{
"uuid": "741007c9-3577-42a4-a436-672fd572c6af",
"tags": [],
"format-version": "0.1",
"name": "Differential gene expression analysis of paired-end NGS data using FastQC, Trimmomatic, HISAT2, 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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.N1.fastq.gz\"}",
"id": 0,
"uuid": "520257e7-1daa-4a80-9c54-2cfd55303823",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.N2.fastq.gz\"}",
"id": 1,
"uuid": "2d333097-2a2f-4f0b-be21-fa849e1ca126",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.N3.fastq.gz\"}",
"id": 2,
"uuid": "d8365f59-c03a-4736-b7f6-bd2e0e0757d6",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.N4.fastq.gz\"}",
"id": 3,
"uuid": "e541340d-ed4d-4d35-aec9-c050a2154647",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R2.N1.fastq.gz\"}",
"id": 4,
"uuid": "cd100282-8035-48cf-83e1-854e5774f82e",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_ctr.R2.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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R2.N2.fastq.gz\"}",
"id": 5,
"uuid": "99f14acf-4230-401c-b42a-9bc7860f6b69",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_ctr.R2.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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R2.N3.fastq.gz\"}",
"id": 6,
"uuid": "c8114f60-3923-4bdb-89d1-133fed4b5e2c",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_ctr.R2.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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R2.N4.fastq.gz\"}",
"id": 7,
"uuid": "5eeace75-07eb-404f-80b6-b5d9c4fc440a",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_ctr.R2.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/training-material/raw/master/raw_data/rna/PE/rna_treat.R1.N1.fastq.gz\"}",
"id": 8,
"uuid": "b665b2d0-ba29-4d4a-a8c2-3c5def576194",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R1.N1.fastq.gz",
"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/training-material/raw/master/raw_data/rna/PE/rna_treat.R1.N2.fastq.gz\"}",
"id": 9,
"uuid": "4375162f-f276-4b97-8caa-4bcd9bfefa83",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R1.N2.fastq.gz",
"description": ""
}
],
"position": {
"top": 1090,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"10": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"name\": \"https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R1.N3.fastq.gz\"}",
"id": 10,
"uuid": "462a7ae2-81cf-4fcc-a981-cdf886f29939",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R1.N3.fastq.gz",
"description": ""
}
],
"position": {
"top": 1210,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"11": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"name\": \"https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R1.N4.fastq.gz\"}",
"id": 11,
"uuid": "be9493f6-5738-42e6-8b98-c9bf12b8f300",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R1.N4.fastq.gz",
"description": ""
}
],
"position": {
"top": 1330,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"12": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"name\": \"https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R2.N1.fastq.gz\"}",
"id": 12,
"uuid": "ea4d2aee-9078-4cb8-b628-7fcba7f0dff4",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R2.N1.fastq.gz",
"description": ""
}
],
"position": {
"top": 1450,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"13": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"name\": \"https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R2.N2.fastq.gz\"}",
"id": 13,
"uuid": "ea712ca8-4cf6-4fe6-bc47-6aa2e8b952d5",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R2.N2.fastq.gz",
"description": ""
}
],
"position": {
"top": 1570,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"14": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"name\": \"https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R2.N3.fastq.gz\"}",
"id": 14,
"uuid": "9a46cda4-8c98-4331-8e82-5c4514c39405",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R2.N3.fastq.gz",
"description": ""
}
],
"position": {
"top": 1690,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"15": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"name\": \"https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R2.N4.fastq.gz\"}",
"id": 15,
"uuid": "afd94065-30ef-433c-9f1a-8c911360fd67",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rna/PE/rna_treat.R2.N4.fastq.gz",
"description": ""
}
],
"position": {
"top": 1810,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"16": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"name\": \"https://github.com/destairdenbi/training-material/raw/master/raw_data/rrbs/hg38.goi.fa\"}",
"id": 16,
"uuid": "7795d0b1-f30a-4dc0-a610-fff91cce38cf",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rrbs/hg38.goi.fa",
"description": ""
}
],
"position": {
"top": 1930,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"17": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"name\": \"https://github.com/destairdenbi/training-material/raw/master/raw_data/rrbs/hg38.goi.gtf\"}",
"id": 17,
"uuid": "52028467-d23a-429b-b2de-1c528fff5d67",
"errors": null,
"name": "Input dataset",
"label": null,
