{
    "uuid": "fc89e580-48de-44ae-8f27-9acb6b3616fc",
    "tags": [],
    "format-version": "0.1",
    "name": "Differential gene expression analysis of single-end NGS data using FastQC, Trimmomatic, BWA, AWK, Infer Experiment, HTSeq-count, 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": "2eeaef8d-472d-43f7-90de-a6fd8cd78fa0",
            "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": "d1c89652-12eb-42ee-86c1-ec0359224875",
            "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": "1c0a968c-e9c4-448f-b362-f7af95fbd086",
            "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": "1f2386b8-1b34-4cc4-bcba-1f773fb316b6",
            "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": "e3d6046d-08ca-4537-af1d-ecb75421af55",
            "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": "99f9cf42-9591-4c63-ab9c-b30c68d96c15",
            "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": "e1fd8299-0c75-4b15-88da-924c913fbe01",
            "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": "7d72ee12-d7c3-4093-9f9f-b0726ae3ddf6",
            "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": "dcd5457e-05c6-4e10-9171-a7fdc063e443",
            "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": "37e0ef6c-ad2a-4545-9a93-4039adb00202",
            "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": "d38b8358-896f-4be6-900c-92213051974a",
            "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": "24158fa7-2cdc-4d8e-8320-2b58ab60aa04",
            "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": "22c9dbbe-7353-414b-b013-5bed55d13bea",
            "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": "50f4a4e9-d227-43fe-93ee-1c0650b8f6b7",
            "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": "a8cd8b78-df82-436e-8ea9-1c18c5776c95",
            "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": "f3e1287b-eea3-467b-8244-3a454b834220",
            "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": "6a672721-2bec-454d-9f97-9e6245a95473",
            "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": "7e4ac6e6-261e-471e-838b-e54d890dafd0",
            "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": "fc9ac76f-6c1d-4733-8b65-be2e7becfe8a",
            "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": "4dac3bec-1be7-4c05-ac92-5ada3da470c1",
            "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": "bc0670a4-14d7-4e80-b7aa-1904ce7fcc3f",
            "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": "e12f25bd-398a-433e-aa0d-8b7321d19f32",
            "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": "0bb9ddb3-30fd-4533-8351-1e37b77b1a7c",
            "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": "217b9f38-7b01-40f0-a922-2d4c82f12238",
            "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": "86f46f16-9472-4d52-ad62-d247ee8b70e7",
            "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": "5f6daa10-3299-4dfd-8dfd-e25aa7b4124a",
            "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": "54ed67ee-acd6-4210-accd-fe698fd0658d",
            "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": "adc0e376-9c19-4dc2-9ce8-98df8b2b853a",
            "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": "14e93643-6f25-433c-8fc6-79e6b151bf8b",
            "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": "12297375-9733-4c84-8c82-261722ac44ae",
            "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": "49f78d23-c8aa-4e32-9fb9-f67ec489a2cd",
            "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": "39d3128f-bde1-44a7-8801-f5ca3d582a4d",
            "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": "234d8046-b0f1-4b8f-861d-fcb032a9b43d",
            "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": "f7ab67fc-c198-4997-abb1-ec62c8de5390",
            "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": "0cd15206-e005-4e53-bdf7-3274af809f2f",
            "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/lparsons/htseq_count/htseq_count/0.9.1",
            "tool_version": "0.9.1",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "counts"
                },
                {
                    "type": "tabular",
                    "name": "othercounts"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "samfile": {
                    "output_name": "bam_output",
                    "id": 27
                },
                "gfffile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 35,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "67b0b160903a",
                "name": "htseq_count",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "12377409-b304-4e15-8cff-3417eff3a0ef",
            "errors": null,
            "name": "htseq-count",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 130,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "type": "tool"
        },
        "36": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "tool_version": "0.9.1",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "counts"
                },
                {
                    "type": "tabular",
                    "name": "othercounts"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "samfile": {
                    "output_name": "bam_output",
                    "id": 28
                },
                "gfffile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 36,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "67b0b160903a",
                "name": "htseq_count",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "5db2f504-41af-4070-9396-9b8711fac273",
            "errors": null,
            "name": "htseq-count",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 250,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "type": "tool"
        },
        "37": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "tool_version": "0.9.1",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "counts"
                },
                {
                    "type": "tabular",
                    "name": "othercounts"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "samfile": {
                    "output_name": "bam_output",
                    "id": 29
                },
                "gfffile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 37,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "67b0b160903a",
