{
    "uuid": "6d2b5012-3ac3-4e21-827a-fdbb7ccafd69",
    "tags": [],
    "format-version": "0.1",
    "name": "Differential gene expression analysis of single-end NGS data using FastQC, Cutadapt, 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": "7bb90140-3a8e-4020-b5ec-4a4134bab9f9",
            "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": "d26e68fb-29e4-44e3-9eb3-7336871c0b0d",
            "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": "b757c6e9-ee58-4b44-a959-757e463dc293",
            "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": "fcf73f91-4c3b-4243-8c28-30a90ab3d5ab",
            "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": "77c0d752-10ea-422f-a68c-ecd2d249ee6d",
            "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": "0f9a3a8b-1426-452b-949a-b6e420cea7d1",
            "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": "6b31c004-1b89-43ec-a89f-e5e250c8fc9f",
            "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": "7e616498-b725-409a-adcd-2ac072c8718a",
            "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": "b903b37f-0ebd-4d9f-82a4-07bc9b123e99",
            "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": "53479132-958b-4b15-8ac7-536e46a5acc8",
            "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": "eec1dc64-88c9-4455-8200-510a7dfc0c86",
            "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/lparsons/cutadapt/cutadapt/1.16.6",
            "tool_version": "1.16.6",
            "outputs": [
                {
                    "type": "fastqsanger",
                    "name": "out1"
                },
                {
                    "type": "txt",
                    "name": "report"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_1": {
                    "output_name": "output",
                    "id": 0
                }
            },
            "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
            "id": 11,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "e4691e1589d3",
                "name": "cutadapt",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "50afa583-ceb6-447f-9207-6eb2c0c8bfb0",
            "errors": null,
            "name": "Cutadapt",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 970,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6",
            "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": "47977771-f031-4b66-b4dc-801a0caaa781",
            "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/lparsons/cutadapt/cutadapt/1.16.6",
            "tool_version": "1.16.6",
            "outputs": [
                {
                    "type": "fastqsanger",
                    "name": "out1"
                },
                {
                    "type": "txt",
                    "name": "report"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_1": {
                    "output_name": "output",
                    "id": 1
                }
            },
            "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
            "id": 13,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "e4691e1589d3",
                "name": "cutadapt",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "d07e9c19-76bf-4244-a864-03573d4cb95f",
            "errors": null,
            "name": "Cutadapt",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1090,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6",
            "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": "9379d8f5-9962-4fa2-9c7e-773bce4a1639",
            "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/lparsons/cutadapt/cutadapt/1.16.6",
            "tool_version": "1.16.6",
            "outputs": [
                {
                    "type": "fastqsanger",
                    "name": "out1"
                },
                {
                    "type": "txt",
                    "name": "report"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_1": {
                    "output_name": "output",
                    "id": 2
                }
            },
            "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
            "id": 15,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "e4691e1589d3",
                "name": "cutadapt",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "ed874fff-c053-41d7-bcc5-e1c94bd6e070",
            "errors": null,
            "name": "Cutadapt",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1210,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6",
            "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": "ba3f4c29-e066-47c8-857e-0f46a3a4fc3c",
            "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/lparsons/cutadapt/cutadapt/1.16.6",
            "tool_version": "1.16.6",
            "outputs": [
                {
                    "type": "fastqsanger",
                    "name": "out1"
                },
                {
                    "type": "txt",
                    "name": "report"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_1": {
                    "output_name": "output",
                    "id": 3
                }
            },
            "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
            "id": 17,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "e4691e1589d3",
                "name": "cutadapt",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "f563370a-a2f3-4818-9ff6-f71004bdff6e",
            "errors": null,
            "name": "Cutadapt",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1330,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6",
            "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": "e4e8884b-7cc0-47cb-a644-2016c77314a6",
            "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/lparsons/cutadapt/cutadapt/1.16.6",
            "tool_version": "1.16.6",
            "outputs": [
                {
                    "type": "fastqsanger",
                    "name": "out1"
                },
                {
                    "type": "txt",
                    "name": "report"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_1": {
                    "output_name": "output",
                    "id": 4
                }
            },
            "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
            "id": 19,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "e4691e1589d3",
                "name": "cutadapt",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "0d7338b2-c1e6-4f29-aee7-396fec27e59f",
