diff Galaxy-Workflow-MMuFF.ga @ 5:60a6f2d92058

Adding Galaxy-Workflow-MMuFF.ga (version 1.4 updated for SnpEff v3.2 and snpeff_cds_report v1.2)
author Jim Johnson <jj@umn.edu>
date Sun, 26 May 2013 08:17:53 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-MMuFF.ga	Sun May 26 08:17:53 2013 -0500
@@ -0,0 +1,945 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "MMuFF_Human_v1.4", 
+    "steps": {
+        "0": {
+            "annotation": "Human RNA-seq paired reads left mates", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "Human RNA-seq paired reads left mates", 
+                    "name": "Forward reads fastq"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 240, 
+                "top": 314
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Forward reads fastq\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "Human RNA-seq paired reads right mates", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "Human RNA-seq paired reads right mates", 
+                    "name": "Reverse reads fastq"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 249, 
+                "top": 410
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reverse reads fastq\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "Known SNPs  - dbSNP.vcf", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "Known SNPs  - dbSNP.vcf", 
+                    "name": "VCF file of known variants (dbSNP)"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 2362, 
+                "top": 745
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "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.  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 "
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 4388, 
+                "top": 576
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"VCF file of additional known variants \"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "Convert quality scores to sanger scale", 
+            "id": 4, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Groomer", 
+                    "name": "input_type"
+                }
+            ], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 510, 
+                "top": 291
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fastq_groomer", 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "Convert quality scores to sanger scale", 
+            "id": 5, 
+            "input_connections": {
+                "input_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Groomer", 
+                    "name": "input_type"
+                }
+            ], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 505, 
+                "top": 431
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fastq_groomer", 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "Map paired reads to reference genome", 
+            "id": 6, 
+            "input_connections": {
+                "input1": {
+                    "id": 4, 
+                    "output_name": "output_file"
+                }, 
+                "singlePaired|input2": {
+                    "id": 5, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Tophat for Illumina", 
+                    "name": "singlePaired"
+                }
+            ], 
+            "name": "Tophat for Illumina", 
+            "outputs": [
+                {
+                    "name": "insertions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "deletions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "junctions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "accepted_hits", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 884, 
+                "top": 332
+            }, 
+            "post_job_actions": {
+                "HideDatasetActiondeletions": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "deletions"
+                }, 
+                "HideDatasetActioninsertions": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "insertions"
+                }, 
+                "HideDatasetActionjunctions": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "junctions"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "tophat", 
+            "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", 
+            "tool_version": "1.5.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "Keep only unique mappings - MAPQ of 255\n(255 is the value tophat uses to indicate that reads are uniquely mapped in the genome)", 
+            "id": 7, 
+            "input_connections": {
+                "input1": {
+                    "id": 6, 
+                    "output_name": "accepted_hits"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter SAM or BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1154, 
+                "top": 366
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "samtools_filter", 
+            "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"mapq\": \"\\\"255\\\"\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "input1": {
+                    "id": 7, 
+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "flagstat", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1505, 
+                "top": 323
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "samtools_flagstat", 
+            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "Add Read Group info required by GATK tools", 
+            "id": 9, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 7, 
+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Add or Replace Groups", 
+            "outputs": [
+                {
+                    "name": "outFile", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 1506, 
+                "top": 503
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0", 
+            "tool_state": "{\"rgpl\": \"\\\"ILLUMINA\\\"\", \"outputFormat\": \"\\\"True\\\"\", \"__page__\": 0, \"rgsm\": \"\\\"1\\\"\", \"readGroupOpts\": \"{\\\"rgOpts\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"rgid\": \"\\\"1\\\"\", \"rgpu\": \"\\\"1.5\\\"\", \"rglb\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.56.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "Synchronize paired reads", 
+            "id": 10, 
+            "input_connections": {
+                "input_file": {
+                    "id": 9, 
+                    "output_name": "outFile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Paired Read Mate Fixer", 
+            "outputs": [
+                {
+                    "name": "out_file", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 1841, 
+                "top": 375
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionout_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0", 