                "name": "htseq_count",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "43ee15b2-887b-407e-aca4-02bf903fee15",
            "errors": null,
            "name": "htseq-count",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 370,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "type": "tool"
        },
        "38": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "tool_version": "0.9.1",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "counts"
                },
                {
                    "type": "tabular",
                    "name": "othercounts"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "samfile": {
                    "output_name": "bam_output",
                    "id": 30
                },
                "gfffile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 38,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "67b0b160903a",
                "name": "htseq_count",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "f3c13f6d-c7a0-443c-8273-d4a0f096f561",
            "errors": null,
            "name": "htseq-count",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 490,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "type": "tool"
        },
        "39": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "tool_version": "0.9.1",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "counts"
                },
                {
                    "type": "tabular",
                    "name": "othercounts"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "samfile": {
                    "output_name": "bam_output",
                    "id": 31
                },
                "gfffile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 39,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "67b0b160903a",
                "name": "htseq_count",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "ffde0b58-7f66-42b9-a9f1-cd6258e1ff90",
            "errors": null,
            "name": "htseq-count",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 610,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "type": "tool"
        },
        "40": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "tool_version": "0.9.1",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "counts"
                },
                {
                    "type": "tabular",
                    "name": "othercounts"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "samfile": {
                    "output_name": "bam_output",
                    "id": 32
                },
                "gfffile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 40,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "67b0b160903a",
                "name": "htseq_count",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "313caa70-4d72-40af-9ea0-48c8c15b32de",
            "errors": null,
            "name": "htseq-count",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 730,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "type": "tool"
        },
        "41": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "tool_version": "0.9.1",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "counts"
                },
                {
                    "type": "tabular",
                    "name": "othercounts"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "samfile": {
                    "output_name": "bam_output",
                    "id": 33
                },
                "gfffile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 41,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "67b0b160903a",
                "name": "htseq_count",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "1be6c8cc-4a89-48a3-a054-81f9df5664fd",
            "errors": null,
            "name": "htseq-count",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 850,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "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": "b31a6dcc-d1bb-47f0-b471-b907541998d5",
            "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/lparsons/htseq_count/htseq_count/0.9.1",
            "tool_version": "0.9.1",
            "outputs": [
                {
                    "type": "tabular",
                    "name": "counts"
                },
                {
                    "type": "tabular",
                    "name": "othercounts"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "samfile": {
                    "output_name": "bam_output",
                    "id": 34
                },
                "gfffile": {
                    "output_name": "output",
                    "id": 9
                }
            },
            "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
            "id": 43,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "67b0b160903a",
                "name": "htseq_count",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "c0db713b-c89c-45c0-9b5e-7c9772f2a5b1",
            "errors": null,
            "name": "htseq-count",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 970,
                "left": 670
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1",
            "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": "counts",
                        "id": 43
                    },
                    {
                        "output_name": "counts",
                        "id": 41
                    },
                    {
                        "output_name": "counts",
                        "id": 40
                    },
                    {
                        "output_name": "counts",
                        "id": 39
                    }
                ],
                "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": [
                    {
                        "output_name": "counts",
                        "id": 38
                    },
                    {
                        "output_name": "counts",
                        "id": 37
                    },
                    {
                        "output_name": "counts",
                        "id": 36
                    },
                    {
                        "output_name": "counts",
                        "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": "f6089182-9571-44cf-83f1-430bdfeb5f8d",
            "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"
}