view Galaxy-Workflow-Phenix_workflow.ga @ 1:162c88041ed7 draft

Uploaded
author ulfschaefer
date Tue, 10 May 2016 05:16:08 -0400
parents
children a3f15f50a4af
line wrap: on
line source

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "Phenix workflow", 
    "steps": {
        "0": {
            "annotation": "", 
            "content_id": null, 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Reference fasta"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 116
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Reference fasta\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "576fa42b-080a-4cc4-aff3-2f2eac3fe3b7", 
            "workflow_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "content_id": null, 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "R1 fastq"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 207, 
                "top": 334
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"R1 fastq\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "10a74ae8-b3f1-4409-8502-f6f79a55b071", 
            "workflow_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "content_id": null, 
            "id": 2, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "R2 fastqs"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 211, 
                "top": 462
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"R2 fastqs\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "58fb33f3-4e67-4376-8b82-afab515e9be1", 
            "workflow_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", 
            "id": 3, 
            "input_connections": {
                "fastq_input|fastq_input1": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "fastq_input|fastq_input2": {
                    "id": 2, 
                    "output_name": "output"
                }, 
                "reference_source|ref_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Map with BWA-MEM", 
            "outputs": [
                {
                    "name": "bam_output", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 423.5, 
                "top": 288
            }, 
            "post_job_actions": {
                "RenameDatasetActionbam_output": {
                    "action_arguments": {
                        "newname": "#{fastq_input1 | basename}.bam"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "bam_output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", 
            "tool_version": "0.7.12.1", 
            "type": "tool", 
            "uuid": "e7189b5b-110c-4e8f-ae4e-a85d9e7bf8c3", 
            "workflow_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", 
            "id": 4, 
            "input_connections": {
                "input_bam": {
                    "id": 3, 
                    "output_name": "bam_output"
                }, 
                "ref_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "PHE MPileup", 
            "outputs": [
                {
                    "name": "outvcf", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 634, 
                "top": 126
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutvcf": {
                    "action_arguments": {
                        "newname": "#{input_bam | basename}.vcf"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outvcf"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", 
            "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", 
            "tool_version": "1.0", 
            "type": "tool", 
            "uuid": "6f7b0596-34f3-4588-9094-04edb6848a4b", 
            "workflow_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 
            "id": 5, 
            "input_connections": {
                "input": {
                    "id": 4, 
                    "output_name": "outvcf"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Filter VCF", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 747, 
                "top": 314
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutput": {
                    "action_arguments": {
                        "newname": "#{input | basename}.filtered.vcf"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 
            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"10\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}]\", \"onlygood\": \"\\\"false\\\"\"}", 
            "tool_version": "1.0", 
            "type": "tool", 
            "uuid": "caf82bf3-cccc-47f7-9721-6ef9057173bb", 
            "workflow_outputs": []
        }
    }, 
    "uuid": "d0b49f14-3813-4724-bcee-88a3ce3fb2e8"
}