{
"uuid": "c19b38cc-9377-47f6-9680-baa8e736fe26",
"tags": [],
"format-version": "0.1",
"name": "Differential gene expression analysis of single-end NGS data using FastQC, Trimmomatic, STAR, 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": "6c6453d3-5c49-4089-baec-e8e8b075f8fc",
"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": "9d8e24cb-1f3a-455b-ba5c-e3532797dece",
"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": "8a1c665d-194c-4417-994d-ffe6d23fc0e2",
"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": "28831784-d743-419a-8a52-c1d7e3b59672",
"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": "64e6c967-7b5c-45cb-a78b-1978750cfb5b",
"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": "4e770932-18bf-482c-aa03-b6de34f34f1e",
"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": "63cefabe-23f5-41a6-9450-fb808fd6b316",
"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": "95714105-bbe5-43a6-a4c6-5007e6147d0d",
"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": "2d322f49-6f42-45c5-bb37-f8ccb3260cca",
"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": "4b7c592d-0e9c-4a93-99d6-8c46fe97f065",
"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": "c37b8515-4d06-4d1c-9898-9deed8ee9206",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 10,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"11": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"tool_version": "0.38.0",
"outputs": [
{
"type": "input",
"name": "fastq_out"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_in": {
"output_name": "output",
"id": 0
}
},
"tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 11,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "af87189b-fcf6-4042-aa57-ea94abe91513",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 970,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"12": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"tool_version": "0.72+galaxy1",
"outputs": [
{
"type": "html",
"name": "html_file"
},
{
"type": "txt",
"name": "text_file"
}
],
"workflow_outputs": [],
"input_connections": {
"input_file": {
"output_name": "output",
"id": 1
}
},
"tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
"id": 12,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "5511b49c-e5a6-4950-915f-b3eb9ad86f29",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 130,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"13": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"tool_version": "0.38.0",
"outputs": [
{
"type": "input",
"name": "fastq_out"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_in": {
"output_name": "output",
"id": 1
}
},
"tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 13,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "93721d01-1da1-4055-9cc2-915c222990ad",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1090,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"14": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"tool_version": "0.72+galaxy1",
"outputs": [
{
"type": "html",
"name": "html_file"
},
{
"type": "txt",
"name": "text_file"
}
],
"workflow_outputs": [],
"input_connections": {
"input_file": {
"output_name": "output",
"id": 2
}
},
"tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
"id": 14,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "369fbec0-e2d6-4b44-a7d7-a6dfa53bd0e3",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 250,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"15": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"tool_version": "0.38.0",
"outputs": [
{
"type": "input",
"name": "fastq_out"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_in": {
"output_name": "output",
"id": 2
}
},
"tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 15,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "eac006d3-ec65-4ff2-8ca8-90a40c4a93f1",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1210,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"16": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"tool_version": "0.72+galaxy1",
"outputs": [
{
"type": "html",
"name": "html_file"
},
{
"type": "txt",
"name": "text_file"
}
],
"workflow_outputs": [],
"input_connections": {
"input_file": {
"output_name": "output",
"id": 3
}
},
"tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
