{
    "uuid": "8c8c54b5-a24f-4c72-9e6e-6edbdb946b41",
    "tags": [],
    "format-version": "0.1",
    "name": "Differential gene expression analysis of single-end NGS data using FastQC, Trimmomatic, BWA, AWK, Infer Experiment, featureCounts, DESeq2",
    "version": 0,
    "steps": {
        "0": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N1.fastq.gz\"}",
            "id": 0,
            "uuid": "ef1860e6-b7de-46e6-babe-adcee329895d",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N1.fastq.gz",
                    "description": ""
                }
            ],
            "position": {
                "top": 10,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "1": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N2.fastq.gz\"}",
            "id": 1,
            "uuid": "f3433cf2-01d6-4008-bd23-3e6ed3e0be01",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N2.fastq.gz",
                    "description": ""
                }
            ],
            "position": {
                "top": 130,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "2": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N3.fastq.gz\"}",
            "id": 2,
            "uuid": "8ba843ea-4cd3-40cf-825b-79318980a2b7",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N3.fastq.gz",
                    "description": ""
                }
            ],
            "position": {
                "top": 250,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "3": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N4.fastq.gz\"}",
            "id": 3,
            "uuid": "e8095d7f-0a93-49ff-8606-7c038a6924e4",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N4.fastq.gz",
                    "description": ""
                }
            ],
            "position": {
                "top": 370,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "4": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N1.fastq.gz\"}",
            "id": 4,
            "uuid": "ef2ee4f2-f7cf-4285-8c54-ac175cf738e3",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N1.fastq.gz",
                    "description": ""
                }
            ],
            "position": {
                "top": 490,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "5": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N2.fastq.gz\"}",
            "id": 5,
            "uuid": "89fd41bf-6ee5-4a49-a5ce-9c43ea2a1b41",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N2.fastq.gz",
                    "description": ""
                }
            ],
            "position": {
                "top": 610,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "6": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N3.fastq.gz\"}",
            "id": 6,
            "uuid": "995d36be-cf0e-4493-8efa-02d7a1d1bc32",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N3.fastq.gz",
                    "description": ""
                }
            ],
            "position": {
                "top": 730,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "7": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N4.fastq.gz\"}",
            "id": 7,
            "uuid": "f502d6d7-a580-47c4-93b8-bfd4694f65c0",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N4.fastq.gz",
                    "description": ""
                }
            ],
            "position": {
                "top": 850,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "8": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/hg38.goi.fa\"}",
            "id": 8,
            "uuid": "58f33df6-4708-40b6-a92a-54d4fbca0630",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/hg38.goi.fa",
                    "description": ""
                }
            ],
            "position": {
                "top": 970,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "9": {
            "tool_id": null,
            "tool_version": null,
            "outputs": [],
            "workflow_outputs": [],
            "input_connections": {},
            "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/hg38.goi.gtf\"}",
            "id": 9,
            "uuid": "d9c44bcc-3deb-49e7-934f-efa4f90c5bc7",
            "errors": null,
            "name": "Input dataset",
            "label": null,
            "inputs": [
                {
                    "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/hg38.goi.gtf",
                    "description": ""
                }
            ],
            "position": {
                "top": 1090,
                "left": 10
            },
            "annotation": "",
            "content_id": null,
            "type": "data_input"
        },
        "10": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "tool_version": "0.72+galaxy1",
            "outputs": [
                {
                    "type": "html",
                    "name": "html_file"
                },
                {
                    "type": "txt",
                    "name": "text_file"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input_file": {
                    "output_name": "output",
                    "id": 0
                }
            },
            "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
            "id": 10,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "e7b2202befea",
                "name": "fastqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "c6d6e3d3-4f3b-492c-874c-7f1c7cbff2e3",
            "errors": null,
            "name": "FastQC",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 10,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "type": "tool"
        },
        "11": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "tool_version": "0.38.0",
            "outputs": [
                {
                    "type": "input",
                    "name": "fastq_out"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "readtype|fastq_in": {
                    "output_name": "output",
                    "id": 0
                }
            },
            "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 11,
            "tool_shed_repository": {
                "owner": "pjbriggs",
                "changeset_revision": "898b67846b47",
                "name": "trimmomatic",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "766dc4ad-9794-4458-93b4-08154e305c4b",
            "errors": null,
            "name": "Trimmomatic",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 970,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "type": "tool"
        },
        "12": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "tool_version": "0.72+galaxy1",
            "outputs": [
                {
                    "type": "html",
                    "name": "html_file"
                },
                {
                    "type": "txt",
                    "name": "text_file"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input_file": {
                    "output_name": "output",
                    "id": 1
                }
            },
            "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
