{
    "uuid": "02c96bf2-5c89-435b-9166-1f89ad1f202b",
    "tags": [],
    "format-version": "0.1",
    "name": "Differential gene expression analysis of single-end NGS data using FastQC, Trimmomatic, segemehl, 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": "ee45c8ef-8377-42ba-ac22-3191ee850e32",
            "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": "3f17bcee-a39c-419e-a182-e3ae846a08be",
            "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": "0d7fcda8-fa06-4d0b-b542-6829295f5fb9",
            "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": "8005924b-58c9-457c-80ea-9d7bcb8d4d39",
            "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": "4f25d6b3-ef7f-4088-8097-0fa50ebf70c7",
            "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": "5e879f7e-9d40-407e-8536-0703ccea5d06",
            "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": "bd36cb25-2ecb-4eb4-9b67-775cfc1ac49a",
            "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": "4f0dff42-fb8b-4b66-991d-7a8f810ecef9",
            "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": "1731017c-0a9f-4889-a0bf-67072e8e24ae",
            "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": "c0350187-9c12-4e2d-829d-fb18fb00fa84",
            "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": "991675b8-98cd-47a5-894f-de300bc2e1b3",
            "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": "379d697e-3d23-482c-883f-652182af3da5",
            "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": "efc47be9-d21f-4f3e-ae29-aa3179a66d97",
            "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": "a2885939-27e6-4e59-b1c3-8b35d1be34d9",
            "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": "83c85271-4535-4d60-b796-7277b0d0a269",
            "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": "54b49868-25da-4d79-933b-19ba8148ba13",
            "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": "3041ec7a-fc87-409e-942e-bfaf0803a495",
            "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": "0d6926b9-2ff0-46fd-bb15-c2d72dfea443",
            "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": "0f3b561d-88b3-4183-beaf-b984bfffeb83",
            "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": "999d63ca-4218-48e4-8af5-19f882225a07",
            "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": "6a1f7e00-6b84-4606-a196-c545130bd0e0",
            "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": "895a2a0c-8d31-4e82-b13c-74d19bdac115",
            "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": "9bd55afe-512b-4d23-9f56-161e42ffc55f",
            "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": "06f50a45-fa9c-40f8-ba42-3689b911d98c",
            "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": "39c37e31-5cd1-4325-8b67-bf9668b0896f",
            "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": "8a3d97c8-eaf4-4b2d-8c6e-8e855223f00a",
            "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": "a13844be-eb47-4b4d-b048-d630badf0357",
            "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/rnateam/segemehl/segemehl/0.2.0.4",
            "tool_version": "0.2.0.4",
            "outputs": [
                {
                    "type": "sam",
                    "name": "segemehl_out"
                },
                {
                    "type": "fastq",
                    "name": "segemehl_outunmatched"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_query": {
                    "output_name": "fastq_out",
                    "id": 11
                },
                "refGenomeSource|own_reference_genome": {
                    "output_name": "output",
                    "id": 8
                }
            },
            "tool_state": "{\"maxout\": \"\\\"0\\\"\", \"hitstrategy\": \"\\\"1\\\"\", \"hardclip\": \"\\\"false\\\"\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_query\\\": null, \\\"type\\\": \\\"single\\\"}\", \"jump\": \"\\\"0\\\"\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"own_reference_genome\\\": null}\", \"prime3\": \"\\\"\\\"\", \"nomatchfilename\": \"\\\"false\\\"\", \"__page__\": null, \"autoclip\": \"\\\"false\\\"\", \"clipacc\": \"\\\"70\\\"\", \"evalue\": \"\\\"5.0\\\"\", \"__rerun_remap_job_id__\": null, \"accuracy\": \"\\\"90\\\"\", \"differences\": \"\\\"1\\\"\", \"maxinterval\": \"\\\"100\\\"\", \"polyA\": \"\\\"false\\\"\", \"prime5\": \"\\\"\\\"\", \"minsize\": \"\\\"12\\\"\", \"splitreads\": \"{\\\"__current_case__\\\": 0, \\\"maxsplitevalue\\\": \\\"50.0\\\", \\\"minfraglen\\\": \\\"20\\\", \\\"minfragscore\\\": \\\"18\\\", \\\"minsplicecover\\\": \\\"80\\\", \\\"splicescorescale\\\": \\\"1.0\\\", \\\"splits\\\": \\\"splits\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"false\\\"\", \"bisulfite\": \"\\\"0\\\"\"}",
