view Galaxy-Workflow-MMuFLR_Human_v1.4.ga @ 1:53a99a00d5ec

Deleted selected files
author jjohnson
date Tue, 04 Jun 2013 09:56:10 -0400
parents 4f70b23c497a
children
line wrap: on
line source

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "MMuFLR_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": {}, 
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            "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": {}, 
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            "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": {
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                    "output_name": "junctions"
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            "tool_errors": null, 
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            "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": {
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            "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": []
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        "8": {
            "annotation": "", 
            "id": 8, 
            "input_connections": {
                "input1": {
                    "id": 7, 
                    "output_name": "output1"
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            }, 
            "inputs": [], 
            "name": "flagstat", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 1505, 
                "top": 323
            }, 
            "post_job_actions": {}, 
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            "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
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            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0", 
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        "10": {
            "annotation": "Synchronize paired reads", 
            "id": 10, 
            "input_connections": {
                "input_file": {
                    "id": 9, 
                    "output_name": "outFile"
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            }, 
            "inputs": [], 
            "name": "Paired Read Mate Fixer", 
            "outputs": [
                {
                    "name": "out_file", 
                    "type": "bam"
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            ], 
            "position": {
                "left": 1841, 
                "top": 375
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            "type": "tool", 
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        "11": {
            "annotation": "Remove duplicate reads", 
            "id": 11, 
            "input_connections": {
                "input_file": {
                    "id": 10, 
                    "output_name": "out_file"
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            }, 
            "inputs": [], 
            "name": "Mark Duplicate reads", 
            "outputs": [
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                    "name": "out_file", 
                    "type": "bam"
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                {
                    "name": "html_file", 
                    "type": "html"
                }
            ], 
            "position": {
                "left": 2086, 
                "top": 360
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            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", 
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            "tool_version": "1.56.0", 
            "type": "tool", 
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        "12": {
            "annotation": "Reorder BAM for GATK tools", 
            "id": 12, 
            "input_connections": {
                "inputFile": {
                    "id": 11, 
                    "output_name": "out_file"
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            }, 
            "inputs": [], 
            "name": "Reorder SAM/BAM", 
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                {
                    "name": "outFile", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 2401, 
                "top": 332
            }, 
            "post_job_actions": {}, 
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                    "output_name": "outFile"
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                    "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
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                    "action_type": "HideDatasetAction", 
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            "annotation": "Perform local realignments for indels", 
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                    "output_name": "output_interval"
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            "inputs": [], 
            "name": "Indel Realigner", 
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                    "name": "output_bam", 
                    "type": "bam"
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                    "name": "output_log", 
                    "type": "txt"
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            ], 
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                    "action_type": "HideDatasetAction", 
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            "annotation": "Check again for duplicate reads and eliminate", 
            "id": 15, 
            "input_connections": {
                "input_file": {
                    "id": 14, 
                    "output_name": "output_bam"
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            }, 
            "inputs": [], 
            "name": "Mark Duplicate reads", 
            "outputs": [
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                    "name": "out_file", 
                    "type": "bam"
                }, 
                {
                    "name": "html_file", 
                    "type": "html"
                }
            ], 
            "position": {
                "left": 3174, 
                "top": 318
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            "post_job_actions": {
                "HideDatasetActionhtml_file": {
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                    "action_type": "HideDatasetAction", 
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                "HideDatasetActionout_file": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file"
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        "16": {
            "annotation": "Determine base calls at each position", 
            "id": 16, 
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                    "id": 15, 
                    "output_name": "out_file"
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            "name": "MPileup", 
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                    "name": "output_mpileup", 
                    "type": "pileup"
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                    "name": "output_log", 
                    "type": "txt"
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            "type": "tool", 
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        }, 
        "17": {
            "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele:  .33\nLeave VCF_ID blank for tumor sample", 
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