"id": 16,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "e34ea8a4-a547-4612-b891-eed811ea3354",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 370,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"17": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"tool_version": "0.38.0",
"outputs": [
{
"type": "input",
"name": "fastq_out"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_in": {
"output_name": "output",
"id": 3
}
},
"tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 17,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "9eae30d6-9e4e-4e22-a97e-2adca01e280c",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1330,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"18": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"tool_version": "0.72+galaxy1",
"outputs": [
{
"type": "html",
"name": "html_file"
},
{
"type": "txt",
"name": "text_file"
}
],
"workflow_outputs": [],
"input_connections": {
"input_file": {
"output_name": "output",
"id": 4
}
},
"tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
"id": 18,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "f18c6885-361c-41ef-a181-2e45d288f5fe",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 490,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"19": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"tool_version": "0.38.0",
"outputs": [
{
"type": "input",
"name": "fastq_out"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_in": {
"output_name": "output",
"id": 4
}
},
"tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 19,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "daf61a05-e536-4b82-91c9-2e6586df556e",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1450,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"20": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"tool_version": "0.72+galaxy1",
"outputs": [
{
"type": "html",
"name": "html_file"
},
{
"type": "txt",
"name": "text_file"
}
],
"workflow_outputs": [],
"input_connections": {
"input_file": {
"output_name": "output",
"id": 5
}
},
"tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
"id": 20,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "57d4cd7e-3223-429b-b541-6f67e3d7f079",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 610,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"21": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"tool_version": "0.38.0",
"outputs": [
{
"type": "input",
"name": "fastq_out"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_in": {
"output_name": "output",
"id": 5
}
},
"tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 21,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "09104f88-17b7-4309-b863-3e9d95b65c35",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1570,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"22": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"tool_version": "0.72+galaxy1",
"outputs": [
{
"type": "html",
"name": "html_file"
},
{
"type": "txt",
"name": "text_file"
}
],
"workflow_outputs": [],
"input_connections": {
"input_file": {
"output_name": "output",
"id": 6
}
},
"tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
"id": 22,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "3c9d21c9-c53d-4244-9817-de0cfccab824",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 730,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"23": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"tool_version": "0.38.0",
"outputs": [
{
"type": "input",
"name": "fastq_out"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_in": {
"output_name": "output",
"id": 6
}
},
"tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 23,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "214d845a-e782-4eb9-acef-c2509ce4658d",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1690,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"24": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"tool_version": "0.72+galaxy1",
"outputs": [
{
"type": "html",
"name": "html_file"
},
{
"type": "txt",
"name": "text_file"
}
],
"workflow_outputs": [],
"input_connections": {
"input_file": {
"output_name": "output",
"id": 7
}
},
"tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}",
