{ "uuid": "cd464b56-9a14-4603-8e53-e30440e4235e", "tags": [], "format-version": "0.1", "name": "Differential gene expression analysis of single-end NGS data using FastQC, Cutadapt, BWA, 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/trainings/raw/master/raw_data/rna/SE/rna_ctr.N1.fastq.gz\"}", "id": 0, "uuid": "670be551-0741-4545-ad6f-ca7beaa2a397", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N1.fastq.gz", "description": "" } ], "position": { "top": 10, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "1": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N2.fastq.gz\"}", "id": 1, "uuid": "59d26c44-0b89-4085-afea-ff6cb462643d", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N2.fastq.gz", "description": "" } ], "position": { "top": 130, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "2": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N3.fastq.gz\"}", "id": 2, "uuid": "23b58e8e-9e37-4d51-a72c-853181ecef03", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N3.fastq.gz", "description": "" } ], "position": { "top": 250, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "3": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N4.fastq.gz\"}", "id": 3, "uuid": "6eff2ecd-ce1c-414c-8606-1fdb0b95d8b1", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_ctr.N4.fastq.gz", "description": "" } ], "position": { "top": 370, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "4": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N1.fastq.gz\"}", "id": 4, "uuid": "d3e7fefd-ec77-44e3-850a-05c1239649b2", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N1.fastq.gz", "description": "" } ], "position": { "top": 490, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "5": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N2.fastq.gz\"}", "id": 5, "uuid": "5d2f4163-df8e-4d92-a6c1-b3663e77dbf3", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N2.fastq.gz", "description": "" } ], "position": { "top": 610, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "6": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N3.fastq.gz\"}", "id": 6, "uuid": "68306fea-3664-4518-94f2-ba60d637d665", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N3.fastq.gz", "description": "" } ], "position": { "top": 730, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "7": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N4.fastq.gz\"}", "id": 7, "uuid": "d8cd4891-f579-4ba8-9803-69920a61618b", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/SE/rna_treat.N4.fastq.gz", "description": "" } ], "position": { "top": 850, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "8": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/hg38.goi.fa\"}", "id": 8, "uuid": "5c7e924d-6fbd-4773-972d-a337e351c942", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/hg38.goi.fa", "description": "" } ], "position": { "top": 970, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "9": { "tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/hg38.goi.gtf\"}", "id": 9, "uuid": "b82b60d4-fe6a-4d08-9c92-f93c798d70cd", "errors": null, "name": "Input dataset", "label": null, "inputs": [ { "name": "https://github.com/destairdenbi/trainings/raw/master/raw_data/rna/hg38.goi.gtf", "description": "" } ], "position": { "top": 1090, "left": 10 }, "annotation": "", "content_id": null, "type": "data_input" }, "10": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "tool_version": "0.72+galaxy1", "outputs": [ { "type": "html", "name": "html_file" }, { "type": "txt", "name": "text_file" } ], "workflow_outputs": [], "input_connections": { "input_file": { "output_name": "output", "id": 0 } }, "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}", "id": 10, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e7b2202befea", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "02c872b1-902c-4fd9-8768-1651dab65341", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 10, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "type": "tool" }, "11": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_1": { "output_name": "output", "id": 0 } }, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 11, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "fa9ac884-f553-41f7-a1d3-b39f92de765b", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 970, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "12": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "tool_version": "0.72+galaxy1", "outputs": [ { "type": "html", "name": "html_file" }, { "type": "txt", "name": "text_file" } ], "workflow_outputs": [], "input_connections": { "input_file": { "output_name": "output", "id": 1 } }, "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}", "id": 12, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e7b2202befea", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "5297cdd4-0218-4ca2-8b77-4ac71bd23cc4", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 130, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "type": "tool" }, "13": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_1": { "output_name": "output", "id": 1 } }, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 13, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "545d7fa6-09b4-449a-ad91-e753732c0bbf", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1090, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "14": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "tool_version": "0.72+galaxy1", "outputs": [ { "type": "html", "name": "html_file" }, { "type": "txt", "name": "text_file" } ], "workflow_outputs": [], "input_connections": { "input_file": { "output_name": "output", "id": 