diff Galaxy-Workflow-MMuFF_v1.2.ga @ 2:04e170c09922

Add a workflow for noraml tissue samples.

--- a/Galaxy-Workflow-MMuFF_v1.2.ga	Thu Mar 28 15:06:33 2013 -0500
+++ b/Galaxy-Workflow-MMuFF_v1.2.ga	Fri Apr 12 07:51:45 2013 -0500
@@ -2,23 +2,23 @@
     "a_galaxy_workflow": "true", 
     "annotation": "", 
     "format-version": "0.1", 
-    "name": "MMuFF_v1.2", 
+    "name": "MMuFF_Human_v1.2", 
     "steps": {
         "0": {
-            "annotation": "", 
+            "annotation": "Human RNA-seq paired reads left mates", 
             "id": 0, 
             "input_connections": {}, 
             "inputs": [
                 {
-                    "description": "", 
+                    "description": "Human RNA-seq paired reads left mates", 
                     "name": "Forward reads fastq"
                 }
             ], 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 244, 
-                "top": 313
+                "left": 240, 
+                "top": 287
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -28,20 +28,20 @@
             "user_outputs": []
         }, 
         "1": {
-            "annotation": "", 
+            "annotation": "Human RNA-seq paired reads right mates", 
             "id": 1, 
             "input_connections": {}, 
             "inputs": [
                 {
-                    "description": "", 
+                    "description": "Human RNA-seq paired reads right mates", 
                     "name": "Reverse reads fastq"
                 }
             ], 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 242, 
-                "top": 410
+                "left": 249, 
+                "top": 383
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -51,20 +51,20 @@
             "user_outputs": []
         }, 
         "2": {
-            "annotation": "dbSNP.vcf", 
+            "annotation": "Known SNPs  - dbSNP.vcf", 
             "id": 2, 
             "input_connections": {}, 
             "inputs": [
                 {
-                    "description": "dbSNP.vcf", 
+                    "description": "Known SNPs  - dbSNP.vcf", 
                     "name": "VCF file of known variants (dbSNP)"
                 }
             ], 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 4063, 
-                "top": 532
+                "left": 2327, 
+                "top": 758
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -74,12 +74,12 @@
             "user_outputs": []
         }, 
         "3": {
-            "annotation": "These are locations other than those in dbSNP.  The ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y) even if it is a bogus value at position 1", 
+            "annotation": "These are locations other than those in dbSNP.  This could include variants from the subject normal tissue.  \nThe ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one  entry for  each chromosome: (M,1,2,...,X,Y)", 
             "id": 3, 
             "input_connections": {}, 
             "inputs": [
                 {
-                    "description": "These are locations other than those in dbSNP.  The ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y) even if it is a bogus value at position 1", 
+                    "description": "These are locations other than those in dbSNP.  This could include variants from the subject normal tissue.  \nThe ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one  entry for  each chromosome: (M,1,2,...,X,Y)", 
                     "name": "VCF file of additional known variants "
                 }
             ], 
@@ -87,7 +87,7 @@
             "outputs": [], 
             "position": {
                 "left": 4388, 
-                "top": 573
+                "top": 549
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -97,7 +97,7 @@
             "user_outputs": []
         }, 
         "4": {
-            "annotation": "", 
+            "annotation": "Convert quality scores to sanger scale", 
             "id": 4, 
             "input_connections": {
                 "input_file": {
@@ -120,7 +120,7 @@
             ], 
             "position": {
                 "left": 510, 
-                "top": 288
+                "top": 264
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -131,7 +131,7 @@
             "user_outputs": []
         }, 
         "5": {
-            "annotation": "", 
+            "annotation": "Convert quality scores to sanger scale", 
             "id": 5, 
             "input_connections": {
                 "input_file": {
@@ -154,7 +154,7 @@
             ], 
             "position": {
                 "left": 505, 
-                "top": 428
+                "top": 404
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -165,7 +165,7 @@
             "user_outputs": []
         }, 
         "6": {
-            "annotation": "Use a GATK compatible genome reference.", 
+            "annotation": "Map paired reads to reference genome", 
             "id": 6, 