            "id": 12,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "e7b2202befea",
                "name": "fastqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "8cd22a4f-c141-49b3-aa21-4acca1eeac00",
            "errors": null,
            "name": "FastQC",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 130,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "type": "tool"
        },
        "13": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "tool_version": "0.38.0",
            "outputs": [
                {
                    "type": "input",
                    "name": "fastq_out"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "readtype|fastq_in": {
                    "output_name": "output",
                    "id": 1
                }
            },
            "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 13,
            "tool_shed_repository": {
                "owner": "pjbriggs",
                "changeset_revision": "898b67846b47",
                "name": "trimmomatic",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "278c8167-d56f-4a0b-ba0d-e4d4532f8e88",
            "errors": null,
            "name": "Trimmomatic",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1090,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "type": "tool"
        },
        "14": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "tool_version": "0.72+galaxy1",
            "outputs": [
                {
                    "type": "html",
                    "name": "html_file"
                },
                {
                    "type": "txt",
                    "name": "text_file"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input_file": {
                    "output_name": "output",
                    "id": 2
                }
            },
            "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
            "id": 14,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "e7b2202befea",
                "name": "fastqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "09b42f87-f86c-48a0-8711-2fcdf85220bf",
            "errors": null,
            "name": "FastQC",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 250,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "type": "tool"
        },
        "15": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "tool_version": "0.38.0",
            "outputs": [
                {
                    "type": "input",
                    "name": "fastq_out"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "readtype|fastq_in": {
                    "output_name": "output",
                    "id": 2
                }
            },
            "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 15,
            "tool_shed_repository": {
                "owner": "pjbriggs",
                "changeset_revision": "898b67846b47",
                "name": "trimmomatic",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "86e2195c-f76f-4ac9-90f8-07632a6b9bfb",
            "errors": null,
            "name": "Trimmomatic",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1210,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "type": "tool"
        },
        "16": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "tool_version": "0.72+galaxy1",
            "outputs": [
                {
                    "type": "html",
                    "name": "html_file"
                },
                {
                    "type": "txt",
                    "name": "text_file"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input_file": {
                    "output_name": "output",
                    "id": 3
                }
            },
            "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
            "id": 16,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "e7b2202befea",
                "name": "fastqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "d12977c1-5bc7-4ed2-98f7-dc63858e1614",
            "errors": null,
            "name": "FastQC",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 370,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "type": "tool"
        },
        "17": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "tool_version": "0.38.0",
            "outputs": [
                {
                    "type": "input",
                    "name": "fastq_out"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "readtype|fastq_in": {
                    "output_name": "output",
                    "id": 3
                }
            },
            "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 17,
            "tool_shed_repository": {
                "owner": "pjbriggs",
                "changeset_revision": "898b67846b47",
                "name": "trimmomatic",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "384bb081-ba09-4525-951f-687d804c2f82",
            "errors": null,
            "name": "Trimmomatic",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1330,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "type": "tool"
        },
        "18": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "tool_version": "0.72+galaxy1",
            "outputs": [
                {
                    "type": "html",
                    "name": "html_file"
                },
                {
                    "type": "txt",
                    "name": "text_file"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input_file": {
                    "output_name": "output",
                    "id": 4
                }
            },
            "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
            "id": 18,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "e7b2202befea",
                "name": "fastqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "806620de-06c0-4232-951e-e463f4b1604f",
            "errors": null,
            "name": "FastQC",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 490,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "type": "tool"
        },
        "19": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "tool_version": "0.38.0",
            "outputs": [
                {
                    "type": "input",
                    "name": "fastq_out"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "readtype|fastq_in": {
                    "output_name": "output",
                    "id": 4
                }
            },
            "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 19,
            "tool_shed_repository": {
                "owner": "pjbriggs",
                "changeset_revision": "898b67846b47",
                "name": "trimmomatic",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "a1f99e7e-a23f-4ee5-b492-953251422795",
            "errors": null,
            "name": "Trimmomatic",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1450,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "type": "tool"
        },
        "20": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "tool_version": "0.72+galaxy1",
            "outputs": [
                {
