{ "uuid": "d2a75cf5-02b4-483f-a128-f5eae05f1e47", "tags": [], "format-version": "0.1", "name": "Differential gene expression analysis of paired-end NGS data using FastQC, Cutadapt, 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/training-material/raw/master/raw_data/rna/PE/rna_ctr.R1.N1.fastq.gz\"}", "id": 0, "uuid": "955a9d57-4e6b-4672-88a5-ceb71b645585", "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": "44841575-b232-40e4-abe8-b656c90b4520", "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": "dcf1a062-0ac6-44f5-a09c-e3d9e19c52c8", "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": "b6812c58-6564-4e2b-bc5a-8f8119c3f4d9", "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": "2cc4ccae-6e22-4e75-9a4f-4ac09db466c8", "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": "f1ec0f12-723f-40fb-bf8d-b788fe6de059", "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": "2d1076f1-9be3-439a-8a1e-ab4983d3c495", "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": "801c47af-1a63-4255-b4fd-e947badb95ab", "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": "c1a751dc-2111-45f7-ab8d-7e65323910e6", "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": "37599dc5-28d5-4b03-b74a-74c0adfe73d3", "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": "dc44e10e-299a-4c0e-bea6-b3d11270bcaf", "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": "9df96777-6328-41e7-9038-43f5d10e38f9", "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": "0e8a57d4-9c0b-4419-9a36-737ccee21400", "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": "2f4ba779-dbaa-43c8-add3-11764ff61395", "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": "2d874e7f-1206-4023-9407-a10b1ed5b495", "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": "ceaba7b7-b59b-49ec-bccf-d8ea40be07eb", "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": "ae4c2d61-03e9-473c-8d16-4ad18057638c", "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": "fab214cd-3f8a-4562-b634-327bb9007c45", "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": "acd7a6b4-7f7f-46e8-afd6-c4e4403122fa", "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": "c45e640d-dc02-4c37-ab0a-c79f610bc182", "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": "901d006e-589d-47e2-a4ff-6bc732722549", "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": "92b165f1-b9b4-4b71-82c6-126abba7fba2", "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": "eaf19c13-40aa-4c7f-8bba-001a3b8a7a14", "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": "48707b84-678d-4cb9-87d4-e861510543f8", "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": "931d41bb-4998-4ac2-90fd-883b9354e7bd", "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": "69a68b22-0761-4c79-94a9-b51d14392ac5", "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": "852bb657-f6cb-4d47-9ef0-895cdfc948fa", "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": "22ffcd15-3e7a-41d3-9739-c5d38d8064a0", "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": "e3aa1aee-9488-4ec2-991d-9e6db41fcc12", "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": "0cc16343-0108-484f-9bbc-f9c4d7021d6a", "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": "b19b732a-5934-4a42-bd59-5fbd9f54e1a2", "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": "76a82ca6-d352-4e11-8f61-2b5edb9bb67a", "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": "45403361-a5ed-4a96-aee3-65154a1201e7", "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": "a71be977-1041-47f6-a817-274c52528008", "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": "5ce8945a-0593-4c55-b316-6834714f4d36", "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": "6caa85f2-9d15-41a5-a491-1b5c4f67bee6", "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": "08019417-601e-42ef-81bd-3b7fb686b536", "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": "17f9a2a2-b295-41d5-9235-4b9a3ad879e7", "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": "40e83cd7-edee-45bd-887e-a17da7cf6d50", "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/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "fastqsanger", "name": "out2" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_2": { "output_name": "output", "id": 18 }, "library|input_1": { "output_name": "output", "id": 19 } }, "tool_state": "{\"__page__\": null, \"input_2|__identifier__\": \"\\\"rna_treat.R2.N1.fastq.gz\\\"\", \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"input_1|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 1, \\\"input_1\\\": null, \\\"input_2\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"r2\\\": {\\\"adapters2\\\": [], \\\"anywhere_adapters2\\\": [], \\\"cut2\\\": \\\"0\\\", \\\"front_adapters2\\\": []}, \\\"type\\\": \\\"paired\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 39, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "8d522c94-3ae2-4b93-9bb0-c3fd40c07220", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 2050, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "40": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "fastqsanger", "name": "out2" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_2": { "output_name": "output", "id": 20 }, "library|input_1": { "output_name": "output", "id": 21 } }, "tool_state": "{\"__page__\": null, \"input_2|__identifier__\": \"\\\"rna_ctr.R2.N1.fastq.gz\\\"\", \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"input_1|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 1, \\\"input_1\\\": null, \\\"input_2\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"r2\\\": {\\\"adapters2\\\": [], \\\"anywhere_adapters2\\\": [], \\\"cut2\\\": \\\"0\\\", \\\"front_adapters2\\\": []}, \\\"type\\\": \\\"paired\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 40, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "7bbb8e8c-52d0-47f1-b2e1-d802df74dc35", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1930, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "41": { "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": { "singlePaired|input2": { "output_name": "out2", "id": 39 }, "refGenomeSource|genomeFastaFiles": { "output_name": "output", "id": 16 }, "singlePaired|input1": { "output_name": "out1", "id": 39 } }, "tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 1, \\\"input1\\\": null, \\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\"}\", \"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\": \"\\\"\\\"\", \"input1|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"input2|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"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\\\": \\\"\\\"}\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\"}", "id": 41, "tool_shed_repository": { "owner": "iuc", "changeset_revision": "b9e04854e2bb", "name": "rgrnastar", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "9d7a614a-9540-46bb-8655-b1aa38f22686", "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" }, "42": { "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": { "singlePaired|input2": { "output_name": "out2", "id": 40 }, "refGenomeSource|genomeFastaFiles": { "output_name": "output", "id": 16 }, "singlePaired|input1": { "output_name": "out1", "id": 40 } }, "tool_state": "{\"quantmode_output\": \"{\\\"__current_case__\\\": 0, \\\"quantMode\\\": \\\"-\\\"}\", \"__page__\": null, \"perf\": \"{\\\"outBAMsortingBinsN\\\": \\\"50\\\"}\", \"singlePaired\": \"{\\\"__current_case__\\\": 1, \\\"input1\\\": null, \\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\"}\", \"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\": \"\\\"\\\"\", \"input1|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"input2|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"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\\\": \\\"\\\"}\", \"algo\": \"{\\\"params\\\": {\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}}\"}", "id": 42, "tool_shed_repository": { "owner": "iuc", "changeset_revision": "b9e04854e2bb", "name": "rgrnastar", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "8c65e8cf-c0f0-411b-8f7b-11900857c66a", "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" }, "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": 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": "852b082d-3b6b-42ef-85e2-0e5c3a7490dc", "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": "mapped_reads", "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": "e3dd42e3-a16a-4c3a-ac87-cacf76d5c111", "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": "mapped_reads", "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": "507302bc-4eba-4a94-a617-16a7e572d393", "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": "c895ebd6-c274-4687-99a7-333127240530", "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" }