"id": 24,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "c387cc15-35b7-44f4-9058-92074d98fa51",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 850,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"25": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"tool_version": "0.38.0",
"outputs": [
{
"type": "input",
"name": "fastq_out"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_in": {
"output_name": "output",
"id": 7
}
},
"tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}, {\\\"__index__\\\": 1, \\\"operation\\\": {\\\"__current_case__\\\": 1, \\\"minlen\\\": \\\"20\\\", \\\"name\\\": \\\"MINLEN\\\"}}]\", \"__page__\": null, \"output_logs\": \"\\\"false\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 0, \\\"fastq_in\\\": null, \\\"single_or_paired\\\": \\\"se\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 25,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "cc30c996-ddc1-422d-bdfc-b3ef74336911",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1810,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"26": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1",
"tool_version": "1.1.1",
"outputs": [
{
"type": "input",
"name": "outfile"
}
],
"workflow_outputs": [],
"input_connections": {
"infile": {
"output_name": "output",
"id": 9
}
},
"tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"code\": \"\\\"!/^#/ && $3==\\\\\\\"exon\\\\\\\"{if($7==\\\\\\\"+\\\\\\\"){ p[px++] = $1\\\\\\\"\\\\\\\\t\\\\\\\"$4\\\\\\\"\\\\\\\\t\\\\\\\"$5\\\\\\\"\\\\\\\\t.\\\\\\\\t.\\\\\\\\t\\\\\\\"$7 }else{ n[nx++] = $1\\\\\\\"\\\\\\\\t\\\\\\\"$4\\\\\\\"\\\\\\\\t\\\\\\\"$5\\\\\\\"\\\\\\\\t.\\\\\\\\t.\\\\\\\\t\\\\\\\"$7 } if(nx>1000 && px>1000){ exit } } END{ for(i in p){ print p[i] } for(i in n){ print n[i] } }\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}",
"id": 26,
"tool_shed_repository": {
"owner": "bgruening",
"changeset_revision": "0a8c6b61f0f4",
"name": "text_processing",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "8e24bec7-377a-4e5d-a678-4db396c0008e",
"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/iuc/rgrnastar/rna_star/2.7.2b",
"tool_version": "2.7.2b",
"outputs": [
{
"type": "txt",
"name": "output_log"
},
{
"type": "interval",
"name": "splice_junctions"
},
{
"type": "bam",
"name": "mapped_reads"
}
],
"workflow_outputs": [],
"input_connections": {
"refGenomeSource|genomeFastaFiles": {
"output_name": "output",
"id": 8
},
"singlePaired|input1": {
"output_name": "fastq_out",
"id": 11
}
},
"tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": null, \\\"sPaired\\\": \\\"single\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"twopass\": \"{\\\"__current_case__\\\": 0, \\\"sj_precalculated\\\": \\\"\\\", \\\"twopassMode\\\": \\\"None\\\", \\\"twopass_read_subset\\\": \\\"\\\"}\", \"filter\": \"{\\\"basic_filters\\\": null, \\\"output_params2\\\": {\\\"__current_case__\\\": 1, \\\"output_select2\\\": \\\"no\\\"}}\", \"chimOutType\": \"\\\"\\\"\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\", \"oformat\": \"{\\\"HI_offset\\\": \\\"1\\\", \\\"outSAMattributes\\\": [\\\"NH\\\", \\\"HI\\\", \\\"AS\\\", \\\"nM\\\", \\\"ch\\\"], \\\"outSAMmapqUnique\\\": \\\"60\\\", \\\"outSAMprimaryFlag\\\": \\\"OneBestScore\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"geneSource\\\": \\\"history\\\", \\\"genomeFastaFiles\\\": null, \\\"genomeSAindexNbases\\\": \\\"\\\"}\"}",
"id": 27,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "b9e04854e2bb",
"name": "rgrnastar",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "7e463aa1-f354-483e-b2b4-ed9f3f4aaa36",
"errors": null,
"name": "RNA STAR",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 10,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"type": "tool"
},
"28": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"tool_version": "2.7.2b",
"outputs": [
{
"type": "txt",
"name": "output_log"
},
{
"type": "interval",
"name": "splice_junctions"
},
{
"type": "bam",
"name": "mapped_reads"
}
],
"workflow_outputs": [],
"input_connections": {
"refGenomeSource|genomeFastaFiles": {
"output_name": "output",
"id": 8
},
"singlePaired|input1": {
"output_name": "fastq_out",
"id": 13
}
},
"tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": null, \\\"sPaired\\\": \\\"single\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"twopass\": \"{\\\"__current_case__\\\": 0, \\\"sj_precalculated\\\": \\\"\\\", \\\"twopassMode\\\": \\\"None\\\", \\\"twopass_read_subset\\\": \\\"\\\"}\", \"filter\": \"{\\\"basic_filters\\\": null, \\\"output_params2\\\": {\\\"__current_case__\\\": 1, \\\"output_select2\\\": \\\"no\\\"}}\", \"chimOutType\": \"\\\"\\\"\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\", \"oformat\": \"{\\\"HI_offset\\\": \\\"1\\\", \\\"outSAMattributes\\\": [\\\"NH\\\", \\\"HI\\\", \\\"AS\\\", \\\"nM\\\", \\\"ch\\\"], \\\"outSAMmapqUnique\\\": \\\"60\\\", \\\"outSAMprimaryFlag\\\": \\\"OneBestScore\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"geneSource\\\": \\\"history\\\", \\\"genomeFastaFiles\\\": null, \\\"genomeSAindexNbases\\\": \\\"\\\"}\"}",
"id": 28,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "b9e04854e2bb",
"name": "rgrnastar",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "08080474-1bf4-47f3-87e3-2669f5bd3b3f",
"errors": null,
"name": "RNA STAR",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 130,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"type": "tool"
},
"29": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"tool_version": "2.7.2b",
"outputs": [
{
"type": "txt",
"name": "output_log"
},
{
"type": "interval",
"name": "splice_junctions"
},
{
"type": "bam",
"name": "mapped_reads"
}
],
"workflow_outputs": [],
"input_connections": {
"refGenomeSource|genomeFastaFiles": {
"output_name": "output",
"id": 8
},
"singlePaired|input1": {
"output_name": "fastq_out",
"id": 15
}
},
"tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": null, \\\"sPaired\\\": \\\"single\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"twopass\": \"{\\\"__current_case__\\\": 0, \\\"sj_precalculated\\\": \\\"\\\", \\\"twopassMode\\\": \\\"None\\\", \\\"twopass_read_subset\\\": \\\"\\\"}\", \"filter\": \"{\\\"basic_filters\\\": null, \\\"output_params2\\\": {\\\"__current_case__\\\": 1, \\\"output_select2\\\": \\\"no\\\"}}\", \"chimOutType\": \"\\\"\\\"\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\", \"oformat\": \"{\\\"HI_offset\\\": \\\"1\\\", \\\"outSAMattributes\\\": [\\\"NH\\\", \\\"HI\\\", \\\"AS\\\", \\\"nM\\\", \\\"ch\\\"], \\\"outSAMmapqUnique\\\": \\\"60\\\", \\\"outSAMprimaryFlag\\\": \\\"OneBestScore\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"geneSource\\\": \\\"history\\\", \\\"genomeFastaFiles\\\": null, \\\"genomeSAindexNbases\\\": \\\"\\\"}\"}",
"id": 29,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "b9e04854e2bb",
"name": "rgrnastar",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "828e76f7-7747-46ed-9ea2-ef54145ba75d",
"errors": null,
"name": "RNA STAR",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 250,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"type": "tool"
},
"30": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"tool_version": "2.7.2b",
"outputs": [
{
"type": "txt",
"name": "output_log"
},
{
"type": "interval",
"name": "splice_junctions"
},
{
"type": "bam",
"name": "mapped_reads"
}
],
"workflow_outputs": [],
"input_connections": {
"refGenomeSource|genomeFastaFiles": {
"output_name": "output",
"id": 8
},
"singlePaired|input1": {
"output_name": "fastq_out",
"id": 17
}
},
"tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": null, \\\"sPaired\\\": \\\"single\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"twopass\": \"{\\\"__current_case__\\\": 0, \\\"sj_precalculated\\\": \\\"\\\", \\\"twopassMode\\\": \\\"None\\\", \\\"twopass_read_subset\\\": \\\"\\\"}\", \"filter\": \"{\\\"basic_filters\\\": null, \\\"output_params2\\\": {\\\"__current_case__\\\": 1, \\\"output_select2\\\": \\\"no\\\"}}\", \"chimOutType\": \"\\\"\\\"\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\", \"oformat\": \"{\\\"HI_offset\\\": \\\"1\\\", \\\"outSAMattributes\\\": [\\\"NH\\\", \\\"HI\\\", \\\"AS\\\", \\\"nM\\\", \\\"ch\\\"], \\\"outSAMmapqUnique\\\": \\\"60\\\", \\\"outSAMprimaryFlag\\\": \\\"OneBestScore\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"geneSource\\\": \\\"history\\\", \\\"genomeFastaFiles\\\": null, \\\"genomeSAindexNbases\\\": \\\"\\\"}\"}",
"id": 30,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "b9e04854e2bb",
"name": "rgrnastar",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "03a3db9c-8b6e-4116-8356-e91a9efacbdb",