                    "type": "html",
                    "name": "html_file"
                },
                {
                    "type": "txt",
                    "name": "text_file"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input_file": {
                    "output_name": "output",
                    "id": 5
                }
            },
            "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
            "id": 20,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "e7b2202befea",
                "name": "fastqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "654d553c-be6e-4f00-83d0-7b2b1b898dc2",
            "errors": null,
            "name": "FastQC",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 610,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "type": "tool"
        },
        "21": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "tool_version": "0.38.0",
            "outputs": [
                {
                    "type": "input",
                    "name": "fastq_out"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "readtype|fastq_in": {
                    "output_name": "output",
                    "id": 5
                }
            },
            "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 21,
            "tool_shed_repository": {
                "owner": "pjbriggs",
                "changeset_revision": "898b67846b47",
                "name": "trimmomatic",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "7196f3d6-f028-4da5-b363-0b84f84f3b2a",
            "errors": null,
            "name": "Trimmomatic",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1570,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "type": "tool"
        },
        "22": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "tool_version": "0.72+galaxy1",
            "outputs": [
                {
                    "type": "html",
                    "name": "html_file"
                },
                {
                    "type": "txt",
                    "name": "text_file"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input_file": {
                    "output_name": "output",
                    "id": 6
                }
            },
            "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
            "id": 22,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "e7b2202befea",
                "name": "fastqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "34940598-7361-4a85-83e6-0daac5b7c9d5",
            "errors": null,
            "name": "FastQC",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 730,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "type": "tool"
        },
        "23": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "tool_version": "0.38.0",
            "outputs": [
                {
                    "type": "input",
                    "name": "fastq_out"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "readtype|fastq_in": {
                    "output_name": "output",
                    "id": 6
                }
            },
            "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 23,
            "tool_shed_repository": {
                "owner": "pjbriggs",
                "changeset_revision": "898b67846b47",
                "name": "trimmomatic",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "763c268d-1dcb-40cd-8a15-90ac2444eac2",
            "errors": null,
            "name": "Trimmomatic",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1690,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "type": "tool"
        },
        "24": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "tool_version": "0.72+galaxy1",
            "outputs": [
                {
                    "type": "html",
                    "name": "html_file"
                },
                {
                    "type": "txt",
                    "name": "text_file"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input_file": {
                    "output_name": "output",
                    "id": 7
                }
            },
            "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
            "id": 24,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "e7b2202befea",
                "name": "fastqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "5873a1b0-ac45-4682-bcc7-5ae60bf651a7",
            "errors": null,
            "name": "FastQC",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 850,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
            "type": "tool"
        },
        "25": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "tool_version": "0.38.0",
            "outputs": [
                {
                    "type": "input",
                    "name": "fastq_out"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "readtype|fastq_in": {
                    "output_name": "output",
                    "id": 7
                }
            },
            "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 25,
            "tool_shed_repository": {
                "owner": "pjbriggs",
                "changeset_revision": "898b67846b47",
                "name": "trimmomatic",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "21fd6743-72da-4ad3-be7b-beb768875ee8",
            "errors": null,
            "name": "Trimmomatic",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1810,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
            "type": "tool"
        },
        "26": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1",
            "tool_version": "1.1.1",
            "outputs": [
                {
                    "type": "input",
                    "name": "outfile"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "infile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"code\": \"\\\"!/^#/ && $3==\\\\\\\"exon\\\\\\\"{if($7==\\\\\\\"+\\\\\\\"){ p[px++] = $1\\\\\\\"\\\\\\\\t\\\\\\\"$4\\\\\\\"\\\\\\\\t\\\\\\\"$5\\\\\\\"\\\\\\\\t.\\\\\\\\t.\\\\\\\\t\\\\\\\"$7 }else{ n[nx++] = $1\\\\\\\"\\\\\\\\t\\\\\\\"$4\\\\\\\"\\\\\\\\t\\\\\\\"$5\\\\\\\"\\\\\\\\t.\\\\\\\\t.\\\\\\\\t\\\\\\\"$7 } if(nx>1000 && px>1000){ exit } } END{ for(i in p){ print p[i] } for(i in n){ print n[i] } }\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}",
            "id": 26,
            "tool_shed_repository": {
                "owner": "bgruening",
                "changeset_revision": "0a8c6b61f0f4",
                "name": "text_processing",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "2846bcea-3061-4589-ab67-b730612bb143",
            "errors": null,
            "name": "Text reformatting",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1930,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1",
            "type": "tool"
        },
        "27": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "tool_version": "0.7.17.4",
            "outputs": [
                {
                    "type": "bam",
                    "name": "bam_output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "reference_source|ref_file": {
