{ "uuid": "c6e313ad-a73f-421f-a48b-2c3e43d3ab90", "tags": [], "format-version": "0.1", "name": "Differential gene expression analysis of paired-end NGS data using FastQC, PRINSEQ, BWA, 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": "5105f210-9bd8-4c27-9054-68689ec7f2e3", "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": "cfd7ddb8-9727-441e-ad54-0a727bf63bb4", "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": "9968a7c8-06f4-442a-8016-ce8e7e842916", "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": "12ebe65e-f69b-45f7-9827-285a02769824", "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": "b55bc2f2-6bf7-4aa1-a7c4-bf5a8cdc7658", "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": "c101cf76-f8ab-45c3-9b2b-137581c444e1", "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": "203ad2e0-86aa-498b-a1d1-7f900e1a3d9f", "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": "01a2bee0-6423-4cb4-bf60-17835f078af3", "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": "d8b4189d-7d67-47e3-91d9-6e7f08638c4a", "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": "66e37e02-bf06-48c4-9b02-7e4127897037", "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": "2c938f59-a6c5-4c32-af7c-dccffe02883d", "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": "77f96146-6ab5-4887-904e-9048e17a8b84", "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": "b803279d-1df5-4180-94ff-90cb0de24dc0", "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": "2531d85d-7906-49d5-99ba-a3af43da3a68", "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": "319fa57b-aa6e-437f-a308-d60d9c001bdf", "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": "13d4f7d7-6c29-4e7c-a16d-199190749e20", "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": "c0f883cf-8c04-4b65-9364-3600009364e1", "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": "793181af-408c-40d5-adef-6c34889af32d", "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": "b7bc50d5-e136-4621-99ed-1996ad780f66", "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": "5d9f82f0-f28e-4834-a8bd-f7344098d248", "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": "ea598c82-674c-4b3e-84f5-f0051a199370", "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": "9e35c8d4-3901-42eb-8b1c-9397c6220ebf", "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": "c6f3c287-10f5-4f4f-a6c0-3b17489a395d", "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": "88e99523-1653-49ae-94c4-54e600d52a26", "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": "40b0607b-60dd-425c-a39b-6661d1ca3f98", "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": "f7fde7d8-59f9-4214-a9ca-1cc74a7a7c9e", "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": "7d0e6e55-9105-481b-bd2f-6ba84802ad55", "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": "72d2df6c-c448-4042-89d9-4a8251c6fffc", "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": "9f4e4a88-6a38-437a-84bb-912efae5cbbc", "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": "3e8badb2-95e9-4015-8474-bd89224ea93c", "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": "82aa8584-c944-4821-a1ba-fd11a2a4518f", "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": "50d70622-dedd-43b2-9ed9-1da06c9f519b", "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": "cda71b47-d7a5-4c02-907f-04a7dee0e014", "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": "e8130ce0-8dba-40db-ba5d-a186bf881db1", "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": "0b2d5d7e-4509-4826-a390-3a751fe4c7ca", "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": "68971819-4c35-4b49-97a3-a839975e9d01", "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": "0fb35495-a5ce-454d-b5cf-0e4a1502edc7", "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": "7b8adb21-6036-4f15-b349-b2832d83f44a", "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": "a260e026-7b1f-4054-b406-83faa3958139", "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/iuc/prinseq/prinseq/0.20.4", "tool_version": "0.20.4", "outputs": [ { "type": "input", "name": "good_sequences_1_file" }, { "type": "input", "name": "good_sequences_1_singletons_file" }, { "type": "input", "name": "rejected_sequence_1_file" }, { "type": "input", "name": "good_sequences_2_file" }, { "type": "input", "name": "good_sequences_2_singletons_file" }, { "type": "input", "name": "rejected_sequence_2_file" } ], "workflow_outputs": [], "input_connections": { "seq_type|input_mate1": { "output_name": "output", "id": 19 }, "seq_type|input_mate2": { "output_name": "output", "id": 18 } }, "tool_state": "{\"seq_type\": \"{\\\"__current_case__\\\": 1, \\\"input_mate1\\\": null, \\\"input_mate2\\\": null, \\\"seq_type_opt\\\": \\\"paired\\\"}\", \"__page__\": null, \"filter_treatments\": \"{\\\"__current_case__\\\": 0, \\\"apply_filter_treatments\\\": \\\"true\\\", \\\"base_content_filter_treatments\\\": {\\\"GC_perc_content_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_GC_perc_content_filter_treatments\\\": \\\"false\\\"}, \\\"N_number_content_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_N_number_content_filter_treatments\\\": \\\"false\\\"}, \\\"N_percentage_content_filter_treatments\\\": {\\\"N_percentage_content_filter_treatment_value\\\": \\\"2\\\", \\\"__current_case__\\\": 