            "id": 27,
            "tool_shed_repository": {
                "owner": "rnateam",
                "changeset_revision": "9c0d4ec99ba9",
                "name": "segemehl",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "6a52b917-44d2-445f-8fb9-9be2873cd9e8",
            "errors": null,
            "name": "segemehl",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 10,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "type": "tool"
        },
        "28": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "tool_version": "0.2.0.4",
            "outputs": [
                {
                    "type": "sam",
                    "name": "segemehl_out"
                },
                {
                    "type": "fastq",
                    "name": "segemehl_outunmatched"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_query": {
                    "output_name": "fastq_out",
                    "id": 13
                },
                "refGenomeSource|own_reference_genome": {
                    "output_name": "output",
                    "id": 8
                }
            },
            "tool_state": "{\"maxout\": \"\\\"0\\\"\", \"hitstrategy\": \"\\\"1\\\"\", \"hardclip\": \"\\\"false\\\"\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_query\\\": null, \\\"type\\\": \\\"single\\\"}\", \"jump\": \"\\\"0\\\"\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"own_reference_genome\\\": null}\", \"prime3\": \"\\\"\\\"\", \"nomatchfilename\": \"\\\"false\\\"\", \"__page__\": null, \"autoclip\": \"\\\"false\\\"\", \"clipacc\": \"\\\"70\\\"\", \"evalue\": \"\\\"5.0\\\"\", \"__rerun_remap_job_id__\": null, \"accuracy\": \"\\\"90\\\"\", \"differences\": \"\\\"1\\\"\", \"maxinterval\": \"\\\"100\\\"\", \"polyA\": \"\\\"false\\\"\", \"prime5\": \"\\\"\\\"\", \"minsize\": \"\\\"12\\\"\", \"splitreads\": \"{\\\"__current_case__\\\": 0, \\\"maxsplitevalue\\\": \\\"50.0\\\", \\\"minfraglen\\\": \\\"20\\\", \\\"minfragscore\\\": \\\"18\\\", \\\"minsplicecover\\\": \\\"80\\\", \\\"splicescorescale\\\": \\\"1.0\\\", \\\"splits\\\": \\\"splits\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"false\\\"\", \"bisulfite\": \"\\\"0\\\"\"}",
            "id": 28,
            "tool_shed_repository": {
                "owner": "rnateam",
                "changeset_revision": "9c0d4ec99ba9",
                "name": "segemehl",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "8fd1a547-a634-4a33-b08d-3242d093abcd",
            "errors": null,
            "name": "segemehl",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 130,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "type": "tool"
        },
        "29": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "tool_version": "0.2.0.4",
            "outputs": [
                {
                    "type": "sam",
                    "name": "segemehl_out"
                },
                {
                    "type": "fastq",
                    "name": "segemehl_outunmatched"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_query": {
                    "output_name": "fastq_out",
                    "id": 15
                },
                "refGenomeSource|own_reference_genome": {
                    "output_name": "output",
                    "id": 8
                }
            },
            "tool_state": "{\"maxout\": \"\\\"0\\\"\", \"hitstrategy\": \"\\\"1\\\"\", \"hardclip\": \"\\\"false\\\"\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_query\\\": null, \\\"type\\\": \\\"single\\\"}\", \"jump\": \"\\\"0\\\"\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"own_reference_genome\\\": null}\", \"prime3\": \"\\\"\\\"\", \"nomatchfilename\": \"\\\"false\\\"\", \"__page__\": null, \"autoclip\": \"\\\"false\\\"\", \"clipacc\": \"\\\"70\\\"\", \"evalue\": \"\\\"5.0\\\"\", \"__rerun_remap_job_id__\": null, \"accuracy\": \"\\\"90\\\"\", \"differences\": \"\\\"1\\\"\", \"maxinterval\": \"\\\"100\\\"\", \"polyA\": \"\\\"false\\\"\", \"prime5\": \"\\\"\\\"\", \"minsize\": \"\\\"12\\\"\", \"splitreads\": \"{\\\"__current_case__\\\": 0, \\\"maxsplitevalue\\\": \\\"50.0\\\", \\\"minfraglen\\\": \\\"20\\\", \\\"minfragscore\\\": \\\"18\\\", \\\"minsplicecover\\\": \\\"80\\\", \\\"splicescorescale\\\": \\\"1.0\\\", \\\"splits\\\": \\\"splits\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"false\\\"\", \"bisulfite\": \"\\\"0\\\"\"}",