"inputs": [
{
"name": "https://github.com/destairdenbi/training-material/raw/master/raw_data/rrbs/hg38.goi.gtf",
"description": ""
}
],
"position": {
"top": 2050,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_input"
},
"18": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
"id": 18,
"uuid": "ba73badc-06b7-4b59-ae46-caffa2eebed2",
"errors": null,
"name": "Input dataset collection",
"label": null,
"inputs": [
{
"name": "Input Dataset Collection",
"description": ""
}
],
"position": {
"top": 2170,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_collection_input"
},
"19": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
"id": 19,
"uuid": "54f8c4a2-076d-4b49-b8d3-be6018ee0a12",
"errors": null,
"name": "Input dataset collection",
"label": null,
"inputs": [
{
"name": "Input Dataset Collection",
"description": ""
}
],
"position": {
"top": 2290,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_collection_input"
},
"20": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
"id": 20,
"uuid": "144e6b49-0358-4e30-853f-6f7f28c8f97a",
"errors": null,
"name": "Input dataset collection",
"label": null,
"inputs": [
{
"name": "Input Dataset Collection",
"description": ""
}
],
"position": {
"top": 2410,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_collection_input"
},
"21": {
"tool_id": null,
"tool_version": null,
"outputs": [],
"workflow_outputs": [],
"input_connections": {},
"tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
"id": 21,
"uuid": "9f374041-56a9-4117-800f-de879e8a9a7a",
"errors": null,
"name": "Input dataset collection",
"label": null,
"inputs": [
{
"name": "Input Dataset Collection",
"description": ""
}
],
"position": {
"top": 2530,
"left": 10
},
"annotation": "",
"content_id": null,
"type": "data_collection_input"
},
"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": 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": 22,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "86b67406-c6c9-4555-b04a-a345b2181f76",
"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"
},
"23": {
"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": 23,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "e1f767b0-e91e-4c6c-b0cb-77e7d91b8d7a",
"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"
},
"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": 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": 24,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "3652e4ee-ab6e-477d-89c0-da3a839cdcf7",
"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"
},
"25": {
"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": 25,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "e8f13ad5-7339-4d85-a21b-b2d0601992aa",
"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"
},
"26": {
"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": 26,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "21582d4a-cfff-483f-a848-d6a488358bc8",
"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"
},
"27": {
"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": 27,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "180c1ef5-9f90-4656-a509-da1829d9efa3",
"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"
},
"28": {
"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": 28,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "e4045cfd-0cdc-4df9-9761-8675ec6d5271",
"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"
},
"29": {
"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": 29,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "b7f6bb7e-668f-420a-b47f-62eb718bf7db",
"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"
},
"30": {
"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": 8
}
},
"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": 30,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "4d073fd2-9d02-4b6d-b2dc-8a65035e28cc",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 970,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"31": {
"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": 9
}
},
"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": 31,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "3b8e52c7-1833-4d86-9d8c-d3f1d1ed9b99",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1090,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"32": {
"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": 10
}
},
"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": 32,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "99cbc45d-7f08-49cb-b5f7-1ad8aac5c855",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1210,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"33": {
"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": 11
}
},
"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": 33,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "4b01cb4a-5570-4b15-97cd-c04d06b4a8fc",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1330,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"34": {
"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": 12
}
},
"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": 34,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "39ca40d2-3268-4e86-beb7-b15bcfe1b3ed",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1450,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"35": {
