# HG changeset patch
# User ulfschaefer
# Date 1467367741 14400
# Node ID 2e5a83c0f78fbd3c684ac3f5a3ba9cb7e5b15625
# Parent  b26e4f861e08227c1de7187bb03a453b8bdc7d9c
Uploaded

diff -r b26e4f861e08 -r 2e5a83c0f78f Galaxy-Workflow-Phenix_workflow.ga
--- a/Galaxy-Workflow-Phenix_workflow.ga	Thu Jun 16 11:08:38 2016 -0400
+++ b/Galaxy-Workflow-Phenix_workflow.ga	Fri Jul 01 06:09:01 2016 -0400
@@ -20,14 +20,14 @@
             "outputs": [], 
             "position": {
                 "left": 200, 
-                "top": 116
+                "top": 128
             }, 
             "tool_errors": null, 
             "tool_id": null, 
             "tool_state": "{\"name\": \"Reference fasta\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "8d026baa-8283-4463-b8ee-6521e4fb616a", 
+            "uuid": "2f18889e-5448-460b-8167-e04125fd51cf", 
             "workflow_outputs": []
         }, 
         "1": {
@@ -45,15 +45,15 @@
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 207, 
-                "top": 334
+                "left": 189, 
+                "top": 296
             }, 
             "tool_errors": null, 
             "tool_id": null, 
             "tool_state": "{\"name\": \"R1 fastq\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "d35a85d2-12c5-4397-9484-b1ce0e339779", 
+            "uuid": "5c634897-4a61-4a99-87c6-d4e23404af6c", 
             "workflow_outputs": []
         }, 
         "2": {
@@ -72,14 +72,14 @@
             "outputs": [], 
             "position": {
                 "left": 211, 
-                "top": 462
+                "top": 474
             }, 
             "tool_errors": null, 
             "tool_id": null, 
             "tool_state": "{\"name\": \"R2 fastqs\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "d7684e32-fa77-4b38-b686-478e2117a2ae", 
+            "uuid": "59c1e55a-eda7-4570-be94-d2d3dca0eb25", 
             "workflow_outputs": []
         }, 
         "3": {
@@ -111,7 +111,7 @@
             ], 
             "position": {
                 "left": 423.5, 
-                "top": 288
+                "top": 300
             }, 
             "post_job_actions": {
                 "RenameDatasetActionbam_output": {
@@ -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": "866b5ac0-33f9-48c5-a5e0-f5f52396f3c9", 
+            "uuid": "104fb0fa-de5b-4202-a8c3-2e8f0fa1321d", 
             "workflow_outputs": []
         }, 
         "4": {
@@ -155,7 +155,7 @@
             ], 
             "position": {
                 "left": 634, 
-                "top": 126
+                "top": 138
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutvcf": {
@@ -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": "e1d89cee-dcbf-4973-9310-c0861b5595c1", 
+            "uuid": "c44a1cad-8e62-4506-84bb-1c4a15f049ca", 
             "workflow_outputs": []
         }, 
         "5": {
@@ -199,7 +199,7 @@
             ], 
             "position": {
                 "left": 747, 
-                "top": 314
+                "top": 326
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -212,12 +212,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 
-            "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"false\\\"\", \"__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_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_version": "1.0", 
             "type": "tool", 
-            "uuid": "5677c0b1-1ef2-43c4-b762-43485541f6ab", 
+            "uuid": "51251f05-75d4-4d89-b757-2248b934d630", 
             "workflow_outputs": []
         }
     }, 
-    "uuid": "602a039a-deb5-45dc-bace-697bb32b974a"
+    "uuid": "878b2c0c-3b8a-4800-85fe-2c4f6d47adcf"
 }
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