            "id": 29,
            "tool_shed_repository": {
                "owner": "rnateam",
                "changeset_revision": "9c0d4ec99ba9",
                "name": "segemehl",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "bac35896-5c9e-401f-9125-a92ec2de135b",
            "errors": null,
            "name": "segemehl",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 250,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "type": "tool"
        },
        "30": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "tool_version": "0.2.0.4",
            "outputs": [
                {
                    "type": "sam",
                    "name": "segemehl_out"
                },
                {
                    "type": "fastq",
                    "name": "segemehl_outunmatched"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_query": {
                    "output_name": "fastq_out",
                    "id": 17
                },
                "refGenomeSource|own_reference_genome": {
                    "output_name": "output",
                    "id": 8
                }
            },
            "tool_state": "{\"maxout\": \"\\\"0\\\"\", \"hitstrategy\": \"\\\"1\\\"\", \"hardclip\": \"\\\"false\\\"\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_query\\\": null, \\\"type\\\": \\\"single\\\"}\", \"jump\": \"\\\"0\\\"\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"own_reference_genome\\\": null}\", \"prime3\": \"\\\"\\\"\", \"nomatchfilename\": \"\\\"false\\\"\", \"__page__\": null, \"autoclip\": \"\\\"false\\\"\", \"clipacc\": \"\\\"70\\\"\", \"evalue\": \"\\\"5.0\\\"\", \"__rerun_remap_job_id__\": null, \"accuracy\": \"\\\"90\\\"\", \"differences\": \"\\\"1\\\"\", \"maxinterval\": \"\\\"100\\\"\", \"polyA\": \"\\\"false\\\"\", \"prime5\": \"\\\"\\\"\", \"minsize\": \"\\\"12\\\"\", \"splitreads\": \"{\\\"__current_case__\\\": 0, \\\"maxsplitevalue\\\": \\\"50.0\\\", \\\"minfraglen\\\": \\\"20\\\", \\\"minfragscore\\\": \\\"18\\\", \\\"minsplicecover\\\": \\\"80\\\", \\\"splicescorescale\\\": \\\"1.0\\\", \\\"splits\\\": \\\"splits\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"false\\\"\", \"bisulfite\": \"\\\"0\\\"\"}",
            "id": 30,
            "tool_shed_repository": {
                "owner": "rnateam",
                "changeset_revision": "9c0d4ec99ba9",
                "name": "segemehl",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "e925c8a4-547a-446c-a5d1-1e534897c70e",
            "errors": null,
            "name": "segemehl",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 370,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "type": "tool"
        },
        "31": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "tool_version": "0.2.0.4",
            "outputs": [
                {
                    "type": "sam",
                    "name": "segemehl_out"
                },
                {
                    "type": "fastq",
                    "name": "segemehl_outunmatched"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_query": {
                    "output_name": "fastq_out",
                    "id": 19
                },
                "refGenomeSource|own_reference_genome": {
                    "output_name": "output",
                    "id": 8
                }
            },
            "tool_state": "{\"maxout\": \"\\\"0\\\"\", \"hitstrategy\": \"\\\"1\\\"\", \"hardclip\": \"\\\"false\\\"\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_query\\\": null, \\\"type\\\": \\\"single\\\"}\", \"jump\": \"\\\"0\\\"\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"own_reference_genome\\\": null}\", \"prime3\": \"\\\"\\\"\", \"nomatchfilename\": \"\\\"false\\\"\", \"__page__\": null, \"autoclip\": \"\\\"false\\\"\", \"clipacc\": \"\\\"70\\\"\", \"evalue\": \"\\\"5.0\\\"\", \"__rerun_remap_job_id__\": null, \"accuracy\": \"\\\"90\\\"\", \"differences\": \"\\\"1\\\"\", \"maxinterval\": \"\\\"100\\\"\", \"polyA\": \"\\\"false\\\"\", \"prime5\": \"\\\"\\\"\", \"minsize\": \"\\\"12\\\"\", \"splitreads\": \"{\\\"__current_case__\\\": 0, \\\"maxsplitevalue\\\": \\\"50.0\\\", \\\"minfraglen\\\": \\\"20\\\", \\\"minfragscore\\\": \\\"18\\\", \\\"minsplicecover\\\": \\\"80\\\", \\\"splicescorescale\\\": \\\"1.0\\\", \\\"splits\\\": \\\"splits\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"false\\\"\", \"bisulfite\": \"\\\"0\\\"\"}",