"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": 13
}
},
"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": 35,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "2161dfda-2656-40fc-8761-d548ec8a99a8",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1570,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"36": {
"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": 14
}
},
"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": 36,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "bee54a3f-0b31-4e78-ae95-3eb107c51a80",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1690,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"37": {
"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": 15
}
},
"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": 37,
"tool_shed_repository": {
"owner": "devteam",
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "5b7d62e6-dff0-4234-a195-73f35fcc0d92",
"errors": null,
"name": "FastQC",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1810,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"type": "tool"
},
"38": {
"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": 17
}
},
"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": 38,
"tool_shed_repository": {
"owner": "bgruening",
"changeset_revision": "0a8c6b61f0f4",
"name": "text_processing",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "f3663bbe-4196-4af2-80e0-cb9feba03655",
"errors": null,
"name": "Text reformatting",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 2170,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1",
"type": "tool"
},
"39": {
"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_r1_paired"
},
{
"type": "input",
"name": "fastq_out_r2_paired"
},
{
"type": "input",
"name": "fastq_out_r1_unpaired"
},
{
"type": "input",
"name": "fastq_out_r2_unpaired"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_r2_in": {
"output_name": "output",
"id": 18
},
"readtype|fastq_r1_in": {
"output_name": "output",
"id": 19
}
},
"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, \"fastq_r1_in|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 1, \\\"fastq_r1_in\\\": null, \\\"fastq_r2_in\\\": null, \\\"single_or_paired\\\": \\\"pair_of_files\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"fastq_r2_in|__identifier__\": \"\\\"rna_treat.R2.N1.fastq.gz\\\"\", \"output_logs\": \"\\\"false\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 39,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "63f2d8a9-ae46-4ac1-b81b-0951bd5cf672",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 2050,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"40": {
"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_r1_paired"
},
{
"type": "input",
"name": "fastq_out_r2_paired"
},
{
"type": "input",
"name": "fastq_out_r1_unpaired"
},
{
"type": "input",
"name": "fastq_out_r2_unpaired"
}
],
"workflow_outputs": [],
"input_connections": {
"readtype|fastq_r2_in": {
"output_name": "output",
"id": 20
},
"readtype|fastq_r1_in": {
"output_name": "output",
"id": 21
}
},
"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, \"fastq_r1_in|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"output_err\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 1, \\\"fastq_r1_in\\\": null, \\\"fastq_r2_in\\\": null, \\\"single_or_paired\\\": \\\"pair_of_files\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\", \"fastq_r2_in|__identifier__\": \"\\\"rna_ctr.R2.N1.fastq.gz\\\"\", \"output_logs\": \"\\\"false\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"id": 40,
"tool_shed_repository": {
"owner": "pjbriggs",
"changeset_revision": "898b67846b47",
"name": "trimmomatic",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "14fe4c40-a5d0-4452-b2d2-8bd0fb65729e",
"errors": null,
"name": "Trimmomatic",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 1930,
"left": 230
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
"type": "tool"
},
"41": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4",
"tool_version": "2.1.0+galaxy4",
"outputs": [
{
"type": "bam",
"name": "output_alignments"
}
],
"workflow_outputs": [],
"input_connections": {
"reference_genome|history_item": {
"output_name": "output",
"id": 16
},
"library|input_2": {
"output_name": "fastq_out_r2_paired",
"id": 39
},
"library|input_1": {
"output_name": "fastq_out_r1_paired",
"id": 39
}
},
"tool_state": "{\"adv\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 0, \\\"alignment_options_selector\\\": \\\"defaults\\\"}, \\\"input_options\\\": {\\\"__current_case__\\\": 0, \\\"input_options_selector\\\": \\\"defaults\\\"}, \\\"other_options\\\": {\\\"__current_case__\\\": 0, \\\"other_options_selector\\\": \\\"defaults\\\"}, \\\"output_options\\\": {\\\"__current_case__\\\": 0, \\\"output_options_selector\\\": \\\"defaults\\\"}, \\\"reporting_options\\\": {\\\"__current_case__\\\": 0, \\\"reporting_options_selector\\\": \\\"defaults\\\"}, \\\"scoring_options\\\": {\\\"__current_case__\\\": 0, \\\"scoring_options_selector\\\": \\\"defaults\\\"}, \\\"spliced_options\\\": {\\\"__current_case__\\\": 0, \\\"spliced_options_selector\\\": \\\"defaults\\\"}}\", \"__page__\": null, \"input_2|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"sum\": \"{\\\"new_summary\\\": \\\"false\\\", \\\"summary_file\\\": \\\"false\\\"}\", \"input_1|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"library\": \"{\\\"__current_case__\\\": 1, \\\"input_1\\\": null, \\\"input_2\\\": null, \\\"paired_options\\\": {\\\"__current_case__\\\": 0, \\\"paired_options_selector\\\": \\\"defaults\\\"}, \\\"rna_strandness\\\": \\\"\\\", \\\"type\\\": \\\"paired\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 1, \\\"history_item\\\": null, \\\"source\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
