{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "MMuFLR_Human_from_MPileup_v1.4", 
    "steps": {
        "0": {
            "annotation": "Tabular output from SAMtools mpileup", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Tabular output from SAMtools mpileup", 
                    "name": "Output from SAMtools MPileup"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 273
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Output from SAMtools MPileup\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "Known SNPs  - dbSNP.vcf", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Known SNPs  - dbSNP.vcf", 
                    "name": "VCF file of known variants (dbSNP)"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 432, 
                "top": 403
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "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": 2, 
            "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": 818, 
                "top": 453
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"VCF file of additional known variants \"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele:  .33\nLeave VCF_ID blank for tumor sample", 
            "id": 3, 
            "input_connections": {
                "input_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "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": 459, 
                "top": 200
            }, 
            "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": []
        }, 
        "4": {
            "annotation": "Annotate the ID field with dbSNP IDs.", 
            "id": 4, 
            "input_connections": {
                "dbSnp": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "input": {
                    "id": 3, 
                    "output_name": "output_file"
                }
            }, 
            "inputs": [], 
            "name": "SnpSift Annotate", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 751, 
                "top": 256
            }, 
            "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": []
        }, 
        "5": {
            "annotation": "Annotate the ID field with users known variant IDs.", 
            "id": 5, 
            "input_connections": {
                "dbSnp": {
                    "id": 2, 
                    "output_name": "output"
                }, 
                "input": {
                    "id": 4, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "SnpSift Annotate", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 1134, 
                "top": 284
            }, 
            "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": []
        }, 
        "6": {
            "annotation": "Filter out chrM variations and any variant with an annotated ID", 
            "id": 6, 
            "input_connections": {
                "input": {
                    "id": 5, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "SnpSift Filter", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 1488, 
                "top": 378
            }, 
            "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": []
        }, 
        "7": {
            "annotation": "", 
            "id": 7, 
            "input_connections": {
                "input": {
                    "id": 6, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "SnpEff", 
            "outputs": [
                {
                    "name": "snpeff_output", 
                    "type": "vcf"
                }, 
                {
                    "name": "statsFile", 
                    "type": "html"
                }
            ], 
            "position": {
                "left": 1728, 
                "top": 310
            }, 
            "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": []
        }, 
        "8": {
            "annotation": "Filter SnpEffects keeping FRAME_SHIFT \nvariants", 
            "id": 8, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "snpeff_output"
                }
            }, 
            "inputs": [], 
            "name": "SnpSift Filter", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 2061, 
                "top": 310
            }, 
            "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": []
        }, 
        "9": {
            "annotation": "Filter SnpEffects keeping NON_SYNONYMOUS_CODING variants", 
            "id": 9, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "snpeff_output"
                }
            }, 
            "inputs": [], 
            "name": "SnpSift Filter", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 2058, 
                "top": 475
            }, 
            "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": []
        }, 
        "10": {
            "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", 
            "id": 10, 
            "input_connections": {
                "snp_effect_vcf": {
                    "id": 8, 
                    "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": 2491, 
                "top": 226
            }, 
            "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": []
        }, 
        "11": {
            "annotation": "Ignore variations in SPLICE donor/acceptor regions", 
            "id": 11, 
            "input_connections": {
                "input": {
                    "id": 9, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "SnpSift Filter", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 2281, 
                "top": 409
            }, 
            "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": []
        }, 
        "12": {
            "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", 
            "id": 12, 
            "input_connections": {
                "snp_effect_vcf": {
                    "id": 11, 
                    "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": 2497, 
                "top": 381
            }, 
            "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": []
        }
    }
}