             "input_connections": {
                 "input1": {
@@ -177,12 +177,7 @@
                     "output_name": "output_file"
                 }
             }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Tophat for Illumina", 
-                    "name": "refGenomeSource"
-                }
-            ], 
+            "inputs": [], 
             "name": "Tophat for Illumina", 
             "outputs": [
                 {
@@ -204,7 +199,7 @@
             ], 
             "position": {
                 "left": 884, 
-                "top": 329
+                "top": 305
             }, 
             "post_job_actions": {
                 "HideDatasetActiondeletions": {
@@ -225,13 +220,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "tophat", 
-            "tool_state": "{\"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"1\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"use_junctions\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"80\\\"}\"}", 
+            "tool_state": "{\"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"1\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"use_junctions\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"80\\\"}\"}", 
             "tool_version": "1.5.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "7": {
-            "annotation": "", 
+            "annotation": "Keep only mappings with MAPQ of 255", 
             "id": 7, 
             "input_connections": {
                 "input1": {
@@ -249,7 +244,7 @@
             ], 
             "position": {
                 "left": 1154, 
-                "top": 363
+                "top": 339
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput1": {
@@ -284,7 +279,7 @@
             ], 
             "position": {
                 "left": 1505, 
-                "top": 320
+                "top": 296
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -295,7 +290,7 @@
             "user_outputs": []
         }, 
         "9": {
-            "annotation": "", 
+            "annotation": "Add Read Group info required by GATK tools", 
             "id": 9, 
             "input_connections": {
                 "inputFile": {
@@ -313,7 +308,7 @@
             ], 
             "position": {
                 "left": 1506, 
-                "top": 500
+                "top": 476
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -324,7 +319,7 @@
             "user_outputs": []
         }, 
         "10": {
-            "annotation": "", 
+            "annotation": "Synchronize paired reads", 
             "id": 10, 
             "input_connections": {
                 "input_file": {
@@ -342,7 +337,7 @@
             ], 
             "position": {
                 "left": 1841, 
-                "top": 372
+                "top": 348
             }, 
             "post_job_actions": {
                 "HideDatasetActionout_file": {
@@ -359,7 +354,7 @@
             "user_outputs": []
         }, 
         "11": {
-            "annotation": "", 
+            "annotation": "Remove duplicate reads", 
             "id": 11, 
             "input_connections": {
                 "input_file": {
@@ -381,7 +376,7 @@
             ], 
             "position": {
                 "left": 2086, 
-                "top": 357
+                "top": 333
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -392,7 +387,7 @@
             "user_outputs": []
         }, 
         "12": {
-            "annotation": "Set to same GATK compatible genome reference as tophat", 
+            "annotation": "Reorder BAM for GATK tools", 
             "id": 12, 
             "input_connections": {
                 "inputFile": {
@@ -400,12 +395,7 @@
                     "output_name": "out_file"
                 }
             }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Reorder SAM/BAM", 
-                    "name": "source"
-                }
-            ], 
+            "inputs": [], 
             "name": "Reorder SAM/BAM", 
             "outputs": [
                 {
@@ -414,32 +404,31 @@
                 }
             ], 
             "position": {
-                "left": 2395, 
-                "top": 323
+                "left": 2401, 
+                "top": 305
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0", 
-            "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}", 
+            "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}", 
             "tool_version": "1.56.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "13": {
-            "annotation": "Set genome reference to same GATK compatible reference as tophat", 
+            "annotation": "", 
             "id": 13, 
             "input_connections": {
                 "reference_source|input_bam": {
                     "id": 12, 
                     "output_name": "outFile"
+                }, 
+                "rod_bind_0|rod_bind_type|input_rod": {
+                    "id": 2, 