                    "output_name": "output",
                    "id": 8
                },
                "input_type|fastq_input1": {
                    "output_name": "fastq_out",
                    "id": 11
                }
            },
            "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 27,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "01ac0a5fedc3",
                "name": "bwa",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "234039d1-b35e-49fe-88b3-63f4c0f6188f",
            "errors": null,
            "name": "Map with BWA",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 10,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "type": "tool"
        },
        "28": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "tool_version": "0.7.17.4",
            "outputs": [
                {
                    "type": "bam",
                    "name": "bam_output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "reference_source|ref_file": {
                    "output_name": "output",
                    "id": 8
                },
                "input_type|fastq_input1": {
                    "output_name": "fastq_out",
                    "id": 13
                }
            },
            "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 28,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "01ac0a5fedc3",
                "name": "bwa",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "75376316-fd90-41fa-85fd-20ff56bf4c6a",
            "errors": null,
            "name": "Map with BWA",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 130,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "type": "tool"
        },
        "29": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "tool_version": "0.7.17.4",
            "outputs": [
                {
                    "type": "bam",
                    "name": "bam_output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "reference_source|ref_file": {
                    "output_name": "output",
                    "id": 8
                },
                "input_type|fastq_input1": {
                    "output_name": "fastq_out",
                    "id": 15
                }
            },
            "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 29,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "01ac0a5fedc3",
                "name": "bwa",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "aba4f4d0-2772-441f-b618-2a1156f14e0d",
            "errors": null,
            "name": "Map with BWA",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 250,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "type": "tool"
        },
        "30": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "tool_version": "0.7.17.4",
            "outputs": [
                {
                    "type": "bam",
                    "name": "bam_output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "reference_source|ref_file": {
                    "output_name": "output",
                    "id": 8
                },
                "input_type|fastq_input1": {
                    "output_name": "fastq_out",
                    "id": 17
                }
            },
            "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 30,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "01ac0a5fedc3",
                "name": "bwa",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "4402bafd-24b6-4a8f-ad09-38a7735b2b23",
            "errors": null,
            "name": "Map with BWA",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 370,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "type": "tool"
        },
        "31": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "tool_version": "0.7.17.4",
            "outputs": [
                {
                    "type": "bam",
                    "name": "bam_output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "reference_source|ref_file": {
                    "output_name": "output",
                    "id": 8
                },
                "input_type|fastq_input1": {
                    "output_name": "fastq_out",
                    "id": 19
                }
            },
            "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 31,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "01ac0a5fedc3",
                "name": "bwa",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "d326be0d-41c7-41fb-89f0-c00bdd6685f1",
            "errors": null,
            "name": "Map with BWA",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 490,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "type": "tool"
        },
        "32": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "tool_version": "0.7.17.4",
            "outputs": [
                {
                    "type": "bam",
                    "name": "bam_output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "reference_source|ref_file": {
                    "output_name": "output",
                    "id": 8
                },
                "input_type|fastq_input1": {
                    "output_name": "fastq_out",
                    "id": 21
                }
            },
            "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 32,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "01ac0a5fedc3",
                "name": "bwa",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "5285f6dc-4887-4e50-8662-5a33328304a6",
            "errors": null,
            "name": "Map with BWA",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 610,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "type": "tool"
        },
        "33": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "tool_version": "0.7.17.4",
            "outputs": [
                {
                    "type": "bam",
                    "name": "bam_output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "reference_source|ref_file": {
                    "output_name": "output",
                    "id": 8
                },
                "input_type|fastq_input1": {
                    "output_name": "fastq_out",
                    "id": 23
                }
            },
            "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 33,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "01ac0a5fedc3",
                "name": "bwa",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "4fc24b78-6133-407f-9fb4-0c65a57f1852",
            "errors": null,
            "name": "Map with BWA",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 730,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "type": "tool"
        },
        "34": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "tool_version": "0.7.17.4",
            "outputs": [
                {
                    "type": "bam",
                    "name": "bam_output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "reference_source|ref_file": {
                    "output_name": "output",
                    "id": 8
                },
                "input_type|fastq_input1": {