0, \\\"apply_N_percentage_content_filter_treatments\\\": \\\"true\\\"}, \\\"__current_case__\\\": 0, \\\"apply_base_content_filter_treatments\\\": \\\"true\\\", \\\"apply_other_base_content_filter_treatments\\\": \\\"false\\\"}, \\\"complexity_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_complexity_filter_treatments\\\": \\\"false\\\"}, \\\"length_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_length_filter_treatments\\\": \\\"true\\\", \\\"max_length_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_max_length_filter_treatments\\\": \\\"false\\\"}, \\\"min_length_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_min_length_filter_treatments\\\": \\\"true\\\", \\\"min_length_filter_treatment_value\\\": \\\"20\\\"}}, \\\"quality_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_quality_filter_treatments\\\": \\\"true\\\", \\\"max_quality_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_max_quality_filter_treatments\\\": \\\"false\\\"}, \\\"mean_quality_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_mean_quality_filter_treatments\\\": \\\"true\\\", \\\"max_mean_quality_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_max_mean_quality_filter_treatments\\\": \\\"false\\\"}, \\\"min_mean_quality_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_min_mean_quality_filter_treatments\\\": \\\"true\\\", \\\"min_mean_quality_filter_treatment_value\\\": \\\"20\\\"}}, \\\"min_quality_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_min_quality_filter_treatments\\\": \\\"false\\\"}}}\", \"__rerun_remap_job_id__\": null, \"trimming_treatments\": \"{\\\"__current_case__\\\": 0, \\\"apply_trimming_treatments\\\": \\\"true\\\", \\\"length_trimming_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_length_trimming_treatments\\\": \\\"false\\\"}, \\\"position_trimming_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_position_trimming_treatments\\\": \\\"false\\\"}, \\\"quality_trimming_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_quality_trimming_treatments\\\": \\\"true\\\", \\\"left_quality_trimming_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_left_quality_trimming_treatments\\\": \\\"false\\\"}, \\\"right_quality_trimming_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_right_quality_trimming_treatments\\\": \\\"true\\\", \\\"right_quality_trimming_treatment_value\\\": \\\"20\\\"}, \\\"rule_quality_trimming_treatments\\\": \\\"lt\\\", \\\"step_quality_trimming_treatments\\\": \\\"1\\\", \\\"type_quality_trimming_treatments\\\": \\\"mean\\\", \\\"window_quality_trimming_treatments\\\": \\\"4\\\"}, \\\"tail_trimming_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_tail_trimming_treatments\\\": \\\"false\\\"}}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 39, "tool_shed_repository": { "owner": "iuc", "changeset_revision": "02befcb391f5", "name": "prinseq", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "01599026-59ad-45ed-89d0-f1d280820504", "errors": null, "name": "PRINSEQ", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 2050, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4", "type": "tool" }, "40": { "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4", "tool_version": "0.20.4", "outputs": [ { "type": "input", "name": "good_sequences_1_file" }, { "type": "input", "name": "good_sequences_1_singletons_file" }, { "type": "input", "name": "rejected_sequence_1_file" }, { "type": "input", "name": "good_sequences_2_file" }, { "type": "input", "name": "good_sequences_2_singletons_file" }, { "type": "input", "name": "rejected_sequence_2_file" } ], "workflow_outputs": [], "input_connections": { "seq_type|input_mate1": { "output_name": "output", "id": 21 }, "seq_type|input_mate2": { "output_name": "output", "id": 20 } }, "tool_state": "{\"seq_type\": \"{\\\"__current_case__\\\": 1, \\\"input_mate1\\\": null, \\\"input_mate2\\\": null, \\\"seq_type_opt\\\": \\\"paired\\\"}\", \"__page__\": null, \"filter_treatments\": \"{\\\"__current_case__\\\": 0, \\\"apply_filter_treatments\\\": \\\"true\\\", \\\"base_content_filter_treatments\\\": {\\\"GC_perc_content_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_GC_perc_content_filter_treatments\\\": \\\"false\\\"}, \\\"N_number_content_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_N_number_content_filter_treatments\\\": \\\"false\\\"}, \\\"N_percentage_content_filter_treatments\\\": {\\\"N_percentage_content_filter_treatment_value\\\": \\\"2\\\", \\\"__current_case__\\\": 0, \\\"apply_N_percentage_content_filter_treatments\\\": \\\"true\\\"}, \\\"__current_case__\\\": 