+                    "output_name": "output"
                 }
             }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Realigner Target Creator", 
-                    "name": "reference_source"
-                }
-            ], 
+            "inputs": [], 
             "name": "Realigner Target Creator", 
             "outputs": [
                 {
@@ -453,7 +442,7 @@
             ], 
             "position": {
                 "left": 2565, 
-                "top": 515
+                "top": 491
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput_log": {
@@ -464,13 +453,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "gatk_realigner_target_creator", 
-            "tool_state": "{\"__page__\": 0, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[{\\\"__index__\\\": 0, \\\"rod_bind_type\\\": {\\\"rod_bind_type_selector\\\": \\\"dbsnp\\\", \\\"__current_case__\\\": 0, \\\"input_rod\\\": null}}]\"}", 
+            "tool_state": "{\"__page__\": 0, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[{\\\"__index__\\\": 0, \\\"rod_bind_type\\\": {\\\"rod_bind_type_selector\\\": \\\"dbsnp\\\", \\\"__current_case__\\\": 0, \\\"input_rod\\\": null}}]\"}", 
             "tool_version": "0.0.4", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "14": {
-            "annotation": "Set genome reference to same GATK compatible reference as tophat", 
+            "annotation": "Perform local realignments for indels", 
             "id": 14, 
             "input_connections": {
                 "reference_source|input_bam": {
@@ -482,12 +471,7 @@
                     "output_name": "output_interval"
                 }
             }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Indel Realigner", 
-                    "name": "reference_source"
-                }
-            ], 
+            "inputs": [], 
             "name": "Indel Realigner", 
             "outputs": [
                 {
@@ -501,7 +485,7 @@
             ], 
             "position": {
                 "left": 2811, 
-                "top": 348
+                "top": 324
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput_log": {
@@ -512,13 +496,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "gatk_indel_realigner", 
-            "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}", 
+            "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}", 
             "tool_version": "0.0.6", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "15": {
-            "annotation": "", 
+            "annotation": "Check again for duplicate reads and eliminate", 
             "id": 15, 
             "input_connections": {
                 "input_file": {
@@ -540,7 +524,7 @@
             ], 
             "position": {
                 "left": 3174, 
-                "top": 315
+                "top": 291
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             "post_job_actions": {
                 "HideDatasetActionhtml_file": {
@@ -562,7 +546,7 @@
             "user_outputs": []
         }, 
         "16": {
-            "annotation": "Set genome reference to same GATK compatible reference as tophat", 
+            "annotation": "Determine base calls at each position", 
             "id": 16, 
             "input_connections": {
                 "reference_source|input_bams_0|input_bam": {
@@ -570,12 +554,7 @@
                     "output_name": "out_file"
                 }
             }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool MPileup", 
-                    "name": "reference_source"
-                }
-            ], 
+            "inputs": [], 
             "name": "MPileup", 
             "outputs": [
                 {
@@ -589,7 +568,7 @@
             ], 
             "position": {
                 "left": 3554, 
-                "top": 289
+                "top": 265
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput_log": {
@@ -605,13 +584,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "samtools_mpileup", 
-            "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"2500\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"20\\\", \\\"disable_probabilistic_realignment\\\": \\\"True\\\", \\\"skip_anomalous_read_pairs\\\": \\\"True\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", 
+            "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"2500\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"20\\\", \\\"disable_probabilistic_realignment\\\": \\\"True\\\", \\\"skip_anomalous_read_pairs\\\": \\\"True\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", 
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             "type": "tool", 
             "user_outputs": []
         }, 
         "17": {
-            "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele:  .33", 
+            "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele:  .33\nLeave VCF_ID blank for tumor sample", 
             "id": 17, 
             "input_connections": {