            "id": 31,
            "tool_shed_repository": {
                "owner": "rnateam",
                "changeset_revision": "9c0d4ec99ba9",
                "name": "segemehl",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "3f441e49-3194-4502-93de-39ee4e53d090",
            "errors": null,
            "name": "segemehl",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 490,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "type": "tool"
        },
        "32": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "tool_version": "0.2.0.4",
            "outputs": [
                {
                    "type": "sam",
                    "name": "segemehl_out"
                },
                {
                    "type": "fastq",
                    "name": "segemehl_outunmatched"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_query": {
                    "output_name": "fastq_out",
                    "id": 21
                },
                "refGenomeSource|own_reference_genome": {
                    "output_name": "output",
                    "id": 8
                }
            },
            "tool_state": "{\"maxout\": \"\\\"0\\\"\", \"hitstrategy\": \"\\\"1\\\"\", \"hardclip\": \"\\\"false\\\"\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_query\\\": null, \\\"type\\\": \\\"single\\\"}\", \"jump\": \"\\\"0\\\"\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"own_reference_genome\\\": null}\", \"prime3\": \"\\\"\\\"\", \"nomatchfilename\": \"\\\"false\\\"\", \"__page__\": null, \"autoclip\": \"\\\"false\\\"\", \"clipacc\": \"\\\"70\\\"\", \"evalue\": \"\\\"5.0\\\"\", \"__rerun_remap_job_id__\": null, \"accuracy\": \"\\\"90\\\"\", \"differences\": \"\\\"1\\\"\", \"maxinterval\": \"\\\"100\\\"\", \"polyA\": \"\\\"false\\\"\", \"prime5\": \"\\\"\\\"\", \"minsize\": \"\\\"12\\\"\", \"splitreads\": \"{\\\"__current_case__\\\": 0, \\\"maxsplitevalue\\\": \\\"50.0\\\", \\\"minfraglen\\\": \\\"20\\\", \\\"minfragscore\\\": \\\"18\\\", \\\"minsplicecover\\\": \\\"80\\\", \\\"splicescorescale\\\": \\\"1.0\\\", \\\"splits\\\": \\\"splits\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"false\\\"\", \"bisulfite\": \"\\\"0\\\"\"}",
            "id": 32,
            "tool_shed_repository": {
                "owner": "rnateam",
                "changeset_revision": "9c0d4ec99ba9",
                "name": "segemehl",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "ad85061f-b1f4-4f92-b681-324abcf132a6",
            "errors": null,
            "name": "segemehl",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 610,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "type": "tool"
        },
        "33": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "tool_version": "0.2.0.4",
            "outputs": [
                {
                    "type": "sam",
                    "name": "segemehl_out"
                },
                {
                    "type": "fastq",
                    "name": "segemehl_outunmatched"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_query": {
                    "output_name": "fastq_out",
                    "id": 23
                },
                "refGenomeSource|own_reference_genome": {
                    "output_name": "output",
                    "id": 8
                }
            },
            "tool_state": "{\"maxout\": \"\\\"0\\\"\", \"hitstrategy\": \"\\\"1\\\"\", \"hardclip\": \"\\\"false\\\"\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_query\\\": null, \\\"type\\\": \\\"single\\\"}\", \"jump\": \"\\\"0\\\"\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"own_reference_genome\\\": null}\", \"prime3\": \"\\\"\\\"\", \"nomatchfilename\": \"\\\"false\\\"\", \"__page__\": null, \"autoclip\": \"\\\"false\\\"\", \"clipacc\": \"\\\"70\\\"\", \"evalue\": \"\\\"5.0\\\"\", \"__rerun_remap_job_id__\": null, \"accuracy\": \"\\\"90\\\"\", \"differences\": \"\\\"1\\\"\", \"maxinterval\": \"\\\"100\\\"\", \"polyA\": \"\\\"false\\\"\", \"prime5\": \"\\\"\\\"\", \"minsize\": \"\\\"12\\\"\", \"splitreads\": \"{\\\"__current_case__\\\": 0, \\\"maxsplitevalue\\\": \\\"50.0\\\", \\\"minfraglen\\\": \\\"20\\\", \\\"minfragscore\\\": \\\"18\\\", \\\"minsplicecover\\\": \\\"80\\\", \\\"splicescorescale\\\": \\\"1.0\\\", \\\"splits\\\": \\\"splits\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"false\\\"\", \"bisulfite\": \"\\\"0\\\"\"}",
            "id": 33,
            "tool_shed_repository": {
                "owner": "rnateam",
