeset 16:55bfe9d1888e draft

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Uploaded
author ulfschaefer
date Tue, 12 Jul 2016 09:56:33 -0400
parents 48c41c6ad84e
children f7494340ae7f
files Galaxy-Workflow-Phenix_workflow.ga
diffstat 1 files changed, 68 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- 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