                 "input_file": {
@@ -634,13 +613,13 @@
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             "position": {
                 "left": 4029, 
-                "top": 320
+                "top": 296
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0", 
-            "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}", 
-            "tool_version": "2.0", 
+            "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}", 
+            "tool_version": "2.2", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -667,7 +646,7 @@
             ], 
             "position": {
                 "left": 4421, 
-                "top": 309
+                "top": 285
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput": {
@@ -706,7 +685,7 @@
             ], 
             "position": {
                 "left": 4724, 
-                "top": 457
+                "top": 433
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput": {
@@ -741,7 +720,7 @@
             ], 
             "position": {
                 "left": 5043, 
-                "top": 507
+                "top": 483
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -752,7 +731,7 @@
             "user_outputs": []
         }, 
         "21": {
-            "annotation": "Use Genome from Ensembl, e.g GRCh37.68 for Human, so we get Ensembl transcript ID info", 
+            "annotation": "Use Genome from Ensembl, e.g GRCh37.68 so we get ensembl transcript name info", 
             "id": 21, 
             "input_connections": {
                 "input": {
@@ -760,12 +739,7 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool SnpEff", 
-                    "name": "genomeVersion"
-                }
-            ], 
+            "inputs": [], 
             "name": "SnpEff", 
             "outputs": [
                 {
@@ -779,7 +753,7 @@
             ], 
             "position": {
                 "left": 5277, 
-                "top": 466
+                "top": 442
             }, 
             "post_job_actions": {
                 "HideDatasetActionstatsFile": {
@@ -790,7 +764,7 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/3.1", 
-            "tool_state": "{\"filterHomHet\": \"\\\"\\\"\", \"outputFormat\": \"\\\"vcf\\\"\", \"filterOut\": \"[\\\"downstream\\\", \\\"intergenic\\\", \\\"intron\\\", \\\"upstream\\\", \\\"utr\\\"]\", \"inputFormat\": \"\\\"vcf\\\"\", \"filterIn\": \"\\\"\\\"\", \"__page__\": 0, \"udLength\": \"\\\"0\\\"\", \"genomeVersion\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"offset\": \"\\\"\\\"\", \"input\": \"null\"}", 
+            "tool_state": "{\"filterHomHet\": \"\\\"\\\"\", \"outputFormat\": \"\\\"vcf\\\"\", \"filterOut\": \"[\\\"downstream\\\", \\\"intergenic\\\", \\\"intron\\\", \\\"upstream\\\", \\\"utr\\\"]\", \"inputFormat\": \"\\\"vcf\\\"\", \"filterIn\": \"\\\"\\\"\", \"__page__\": 0, \"udLength\": \"\\\"0\\\"\", \"genomeVersion\": \"\\\"GRCh37.68\\\"\", \"offset\": \"\\\"\\\"\", \"input\": \"null\"}", 
             "tool_version": "3.1", 
             "type": "tool", 
             "user_outputs": []
@@ -814,7 +788,7 @@
             ], 
             "position": {
                 "left": 5595, 
-                "top": 429
+                "top": 405
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -842,8 +816,8 @@
                 }
             ], 
             "position": {
-                "left": 5595, 
-                "top": 575
+                "left": 5600, 
+                "top": 584
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -879,8 +853,8 @@
                 }
             ], 
             "position": {
-                "left": 5832, 
-                "top": 395
+                "left": 5810, 
+                "top": 364
             }, 
             "post_job_actions": {
                 "HideDatasetActionhtml_report": {
@@ -900,7 +874,7 @@
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.0", 
+            "tool_id": "SnpEff-cds-report", 
             "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"FRAME_SHIFT\\\"\", \"all_effects\": \"\\\"False\\\"\", \"polya\": \"\\\"5\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", 
             "tool_version": "1.0", 
             "type": "tool", 
@@ -932,8 +906,8 @@
                 }
             ], 
             "position": {
-                "left": 5838, 
-                "top": 549
+                "left": 5820, 
+                "top": 537
             }, 
             "post_job_actions": {
                 "HideDatasetActionhtml_report": {
@@ -953,11 +927,11 @@
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.0", 
+            "tool_id": "SnpEff-cds-report", 
             "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"all_effects\": \"\\\"False\\\"\", \"polya\": \"\\\"5\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", 
             "tool_version": "1.0", 
             "type": "tool", 
             "user_outputs": []
         }
     }
-}
+}
\ No newline at end of file