                "changeset_revision": "9c0d4ec99ba9",
                "name": "segemehl",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "9b7333a4-e014-4e6f-a3e5-49d67333d5bc",
            "errors": null,
            "name": "segemehl",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 730,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "type": "tool"
        },
        "34": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "tool_version": "0.2.0.4",
            "outputs": [
                {
                    "type": "sam",
                    "name": "segemehl_out"
                },
                {
                    "type": "fastq",
                    "name": "segemehl_outunmatched"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_query": {
                    "output_name": "fastq_out",
                    "id": 25
                },
                "refGenomeSource|own_reference_genome": {
                    "output_name": "output",
                    "id": 8
                }
            },
            "tool_state": "{\"maxout\": \"\\\"0\\\"\", \"hitstrategy\": \"\\\"1\\\"\", \"hardclip\": \"\\\"false\\\"\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_query\\\": null, \\\"type\\\": \\\"single\\\"}\", \"jump\": \"\\\"0\\\"\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"own_reference_genome\\\": null}\", \"prime3\": \"\\\"\\\"\", \"nomatchfilename\": \"\\\"false\\\"\", \"__page__\": null, \"autoclip\": \"\\\"false\\\"\", \"clipacc\": \"\\\"70\\\"\", \"evalue\": \"\\\"5.0\\\"\", \"__rerun_remap_job_id__\": null, \"accuracy\": \"\\\"90\\\"\", \"differences\": \"\\\"1\\\"\", \"maxinterval\": \"\\\"100\\\"\", \"polyA\": \"\\\"false\\\"\", \"prime5\": \"\\\"\\\"\", \"minsize\": \"\\\"12\\\"\", \"splitreads\": \"{\\\"__current_case__\\\": 0, \\\"maxsplitevalue\\\": \\\"50.0\\\", \\\"minfraglen\\\": \\\"20\\\", \\\"minfragscore\\\": \\\"18\\\", \\\"minsplicecover\\\": \\\"80\\\", \\\"splicescorescale\\\": \\\"1.0\\\", \\\"splits\\\": \\\"splits\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"false\\\"\", \"bisulfite\": \"\\\"0\\\"\"}",
            "id": 34,
            "tool_shed_repository": {
                "owner": "rnateam",
                "changeset_revision": "9c0d4ec99ba9",
                "name": "segemehl",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "5c2ed4e8-a81f-418f-92f5-4b1abbdea9d1",
            "errors": null,
            "name": "segemehl",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 850,
                "left": 450
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.4",
            "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": "segemehl_out",
                    "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": "3370cc24-8a6a-4604-a54d-a87db3124eab",
            "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": "segemehl_out",
                    "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": "c9262690-42e3-4324-9784-cf6b1abc5482",
            "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": "segemehl_out",
                    "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": "c68f6ba4-994f-4b43-871c-2424beacd4f4",
            "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": "segemehl_out",
                    "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": "85fa3f86-d031-4717-bc8c-fa874a063b09",
            "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": "segemehl_out",
                    "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": "80e0943e-d305-4163-85a5-b49eb087b6e6",
            "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": "segemehl_out",
                    "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": "ae4e2fd8-e33d-4811-b2d9-e16819f2f928",
            "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": "segemehl_out",
                    "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": "e9b1f3f3-53d6-42ab-9cc1-e02bb487dc89",
            "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": "segemehl_out",
                    "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": "b5a9e21a-f66f-426b-ad0c-1f4aeac06712",
            "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": "segemehl_out",
                    "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": "cba0bb82-d499-4570-bf75-3e5e2d42d9f6",
            "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": "4ffce134-8b23-4990-8b80-ac7a164eae16",
            "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"
}