"errors": null,
"name": "RNA STAR",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 370,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"type": "tool"
},
"31": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"tool_version": "2.7.2b",
"outputs": [
{
"type": "txt",
"name": "output_log"
},
{
"type": "interval",
"name": "splice_junctions"
},
{
"type": "bam",
"name": "mapped_reads"
}
],
"workflow_outputs": [],
"input_connections": {
"refGenomeSource|genomeFastaFiles": {
"output_name": "output",
"id": 8
},
"singlePaired|input1": {
"output_name": "fastq_out",
"id": 19
}
},
"tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": null, \\\"sPaired\\\": \\\"single\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"twopass\": \"{\\\"__current_case__\\\": 0, \\\"sj_precalculated\\\": \\\"\\\", \\\"twopassMode\\\": \\\"None\\\", \\\"twopass_read_subset\\\": \\\"\\\"}\", \"filter\": \"{\\\"basic_filters\\\": null, \\\"output_params2\\\": {\\\"__current_case__\\\": 1, \\\"output_select2\\\": \\\"no\\\"}}\", \"chimOutType\": \"\\\"\\\"\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\", \"oformat\": \"{\\\"HI_offset\\\": \\\"1\\\", \\\"outSAMattributes\\\": [\\\"NH\\\", \\\"HI\\\", \\\"AS\\\", \\\"nM\\\", \\\"ch\\\"], \\\"outSAMmapqUnique\\\": \\\"60\\\", \\\"outSAMprimaryFlag\\\": \\\"OneBestScore\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"geneSource\\\": \\\"history\\\", \\\"genomeFastaFiles\\\": null, \\\"genomeSAindexNbases\\\": \\\"\\\"}\"}",
"id": 31,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "b9e04854e2bb",
"name": "rgrnastar",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "d53a178c-57b9-44c9-a603-e4fb39d1c091",
"errors": null,
"name": "RNA STAR",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 490,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"type": "tool"
},
"32": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"tool_version": "2.7.2b",
"outputs": [
{
"type": "txt",
"name": "output_log"
},
{
"type": "interval",
"name": "splice_junctions"
},
{
"type": "bam",
"name": "mapped_reads"
}
],
"workflow_outputs": [],
"input_connections": {
"refGenomeSource|genomeFastaFiles": {
"output_name": "output",
"id": 8
},
"singlePaired|input1": {
"output_name": "fastq_out",
"id": 21
}
},
"tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": null, \\\"sPaired\\\": \\\"single\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"twopass\": \"{\\\"__current_case__\\\": 0, \\\"sj_precalculated\\\": \\\"\\\", \\\"twopassMode\\\": \\\"None\\\", \\\"twopass_read_subset\\\": \\\"\\\"}\", \"filter\": \"{\\\"basic_filters\\\": null, \\\"output_params2\\\": {\\\"__current_case__\\\": 1, \\\"output_select2\\\": \\\"no\\\"}}\", \"chimOutType\": \"\\\"\\\"\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\", \"oformat\": \"{\\\"HI_offset\\\": \\\"1\\\", \\\"outSAMattributes\\\": [\\\"NH\\\", \\\"HI\\\", \\\"AS\\\", \\\"nM\\\", \\\"ch\\\"], \\\"outSAMmapqUnique\\\": \\\"60\\\", \\\"outSAMprimaryFlag\\\": \\\"OneBestScore\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"geneSource\\\": \\\"history\\\", \\\"genomeFastaFiles\\\": null, \\\"genomeSAindexNbases\\\": \\\"\\\"}\"}",
"id": 32,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "b9e04854e2bb",
"name": "rgrnastar",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "3beb024f-06d6-4fcd-a9e9-61585121a3cc",
"errors": null,
"name": "RNA STAR",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 610,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"type": "tool"
},
"33": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"tool_version": "2.7.2b",
"outputs": [
{
"type": "txt",
"name": "output_log"
},
{
"type": "interval",
"name": "splice_junctions"
},
{
"type": "bam",
"name": "mapped_reads"
}
],
"workflow_outputs": [],
"input_connections": {
"refGenomeSource|genomeFastaFiles": {
"output_name": "output",
"id": 8
},
"singlePaired|input1": {
"output_name": "fastq_out",
"id": 23
}
},
"tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": null, \\\"sPaired\\\": \\\"single\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"twopass\": \"{\\\"__current_case__\\\": 0, \\\"sj_precalculated\\\": \\\"\\\", \\\"twopassMode\\\": \\\"None\\\", \\\"twopass_read_subset\\\": \\\"\\\"}\", \"filter\": \"{\\\"basic_filters\\\": null, \\\"output_params2\\\": {\\\"__current_case__\\\": 1, \\\"output_select2\\\": \\\"no\\\"}}\", \"chimOutType\": \"\\\"\\\"\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\", \"oformat\": \"{\\\"HI_offset\\\": \\\"1\\\", \\\"outSAMattributes\\\": [\\\"NH\\\", \\\"HI\\\", \\\"AS\\\", \\\"nM\\\", \\\"ch\\\"], \\\"outSAMmapqUnique\\\": \\\"60\\\", \\\"outSAMprimaryFlag\\\": \\\"OneBestScore\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"geneSource\\\": \\\"history\\\", \\\"genomeFastaFiles\\\": null, \\\"genomeSAindexNbases\\\": \\\"\\\"}\"}",
"id": 33,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "b9e04854e2bb",
"name": "rgrnastar",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "d1541601-27fa-4d78-9fb1-04c70ca68982",
"errors": null,
"name": "RNA STAR",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 730,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"type": "tool"
},
"34": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"tool_version": "2.7.2b",
"outputs": [
{
"type": "txt",
"name": "output_log"
},
{
"type": "interval",
"name": "splice_junctions"
},
{
"type": "bam",
"name": "mapped_reads"
}
],
"workflow_outputs": [],
"input_connections": {
"refGenomeSource|genomeFastaFiles": {
"output_name": "output",
"id": 8
},
"singlePaired|input1": {
"output_name": "fastq_out",
"id": 25
}
},
"tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": null, \\\"sPaired\\\": \\\"single\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"twopass\": \"{\\\"__current_case__\\\": 0, \\\"sj_precalculated\\\": \\\"\\\", \\\"twopassMode\\\": \\\"None\\\", \\\"twopass_read_subset\\\": \\\"\\\"}\", \"filter\": \"{\\\"basic_filters\\\": null, \\\"output_params2\\\": {\\\"__current_case__\\\": 1, \\\"output_select2\\\": \\\"no\\\"}}\", \"chimOutType\": \"\\\"\\\"\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\", \"oformat\": \"{\\\"HI_offset\\\": \\\"1\\\", \\\"outSAMattributes\\\": [\\\"NH\\\", \\\"HI\\\", \\\"AS\\\", \\\"nM\\\", \\\"ch\\\"], \\\"outSAMmapqUnique\\\": \\\"60\\\", \\\"outSAMprimaryFlag\\\": \\\"OneBestScore\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"geneSource\\\": \\\"history\\\", \\\"genomeFastaFiles\\\": null, \\\"genomeSAindexNbases\\\": \\\"\\\"}\"}",
"id": 34,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "b9e04854e2bb",
"name": "rgrnastar",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "2c518664-5c4f-433d-815a-50fc84bb88ef",
"errors": null,
"name": "RNA STAR",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 850,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b",
"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": "mapped_reads",
"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": "0220c204-cb07-46dc-b5f5-266cf1d08160",
"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": "mapped_reads",
"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": "a178c580-9af7-4291-a09a-ec6f4bbd3576",
"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": "mapped_reads",
"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": "a57ae494-b04b-4711-a58c-bae2fcf42a5c",
"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": "mapped_reads",
"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": "9c576b35-b591-4463-8b3b-ff9cb2757bc5",
"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": "mapped_reads",
"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": "39f04e90-ebe1-4504-8fe6-75f6cf933af5",
"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": "mapped_reads",
"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": "e1aba553-412f-4b56-9f0b-bc188eab8735",
"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": "mapped_reads",
"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": "c921e0ca-747e-4280-a494-3b7c7f18c57a",
"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": "mapped_reads",
"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": "8ce58ba3-19af-4135-8f83-d5b10d6651f3",
"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": "mapped_reads",
"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": "357a591b-2b11-4e90-8878-55ab1886b026",
"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": "f46ba3d8-f895-46cb-97dd-acd7af8287e8",
"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"
}