+            "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"input_file\": \"null\", \"out_prefix\": \"\\\"Fix Mate\\\"\", \"sortOrder\": \"\\\"coordinate\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
+            "tool_version": "1.56.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "Remove duplicate reads", 
+            "id": 11, 
+            "input_connections": {
+                "input_file": {
+                    "id": 10, 
+                    "output_name": "out_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Mark Duplicate reads", 
+            "outputs": [
+                {
+                    "name": "out_file", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "html_file", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
+                "left": 2086, 
+                "top": 360
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", 
+            "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
+            "tool_version": "1.56.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "Reorder BAM for GATK tools", 
+            "id": 12, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 11, 
+                    "output_name": "out_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Reorder SAM/BAM", 
+            "outputs": [
+                {
+                    "name": "outFile", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 2401, 
+                "top": 332
+            }, 
+            "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\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.56.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "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": [], 
+            "name": "Realigner Target Creator", 
+            "outputs": [
+                {
+                    "name": "output_interval", 
+                    "type": "gatk_interval"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 2565, 
+                "top": 518
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_log": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_log"
+                }
+            }, 
+            "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__\\\": \\\"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": "Perform local realignments for indels", 
+            "id": 14, 
+            "input_connections": {
+                "reference_source|input_bam": {
+                    "id": 12, 
+                    "output_name": "outFile"
+                }, 
+                "target_intervals": {
+                    "id": 13, 
+                    "output_name": "output_interval"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Indel Realigner", 
+            "outputs": [
+                {
+                    "name": "output_bam", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 2811, 
+                "top": 351
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_log": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_log"
+                }
+            }, 
+            "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__\\\": \\\"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": "Check again for duplicate reads and eliminate", 
+            "id": 15, 
+            "input_connections": {
+                "input_file": {
+                    "id": 14, 
+                    "output_name": "output_bam"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Mark Duplicate reads", 
+            "outputs": [
+                {
+                    "name": "out_file", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "html_file", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
+                "left": 3174, 
+                "top": 318
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionhtml_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "html_file"
+                }, 
+                "HideDatasetActionout_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", 
+            "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
+            "tool_version": "1.56.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "16": {
+            "annotation": "Determine base calls at each position", 
+            "id": 16, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 15, 
+                    "output_name": "out_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 3554, 
+                "top": 292
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_log": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_log"
+                }, 
+                "HideDatasetActionoutput_mpileup": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "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\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", 
+            "tool_version": "0.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "17": {
+            "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": {
+                    "id": 16, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Pileup to VCF", 
+                    "name": "min_base_qual"
+                }
+            ], 
+            "name": "Pileup to VCF", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 4029, 
+                "top": 323
+            }, 
+            "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, \"vcf_id\": \"\\\"\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}", 
+            "tool_version": "2.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "18": {
+            "annotation": "Annotate the ID field with dbSNP IDs.", 
+            "id": 18, 
+            "input_connections": {
+                "dbSnp": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "input": {
+                    "id": 17, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpSift Annotate", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 4321, 
+                "top": 379
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.2", 
+            "tool_state": "{\"annotate\": \"{\\\"id\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"dbSnp\": \"null\", \"annotate_cmd\": \"\\\"False\\\"\", \"__page__\": 0}", 
+            "tool_version": "3.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "19": {
+            "annotation": "Annotate the ID field with users known variant IDs.", 
+            "id": 19, 
+            "input_connections": {
+                "dbSnp": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "input": {
+                    "id": 18, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpSift Annotate", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 4704, 
+                "top": 407
