{ "uuid": "6886e05c-d1f8-41e0-b61a-3f74c138cf47", "tags": [], "format-version": "0.1", "name": "Differential gene expression analysis of paired-end NGS data using FastQC, Trimmomatic, STAR, AWK, Infer Experiment, HTSeq-count, 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": "aa8da882-2108-46cd-8e53-fad2bed6aa98", "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": "de0e87b1-033e-4c98-b7a6-ab7ae81158b7", "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": "b312c342-1068-4f80-b1f1-f7ea69d1f59c", "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": "e44f9a16-d4ea-4f9c-9961-4edde2f07b69", "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": "ba8af493-d1b1-4e58-b992-15773a665577", "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": "85d4865a-11ae-4f6c-94b6-8c2974a742a9", "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": "b167556f-9433-496b-ade3-49cdb1319c90", "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": "42c3130a-7e9b-4a93-8754-60a9f51701b6", "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": "b005275d-2eec-477a-a762-e7b56c02e845", "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": "978f3b2c-5a21-4d81-85b4-63aee873421a", "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": "58c2103c-d6db-43a4-8da3-2c14f3227efb", "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": "325d7533-d32e-44e9-816e-767db473d7ac", "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": "37276f30-e388-492c-82a4-ffe53a6162c5", "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": "e0cde292-295a-4662-b3da-8ad435477c19", "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": "424d069e-a1ce-4281-a2e6-fbaf128cbc19", "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": "0463b653-316c-41d7-b213-f5bb8eaa7394", "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": "45da8519-3c3f-403d-8286-536fdffe7b4b", "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": "01e17307-dfee-438f-b646-9f7df07752cf", "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": "294cb210-c8e5-4f11-b8df-703b27e4cf85", "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": "5813d146-822e-4b13-b1d9-7f533493d178", "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": "f986c7fa-927c-40cf-af82-7a836ffdbf1f", "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": "165866b5-3f38-47c6-8652-e49a596e4a8a", "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": "f59c380b-50d3-4ab7-a137-0ae6c2f14580", "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": "159042a4-e315-468c-96d6-e3e55fd88198", "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": "60cf6fc8-ec68-46e9-867c-49ad04310032", "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": "d68a66b4-7aab-47b0-884f-18e914aa1f93", "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": "1eaa5390-95e8-4a19-a149-3f8ce4b00ea8", "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": "6036b062-9bc3-415e-a01e-aea2b24eac26", "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": "60773062-b3dc-4bf8-947d-35c9ac6d9441", "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": "1e0fda27-1a5e-4147-b45f-6d3ca41ab435", "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": "53482bfe-c929-4309-bfd4-880f33651862", "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": "b15294bd-4442-4cd8-bee6-0f9e6c217fd7", "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": "1d0a0312-0368-48dc-aeb9-05878f1d3777", "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": "8e46446b-db2e-4c40-8a06-de5119a60e1b", "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": "ba8e5eea-a7ae-46f5-91fc-e28ae2fd71e0", "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": "c53e55d2-e930-4569-ae56-2a978d1d9acd", "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": "a06cb669-ffe2-4f38-894e-390de5ff68fd", "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": "77bf94fc-1239-4258-b63f-586c7c94e034", "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": "ebc4cb94-5eec-45bd-a4e3-55d4d53cfb41", "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": "2bd2facf-ead2-42af-8ad3-9a2de4b01196", "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": "cec88303-5b2d-4de2-9b52-fa1204a010b3", "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/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": "fastq_out_r2_paired", "id": 39 }, "refGenomeSource|genomeFastaFiles": { "output_name": "output", "id": 16 }, "singlePaired|input1": { "output_name": "fastq_out_r1_paired", "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": "633619a8-5ef1-4f09-a6cf-8197d61cd6b1", "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": "fastq_out_r2_paired", "id": 40 }, "refGenomeSource|genomeFastaFiles": { "output_name": "output", "id": 16 }, "singlePaired|input1": { "output_name": "fastq_out_r1_paired", "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": "1de05a12-0d4d-4486-8253-7b71ac759ea3", "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/lparsons/htseq_count/htseq_count/0.9.1", "tool_version": "0.9.1", "outputs": [ { "type": "tabular", "name": "counts" }, { "type": "tabular", "name": "othercounts" } ], "workflow_outputs": [], "input_connections": { "samfile": { "output_name": "mapped_reads", "id": 41 }, "gfffile": { "output_name": "output", "id": 17 } }, "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"samfile|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 43, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "25eeb4de-812d-4eee-aa89-ea72b6675a6c", "errors": null, "name": "htseq-count", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 250, "left": 670 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1", "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": "62663e67-5bd3-44ee-b5d7-b5369a13e928", "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/lparsons/htseq_count/htseq_count/0.9.1", "tool_version": "0.9.1", "outputs": [ { "type": "tabular", "name": "counts" }, { "type": "tabular", "name": "othercounts" } ], "workflow_outputs": [], "input_connections": { "samfile": { "output_name": "mapped_reads", "id": 42 }, "gfffile": { "output_name": "output", "id": 17 } }, "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"advanced_options\": \"{\\\"__current_case__\\\": 0, \\\"advanced_options_selector\\\": \\\"simple\\\"}\", \"idattr\": \"\\\"gene_id\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"no\\\"\", \"samfile\": \"null\", \"gfffile\": \"null\", \"minaqual\": \"\\\"0\\\"\", \"mode\": \"\\\"union\\\"\", \"samfile|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 45, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "b51bb7b5-cf29-4278-9b28-24993b332f43", "errors": null, "name": "htseq-count", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 130, "left": 670 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1", "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": "counts", "id": 43 }, "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": { "output_name": "counts", "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": "a323408c-51ab-4da3-bd37-d1f9582517fa", "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" }