                    "output_name": "fastq_out",
                    "id": 25
                }
            },
            "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 34,
            "tool_shed_repository": {
                "owner": "devteam",
                "changeset_revision": "01ac0a5fedc3",
                "name": "bwa",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "5d3afe26-e984-4bd8-ab80-3d530974519a",
            "errors": null,
            "name": "Map with BWA",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 850,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
            "type": "tool"
        },
        "35": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "tool_version": "1.6.4",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "output_short"
                },
                {
                    "type": "tabular",
                    "name": "output_summary"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "alignment": {
                    "output_name": "bam_output",
                    "id": 27
                },
                "anno|reference_gene_sets": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": null}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"extended_parameters\": \"{\\\"R\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"10\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"null\"}",
            "id": 35,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "9301937c9037",
                "name": "featurecounts",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "7593c2b9-d0a2-4bb4-a68d-165a6a4727c7",
            "errors": null,
            "name": "featureCounts",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 130,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "type": "tool"
        },
        "36": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "tool_version": "1.6.4",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "output_short"
                },
                {
                    "type": "tabular",
                    "name": "output_summary"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "alignment": {
                    "output_name": "bam_output",
                    "id": 28
                },
                "anno|reference_gene_sets": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": null}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"extended_parameters\": \"{\\\"R\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"10\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"null\"}",
            "id": 36,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "9301937c9037",
                "name": "featurecounts",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "0e2910ae-d40c-46da-b509-00cf1fbc6cf4",
            "errors": null,
            "name": "featureCounts",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 250,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "type": "tool"
        },
        "37": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "tool_version": "1.6.4",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "output_short"
                },
                {
                    "type": "tabular",
                    "name": "output_summary"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "alignment": {
                    "output_name": "bam_output",
                    "id": 29
                },
                "anno|reference_gene_sets": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": null}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"extended_parameters\": \"{\\\"R\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"10\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"null\"}",
            "id": 37,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "9301937c9037",
                "name": "featurecounts",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "5490529d-909f-464c-8efc-a4fbcaa78c77",
            "errors": null,
            "name": "featureCounts",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 370,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "type": "tool"
        },
        "38": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "tool_version": "1.6.4",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "output_short"
                },
                {
                    "type": "tabular",
                    "name": "output_summary"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "alignment": {
                    "output_name": "bam_output",
                    "id": 30
                },
                "anno|reference_gene_sets": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": null}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"extended_parameters\": \"{\\\"R\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"10\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"null\"}",
            "id": 38,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "9301937c9037",
                "name": "featurecounts",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "16801d1d-e007-411d-8967-48a117d921f8",
            "errors": null,
            "name": "featureCounts",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 490,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "type": "tool"
        },
        "39": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "tool_version": "1.6.4",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "output_short"
                },
                {
                    "type": "tabular",
                    "name": "output_summary"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "alignment": {
                    "output_name": "bam_output",
                    "id": 31
                },
                "anno|reference_gene_sets": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": null}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"extended_parameters\": \"{\\\"R\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"10\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"null\"}",
            "id": 39,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "9301937c9037",
                "name": "featurecounts",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "7be519ce-0687-4ad4-a815-f87635d6084a",
            "errors": null,
            "name": "featureCounts",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 610,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "type": "tool"
        },
        "40": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "tool_version": "1.6.4",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "output_short"
                },
                {
                    "type": "tabular",
                    "name": "output_summary"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "alignment": {
                    "output_name": "bam_output",
                    "id": 32
                },
                "anno|reference_gene_sets": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": null}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"extended_parameters\": \"{\\\"R\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"10\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"null\"}",