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.2", 
+            "tool_state": "{\"annotate\": \"{\\\"id\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"dbSnp\": \"null\", \"annotate_cmd\": \"\\\"False\\\"\", \"__page__\": 0}", 
+            "tool_version": "3.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "20": {
+            "annotation": "Filter out chrM variations and any variant with an annotated ID", 
+            "id": 20, 
+            "input_connections": {
+                "input": {
+                    "id": 19, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpSift Filter", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 5058, 
+                "top": 501
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", 
+            "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"(CHROM !~ 'chrM') & (ID = '')\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", 
+            "tool_version": "3.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "21": {
+            "annotation": "", 
+            "id": 21, 
+            "input_connections": {
+                "input": {
+                    "id": 20, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpEff", 
+            "outputs": [
+                {
+                    "name": "snpeff_output", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "statsFile", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
+                "left": 5298, 
+                "top": 433
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/3.2", 
+            "tool_state": "{\"spliceSiteSize\": \"\\\"2\\\"\", \"filterHomHet\": \"\\\"no_filter\\\"\", \"outputFormat\": \"\\\"vcf\\\"\", \"udLength\": \"\\\"0\\\"\", \"inputFormat\": \"\\\"vcf\\\"\", \"filterIn\": \"\\\"no_filter\\\"\", \"__page__\": 0, \"filterOut\": \"[\\\"no-downstream\\\", \\\"no-intergenic\\\", \\\"no-intron\\\", \\\"no-upstream\\\", \\\"no-utr\\\"]\", \"genomeVersion\": \"\\\"GRCh37.68\\\"\", \"regulation\": \"null\", \"generate_stats\": \"\\\"True\\\"\", \"noLog\": \"\\\"True\\\"\", \"chr\": \"\\\"\\\"\", \"intervals\": \"null\", \"offset\": \"\\\"\\\"\", \"input\": \"null\", \"transcripts\": \"null\", \"annotations\": \"[\\\"hgvs\\\", \\\"lof\\\"]\"}", 
+            "tool_version": "3.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "22": {
+            "annotation": "Filter SnpEffects keeping FRAME_SHIFT \nvariants", 
+            "id": 22, 
+            "input_connections": {
+                "input": {
+                    "id": 21, 
+                    "output_name": "snpeff_output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpSift Filter", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 5631, 
+                "top": 433
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", 
+            "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[*].EFFECT = 'FRAME_SHIFT' )\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", 
+            "tool_version": "3.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "23": {
+            "annotation": "Filter SnpEffects keeping NON_SYNONYMOUS_CODING variants", 
+            "id": 23, 
+            "input_connections": {
+                "input": {
+                    "id": 21, 
+                    "output_name": "snpeff_output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpSift Filter", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 5628, 
+                "top": 598
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", 
+            "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[*].EFFECT = 'NON_SYNONYMOUS_CODING')\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", 
+            "tool_version": "3.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "24": {
+            "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", 
+            "id": 24, 
+            "input_connections": {
+                "snp_effect_vcf": {
+                    "id": 22, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpEff Ensembl CDS", 
+            "outputs": [
+                {
+                    "name": "html_report", 
+                    "type": "html"
+                }, 
+                {
+                    "name": "tsv_report", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "text_report", 
+                    "type": "text"
+                }
+            ], 
+            "position": {
+                "left": 6064, 
+                "top": 345
+            }, 
+            "post_job_actions": {
+                "HideDatasetActiontext_report": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "text_report"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2", 
+            "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"FRAME_SHIFT\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", 
+            "tool_version": "1.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "25": {
+            "annotation": "Ignore variations in SPLICE donor/acceptor regions", 
+            "id": 25, 
+            "input_connections": {
+                "input": {
+                    "id": 23, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpSift Filter", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 5851, 
+                "top": 532
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", 
+            "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"True\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[ANY].EFFECT =~ 'SPLICE' )\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", 
+            "tool_version": "3.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "26": {
+            "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", 
+            "id": 26, 
+            "input_connections": {
+                "snp_effect_vcf": {
+                    "id": 25, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SnpEff Ensembl CDS", 
+            "outputs": [
+                {
+                    "name": "html_report", 
+                    "type": "html"
+                }, 
+                {
+                    "name": "tsv_report", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "text_report", 
+                    "type": "text"
+                }
+            ], 
+            "position": {
+                "left": 6067, 
+                "top": 502
+            }, 
+            "post_job_actions": {
+                "HideDatasetActiontext_report": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "text_report"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2", 
+            "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", 
+            "tool_version": "1.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file