            "errors": null,
            "name": "Cutadapt",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1450,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6",
            "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": "96fbc428-8c4f-4999-849b-e59a1c5206f5",
            "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/lparsons/cutadapt/cutadapt/1.16.6",
            "tool_version": "1.16.6",
            "outputs": [
                {
                    "type": "fastqsanger",
                    "name": "out1"
                },
                {
                    "type": "txt",
                    "name": "report"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_1": {
                    "output_name": "output",
                    "id": 5
                }
            },
            "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
            "id": 21,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "e4691e1589d3",
                "name": "cutadapt",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "2aee7b91-352f-4c24-91a7-3da65d031019",
            "errors": null,
            "name": "Cutadapt",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1570,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6",
            "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": "cb305329-be17-4c6c-836c-8086374ca16f",
            "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/lparsons/cutadapt/cutadapt/1.16.6",
            "tool_version": "1.16.6",
            "outputs": [
                {
                    "type": "fastqsanger",
                    "name": "out1"
                },
                {
                    "type": "txt",
                    "name": "report"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_1": {
                    "output_name": "output",
                    "id": 6
                }
            },
            "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
            "id": 23,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "e4691e1589d3",
                "name": "cutadapt",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "e9ff4297-d59e-4534-a954-84ba82593ac2",
            "errors": null,
            "name": "Cutadapt",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1690,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6",
            "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": "21c8942b-7259-4af5-888f-6daa4b2c6326",
            "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/lparsons/cutadapt/cutadapt/1.16.6",
            "tool_version": "1.16.6",
            "outputs": [
                {
                    "type": "fastqsanger",
                    "name": "out1"
                },
                {
                    "type": "txt",
                    "name": "report"
                }
            ],
            "workflow_outputs": [],
            "input_connections": {
                "library|input_1": {
                    "output_name": "output",
                    "id": 7
                }
            },
            "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
            "id": 25,
            "tool_shed_repository": {
                "owner": "lparsons",
                "changeset_revision": "e4691e1589d3",
                "name": "cutadapt",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "uuid": "611d0216-88fd-4ecb-b19d-81d6d8ee27a5",
            "errors": null,
            "name": "Cutadapt",
            "post_job_actions": {},
            "label": null,
            "inputs": [],
            "position": {
                "top": 1810,
                "left": 230
            },
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6",
            "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": "0ecfd347-f734-41b4-8b05-db1d70ce00c7",
            "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": "out1",
                    "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": "5359c86f-03db-4a56-9deb-ec4d8d747b34",
            "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": "out1",
                    "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": "cc6c4ef5-78af-4620-8d3f-185ea367eb66",
            "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": "out1",
                    "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": "a0c0a568-4529-4b06-865a-499a4b31ddd5",
            "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": "out1",
                    "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": "f8e23e20-91a5-4b11-83fc-57b9fbe5d571",
            "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": "out1",
                    "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": "ef8c0423-f05f-4a61-8887-c1d12009ba0d",
            "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": "out1",
                    "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": "c7118966-2592-491b-8098-c8e24927d4c6",
            "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": "out1",
                    "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": "8bd361fc-3a97-4e73-ba24-1da200b49fed",
            "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": "out1",
                    "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": "7ba774e2-bc2a-4709-8086-034fa2652da9",
            "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": "2c8e02e2-9071-407f-9f5e-e2f08ae52c73",
            "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": "a60786fd-64c6-4fe4-879a-533a4a064b8f",
            "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": "6dfacf50-b569-4ef7-b29f-9474ff6daa69",
            "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": "7409eabc-bee0-407b-a396-1d3c20eb7e8e",
            "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": "8ae4007c-8277-4895-96d7-cdff9053a6e7",
            "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": "75cc41c6-caad-476b-a70e-ca4e34ab13d6",
            "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": "01a8f77d-89bc-414a-a6b2-869f3469395c",
            "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": "6004a91a-7480-4367-b710-494b8d487c85",
            "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": "582568b7-7e81-473f-9e6d-bd51c1158119",
            "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": "63f1c357-bc10-4b00-933c-ec90aa00c620",
            "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"
}