0, \\\"apply_base_content_filter_treatments\\\": \\\"true\\\", \\\"apply_other_base_content_filter_treatments\\\": \\\"false\\\"}, \\\"complexity_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_complexity_filter_treatments\\\": \\\"false\\\"}, \\\"length_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_length_filter_treatments\\\": \\\"true\\\", \\\"max_length_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_max_length_filter_treatments\\\": \\\"false\\\"}, \\\"min_length_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_min_length_filter_treatments\\\": \\\"true\\\", \\\"min_length_filter_treatment_value\\\": \\\"20\\\"}}, \\\"quality_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_quality_filter_treatments\\\": \\\"true\\\", \\\"max_quality_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_max_quality_filter_treatments\\\": \\\"false\\\"}, \\\"mean_quality_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_mean_quality_filter_treatments\\\": \\\"true\\\", \\\"max_mean_quality_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_max_mean_quality_filter_treatments\\\": \\\"false\\\"}, \\\"min_mean_quality_filter_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_min_mean_quality_filter_treatments\\\": \\\"true\\\", \\\"min_mean_quality_filter_treatment_value\\\": \\\"20\\\"}}, \\\"min_quality_filter_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_min_quality_filter_treatments\\\": \\\"false\\\"}}}\", \"__rerun_remap_job_id__\": null, \"trimming_treatments\": \"{\\\"__current_case__\\\": 0, \\\"apply_trimming_treatments\\\": \\\"true\\\", \\\"length_trimming_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_length_trimming_treatments\\\": \\\"false\\\"}, \\\"position_trimming_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_position_trimming_treatments\\\": \\\"false\\\"}, \\\"quality_trimming_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_quality_trimming_treatments\\\": \\\"true\\\", \\\"left_quality_trimming_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_left_quality_trimming_treatments\\\": \\\"false\\\"}, \\\"right_quality_trimming_treatments\\\": {\\\"__current_case__\\\": 0, \\\"apply_right_quality_trimming_treatments\\\": \\\"true\\\", \\\"right_quality_trimming_treatment_value\\\": \\\"20\\\"}, \\\"rule_quality_trimming_treatments\\\": \\\"lt\\\", \\\"step_quality_trimming_treatments\\\": \\\"1\\\", \\\"type_quality_trimming_treatments\\\": \\\"mean\\\", \\\"window_quality_trimming_treatments\\\": \\\"4\\\"}, \\\"tail_trimming_treatments\\\": {\\\"__current_case__\\\": 1, \\\"apply_tail_trimming_treatments\\\": \\\"false\\\"}}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 40, "tool_shed_repository": { "owner": "iuc", "changeset_revision": "02befcb391f5", "name": "prinseq", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "5dc639ea-5e11-43e7-8054-b62b75ecc159", "errors": null, "name": "PRINSEQ", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1930, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4", "type": "tool" }, "41": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "tool_version": "0.7.17.4", "outputs": [ { "type": "bam", "name": "bam_output" } ], "workflow_outputs": [], "input_connections": { "reference_source|ref_file": { "output_name": "output", "id": 16 }, "input_type|fastq_input1": { "output_name": "good_sequences_1_file", "id": 39 }, "input_type|fastq_input2": { "output_name": "good_sequences_2_file", "id": 39 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 0, \\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"fastq_input2\\\": null, \\\"input_type_selector\\\": \\\"paired\\\"}\", \"__rerun_remap_job_id__\": null, \"fastq_input2|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"fastq_input1|__identifier__\": \"\\\"rna_treat.R1.N1.fastq.gz\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 41, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "064b6461-9030-4d84-8e77-b077250c239d", "errors": null, "name": "Map with BWA", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 130, "left": 450 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "type": "tool" }, "42": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "tool_version": "0.7.17.4", "outputs": [ { "type": "bam", "name": "bam_output" } ], "workflow_outputs": [], "input_connections": { "reference_source|ref_file": { "output_name": "output", "id": 16 }, "input_type|fastq_input1": { "output_name": "good_sequences_1_file", "id": 40 }, "input_type|fastq_input2": { "output_name": "good_sequences_2_file", "id": 40 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 0, \\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"fastq_input2\\\": null, \\\"input_type_selector\\\": \\\"paired\\\"}\", \"__rerun_remap_job_id__\": null, \"fastq_input2|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"fastq_input1|__identifier__\": \"\\\"rna_ctr.R1.N1.fastq.gz\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 42, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "b875e381-2301-4f6b-a3b8-8df6e8a1246d", "errors": null, "name": "Map with BWA", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 10, "left": 450 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "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": "bam_output", "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": "6d6016da-a307-4b2a-96e4-6fc3483773e6", "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": "bam_output", "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": "7c24d632-50ee-45f2-a305-fefb88b338fb", "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": "bam_output", "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": "183a85dd-f783-4512-84a6-6824e198642e", "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": "cb558979-99a0-4cf3-9de8-9514b82826f1", "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" }