# HG changeset patch
# User ulfschaefer
# Date 1466080009 14400
# Node ID a3f15f50a4afc3a03920cd70d84c153751aeb240
# Parent  76f76eee913054998382fc3d302c3ac54a16ea31
Uploaded

diff -r 76f76eee9130 -r a3f15f50a4af Galaxy-Workflow-Phenix_workflow.ga
--- a/Galaxy-Workflow-Phenix_workflow.ga	Thu Jun 16 08:17:09 2016 -0400
+++ b/Galaxy-Workflow-Phenix_workflow.ga	Thu Jun 16 08:26:49 2016 -0400
@@ -27,7 +27,7 @@
             "tool_state": "{\"name\": \"Reference fasta\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "576fa42b-080a-4cc4-aff3-2f2eac3fe3b7", 
+            "uuid": "e8f09ff7-1ad7-4798-b4e1-5d28171afb9c", 
             "workflow_outputs": []
         }, 
         "1": {
@@ -53,7 +53,7 @@
             "tool_state": "{\"name\": \"R1 fastq\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "10a74ae8-b3f1-4409-8502-f6f79a55b071", 
+            "uuid": "129fd86e-8b0c-4816-bff0-0ca5916064d7", 
             "workflow_outputs": []
         }, 
         "2": {
@@ -79,7 +79,7 @@
             "tool_state": "{\"name\": \"R2 fastqs\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "58fb33f3-4e67-4376-8b82-afab515e9be1", 
+            "uuid": "4d4064d2-6fe8-4758-973f-3b869fdc5432", 
             "workflow_outputs": []
         }, 
         "3": {
@@ -127,7 +127,7 @@
             "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_version": "0.7.12.1", 
             "type": "tool", 
-            "uuid": "e7189b5b-110c-4e8f-ae4e-a85d9e7bf8c3", 
+            "uuid": "698f08bf-70f5-4fbc-b0b2-d4383bb0f46c", 
             "workflow_outputs": []
         }, 
         "4": {
@@ -171,7 +171,7 @@
             "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", 
             "tool_version": "1.0", 
             "type": "tool", 
-            "uuid": "6f7b0596-34f3-4588-9094-04edb6848a4b", 
+            "uuid": "55618bcb-113c-463d-86a5-07c56f36bd2a", 
             "workflow_outputs": []
         }, 
         "5": {
@@ -182,6 +182,10 @@
                 "input": {
                     "id": 4, 
                     "output_name": "outvcf"
+                }, 
+                "ref_fa": {
+                    "id": 0, 
+                    "output_name": "output"
                 }
             }, 
             "inputs": [], 
@@ -208,12 +212,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 
-            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": 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\\\": \\\"10\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}]\", \"onlygood\": \"\\\"false\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"null\", \"input\": \"null\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"ad_ratio\\\": \\\"0.8\\\", \\\"__current_case__\\\": 2, \\\"snp_filter_type_selector\\\": \\\"ad_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_version": "1.0", 
             "type": "tool", 
-            "uuid": "caf82bf3-cccc-47f7-9721-6ef9057173bb", 
+            "uuid": "9107d008-d037-414d-ad61-715ec3c4b3eb", 
             "workflow_outputs": []
         }
     }, 
-    "uuid": "d0b49f14-3813-4724-bcee-88a3ce3fb2e8"
+    "uuid": "80e0166f-6275-4dfd-b94d-5ce2fd15d6d8"
 }
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