"id": 41,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "3fb01a8c902d",
"name": "hisat2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "30efbd11-6636-47b1-acce-3f0097a27eca",
"errors": null,
"name": "HISAT2",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 130,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4",
"type": "tool"
},
"42": {
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4",
"tool_version": "2.1.0+galaxy4",
"outputs": [
{
"type": "bam",
"name": "output_alignments"
}
],
"workflow_outputs": [],
"input_connections": {
"reference_genome|history_item": {
"output_name": "output",
"id": 16
},
"library|input_2": {
"output_name": "fastq_out_r2_paired",
"id": 40
},
"library|input_1": {
"output_name": "fastq_out_r1_paired",
"id": 40
}
},
"tool_state": "{\"adv\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 0, \\\"alignment_options_selector\\\": \\\"defaults\\\"}, \\\"input_options\\\": {\\\"__current_case__\\\": 0, \\\"input_options_selector\\\": \\\"defaults\\\"}, \\\"other_options\\\": {\\\"__current_case__\\\": 0, \\\"other_options_selector\\\": \\\"defaults\\\"}, \\\"output_options\\\": {\\\"__current_case__\\\": 0, \\\"output_options_selector\\\": \\\"defaults\\\"}, \\\"reporting_options\\\": {\\\"__current_case__\\\": 0, \\\"reporting_options_selector\\\": \\\"defaults\\\"}, \\\"scoring_options\\\": {\\\"__current_case__\\\": 0, \\\"scoring_options_selector\\\": \\\"defaults\\\"}, \\\"spliced_options\\\": {\\\"__current_case__\\\": 0, \\\"spliced_options_selector\\\": \\\"defaults\\\"}}\", \"__page__\": null, \"input_2|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"sum\": \"{\\\"new_summary\\\": \\\"false\\\", \\\"summary_file\\\": \\\"false\\\"}\", \"input_1|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"library\": \"{\\\"__current_case__\\\": 1, \\\"input_1\\\": null, \\\"input_2\\\": null, \\\"paired_options\\\": {\\\"__current_case__\\\": 0, \\\"paired_options_selector\\\": \\\"defaults\\\"}, \\\"rna_strandness\\\": \\\"\\\", \\\"type\\\": \\\"paired\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 1, \\\"history_item\\\": null, \\\"source\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
"id": 42,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "3fb01a8c902d",
"name": "hisat2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "b6aafe4f-62a4-4e07-bf0a-ef1f5f457490",
"errors": null,
"name": "HISAT2",
"post_job_actions": {},
"label": null,
"inputs": [],
"position": {
"top": 10,
"left": 450
},
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4",
"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": "output_alignments",
"id": 41
},
"anno|reference_gene_sets": {
"output_name": "output",
"id": 17
}
},
"tool_state": "{\"alignment|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"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": "4a681edc-b40a-4b12-8035-1887b4660843",
"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"
},
"44": {
"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": "output_alignments",
"id": 42
},
"refgene": {
"output_name": "outfile",
"id": 38
}
},
"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\\\"\", \"input|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\"}",
"id": 44,
"tool_shed_repository": {
"owner": "nilesh",
"changeset_revision": "1a052c827e88",
"name": "rseqc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "fe558230-2520-4c40-a8b2-e5cd641033de",
"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"
},
"45": {
"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": "output_alignments",
"id": 42
},
"anno|reference_gene_sets": {
"output_name": "output",
"id": 17
}
},
"tool_state": "{\"alignment|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"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": 45,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "9301937c9037",
"name": "featurecounts",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "056b6a2f-be9e-4b22-b18a-3934bd1cb4a8",
"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"
},
"46": {
"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
},
"select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
"output_name": "output_short",
"id": 45
}
},
"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": 46,
"tool_shed_repository": {
"owner": "iuc",
"changeset_revision": "0696db066a5b",
"name": "deseq2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"uuid": "f6ef2c01-26a4-4eed-94f7-2e82113b8d6a",
"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"
}