            "id": 40,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "9301937c9037",
                "name": "featurecounts",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "ad211493-f39e-497e-a7bb-0939561df2fb",
            "errors": null,
            "name": "featureCounts",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 730,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "type": "tool"
        },
        "41": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "tool_version": "1.6.4",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "output_short"
                },
                {
                    "type": "tabular",
                    "name": "output_summary"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "alignment": {
                    "output_name": "bam_output",
                    "id": 33
                },
                "anno|reference_gene_sets": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": null}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"extended_parameters\": \"{\\\"R\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"10\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"null\"}",
            "id": 41,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "9301937c9037",
                "name": "featurecounts",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "1bcb8de2-a6f2-4f7a-b27c-1d3e87a2f225",
            "errors": null,
            "name": "featureCounts",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 850,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "type": "tool"
        },
        "42": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1",
            "tool_version": "2.6.4.1",
            "outputs": [
                {
                    "type": "txt",
                    "name": "output"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "input": {
                    "output_name": "bam_output",
                    "id": 34
                },
                "refgene": {
                    "output_name": "outfile",
                    "id": 26
                }
            },
            "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"refgene\": \"null\", \"sample_size\": \"\\\"200000\\\"\", \"mapq\": \"\\\"0\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 42,
            "tool_shed_repository": {
                "owner": "nilesh",
                "changeset_revision": "1a052c827e88",
                "name": "rseqc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "189c66da-c8c3-4924-943a-6902d806d16d",
            "errors": null,
            "name": "Infer Experiment",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 10,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1",
            "type": "tool"
        },
        "43": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "tool_version": "1.6.4",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "output_short"
                },
                {
                    "type": "tabular",
                    "name": "output_summary"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "alignment": {
                    "output_name": "bam_output",
                    "id": 34
                },
                "anno|reference_gene_sets": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": null}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"extended_parameters\": \"{\\\"R\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"10\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"null\"}",
            "id": 43,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "9301937c9037",
                "name": "featurecounts",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "9a338f54-ae9c-49c1-b8d8-5ca54b5e1776",
            "errors": null,
            "name": "featureCounts",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 970,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4",
            "type": "tool"
        },
        "44": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6",
            "tool_version": "2.11.40.6",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "deseq_out"
                },
                {
                    "type": "pdf",
                    "name": "plots"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": [
                    {
                        "output_name": "output_short",
                        "id": 43
                    },
                    {
                        "output_name": "output_short",
                        "id": 41
                    },
                    {
                        "output_name": "output_short",
                        "id": 40
                    },
                    {
                        "output_name": "output_short",
                        "id": 39
                    }
                ],
                "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": [
                    {
                        "output_name": "output_short",
                        "id": 38
                    },
                    {
                        "output_name": "output_short",
                        "id": 37
                    },
                    {
                        "output_name": "output_short",
                        "id": 36
                    },
                    {
                        "output_name": "output_short",
                        "id": 35
                    }
                ]
            },
            "tool_state": "{\"fit_type\": \"\\\"1\\\"\", \"__page__\": null, \"normVST\": \"\\\"false\\\"\", \"tximport\": \"{\\\"__current_case__\\\": 1, \\\"tximport_selector\\\": \\\"count\\\"}\", \"esf\": \"\\\"\\\"\", \"outlier_replace_off\": \"\\\"false\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"auto_mean_filter_off\": \"\\\"false\\\"\", \"header\": \"\\\"true\\\"\", \"normCounts\": \"\\\"false\\\"\", \"outlier_filter_off\": \"\\\"false\\\"\", \"many_contrasts\": \"\\\"false\\\"\", \"batch_factors\": \"null\", \"pdf\": \"\\\"true\\\"\", \"normRLog\": \"\\\"false\\\"\", \"select_data\": \"{\\\"__current_case__\\\": 1, \\\"how\\\": \\\"datasets_per_level\\\", \\\"rep_factorName\\\": [{\\\"__index__\\\": 0, \\\"factorName\\\": \\\"treatment\\\", \\\"rep_factorLevel\\\": [{\\\"__index__\\\": 0, \\\"countsFile\\\": null, \\\"factorLevel\\\": \\\"control\\\"}, {\\\"__index__\\\": 1, \\\"countsFile\\\": null, \\\"factorLevel\\\": \\\"treated\\\"}]}]}\"}",
            "id": 44,
            "tool_shed_repository": {
                "owner": "iuc",
                "changeset_revision": "0696db066a5b",
                "name": "deseq2",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "63cfdbda-ef39-48b5-85ef-4629c4b571f4",
            "errors": null,
            "name": "DESeq2",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 10,
                "left": 890
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6",
            "type": "tool"
        }
    },
    "annotation": "",
    "a_galaxy_workflow": "true"
}