2 } }, "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}", "id": 14, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e7b2202befea", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "54ad5734-642b-4ef1-89a6-8c1f1ce844c5", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 250, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "type": "tool" }, "15": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_1": { "output_name": "output", "id": 2 } }, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 15, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "54060c69-6ee1-4163-a6ee-ea0e9be358f1", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1210, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "16": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "tool_version": "0.72+galaxy1", "outputs": [ { "type": "html", "name": "html_file" }, { "type": "txt", "name": "text_file" } ], "workflow_outputs": [], "input_connections": { "input_file": { "output_name": "output", "id": 3 } }, "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}", "id": 16, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e7b2202befea", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "1ce32dfe-9f55-469d-b19f-be147d5e9c34", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 370, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "type": "tool" }, "17": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_1": { "output_name": "output", "id": 3 } }, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 17, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "c545476e-b840-4779-a5d6-09d00711c2ae", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1330, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "18": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "tool_version": "0.72+galaxy1", "outputs": [ { "type": "html", "name": "html_file" }, { "type": "txt", "name": "text_file" } ], "workflow_outputs": [], "input_connections": { "input_file": { "output_name": "output", "id": 4 } }, "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}", "id": 18, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e7b2202befea", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "4fd09209-1adb-461f-a13f-2b889814b1c9", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 490, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "type": "tool" }, "19": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_1": { "output_name": "output", "id": 4 } }, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 19, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "e48bed78-b9d9-4f0c-a03e-d7eafe6f25e6", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1450, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "20": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "tool_version": "0.72+galaxy1", "outputs": [ { "type": "html", "name": "html_file" }, { "type": "txt", "name": "text_file" } ], "workflow_outputs": [], "input_connections": { "input_file": { "output_name": "output", "id": 5 } }, "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}", "id": 20, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e7b2202befea", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "030491ea-883c-4c08-b689-ae3670a742d1", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 610, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "type": "tool" }, "21": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_1": { "output_name": "output", "id": 5 } }, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 21, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "9047324b-4ff6-4690-bf45-538f53d7b3f6", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1570, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "22": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "tool_version": "0.72+galaxy1", "outputs": [ { "type": "html", "name": "html_file" }, { "type": "txt", "name": "text_file" } ], "workflow_outputs": [], "input_connections": { "input_file": { "output_name": "output", "id": 6 } }, "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}", "id": 22, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e7b2202befea", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "cf73d1b2-5543-43c6-9417-aaf380624122", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 730, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "type": "tool" }, "23": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_1": { "output_name": "output", "id": 6 } }, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 23, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "3d36b370-090a-4b35-9437-340ce61685ce", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1690, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "24": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "tool_version": "0.72+galaxy1", "outputs": [ { "type": "html", "name": "html_file" }, { "type": "txt", "name": "text_file" } ], "workflow_outputs": [], "input_connections": { "input_file": { "output_name": "output", "id": 7 } }, "tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"null\", \"input_file\": \"null\", \"__page__\": null, \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"adapters\": \"null\", \"nogroup\": \"\\\"false\\\"\"}", "id": 24, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e7b2202befea", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "454fbdfe-e41f-4824-bfde-a9e77c7e388a", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 850, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "type": "tool" }, "25": { "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "tool_version": "1.16.6", "outputs": [ { "type": "fastqsanger", "name": "out1" }, { "type": "txt", "name": "report" } ], "workflow_outputs": [], "input_connections": { "library|input_1": { "output_name": "output", "id": 7 } }, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"info_file\\\": \\\"false\\\", \\\"multiple_output\\\": \\\"false\\\", \\\"report\\\": \\\"true\\\", \\\"rest_file\\\": \\\"false\\\", \\\"too_long_file\\\": \\\"false\\\", \\\"too_short_file\\\": \\\"false\\\", \\\"untrimmed_file\\\": \\\"false\\\", \\\"wildcard_file\\\": \\\"false\\\"}\", \"read_mod_options\": \"{\\\"length\\\": \\\"0\\\", \\\"length_tag\\\": \\\"\\\", \\\"nextseq_trim\\\": \\\"0\\\", \\\"prefix\\\": \\\"\\\", \\\"quality_cutoff\\\": \\\"20\\\", \\\"strip_suffix\\\": \\\"\\\", \\\"suffix\\\": \\\"\\\", \\\"trim_n\\\": \\\"false\\\"}\", \"adapter_options\": \"{\\\"count\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"mask_adapter\\\": \\\"false\\\", \\\"match_read_wildcards\\\": \\\" \\\", \\\"no_indels\\\": \\\"false\\\", \\\"no_trim\\\": \\\"false\\\", \\\"overlap\\\": \\\"3\\\"}\", \"library\": \"{\\\"__current_case__\\\": 0, \\\"input_1\\\": null, \\\"r1\\\": {\\\"adapters\\\": [], \\\"anywhere_adapters\\\": [], \\\"cut\\\": \\\"0\\\", \\\"front_adapters\\\": []}, \\\"type\\\": \\\"single\\\"}\", \"filter_options\": \"{\\\"discard\\\": \\\"false\\\", \\\"discard_untrimmed\\\": \\\"false\\\", \\\"max\\\": \\\"0\\\", \\\"max_n\\\": \\\"\\\", \\\"min\\\": \\\"20\\\", \\\"pair_filter\\\": \\\"any\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "id": 25, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "e4691e1589d3", "name": "cutadapt", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "8b14d703-9e2b-48c9-ab39-aeb40d823ea3", "errors": null, "name": "Cutadapt", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1810, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6", "type": "tool" }, "26": { "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1", "tool_version": "1.1.1", "outputs": [ { "type": "input", "name": "outfile" } ], "workflow_outputs": [], "input_connections": { "infile": { "output_name": "output", "id": 9 } }, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"code\": \"\\\"!/^#/ && $3==\\\\\\\"exon\\\\\\\"{if($7==\\\\\\\"+\\\\\\\"){ p[px++] = $1\\\\\\\"\\\\\\\\t\\\\\\\"$4\\\\\\\"\\\\\\\\t\\\\\\\"$5\\\\\\\"\\\\\\\\t.\\\\\\\\t.\\\\\\\\t\\\\\\\"$7 }else{ n[nx++] = $1\\\\\\\"\\\\\\\\t\\\\\\\"$4\\\\\\\"\\\\\\\\t\\\\\\\"$5\\\\\\\"\\\\\\\\t.\\\\\\\\t.\\\\\\\\t\\\\\\\"$7 } if(nx>1000 && px>1000){ exit } } END{ for(i in p){ print p[i] } for(i in n){ print n[i] } }\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}", "id": 26, "tool_shed_repository": { "owner": "bgruening", "changeset_revision": "0a8c6b61f0f4", "name": "text_processing", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "bb2acba1-8c09-415f-bca3-4d89823c6467", "errors": null, "name": "Text reformatting", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 1930, "left": 230 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1", "type": "tool" }, "27": { "tool_id": "toolshed.g2.bx.psu.edu/repos/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": 8 }, "input_type|fastq_input1": { "output_name": "out1", "id": 11 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"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": 27, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "e1d57dbd-3d1f-4265-b657-91dfc356779b", "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" }, "28": { "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": 8 }, "input_type|fastq_input1": { "output_name": "out1", "id": 13 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"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": 28, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "9c74f039-f9ef-4715-ae43-0e9e0a8edd72", "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" }, "29": { "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": 8 }, "input_type|fastq_input1": { "output_name": "out1", "id": 15 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"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": 29, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "82404386-4d2d-4eee-8ed3-e35974d5f00a", "errors": null, "name": "Map with BWA", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 250, "left": 450 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "type": "tool" }, "30": { "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": 8 }, "input_type|fastq_input1": { "output_name": "out1", "id": 17 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"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": 30, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "21b2afb7-5a53-4654-bbd0-3f081c3b5530", "errors": null, "name": "Map with BWA", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 370, "left": 450 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "type": "tool" }, "31": { "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": 8 }, "input_type|fastq_input1": { "output_name": "out1", "id": 19 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"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": 31, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "b332a93f-5659-434c-955a-696bc939f8ae", "errors": null, "name": "Map with BWA", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 490, "left": 450 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "type": "tool" }, "32": { "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": 8 }, "input_type|fastq_input1": { "output_name": "out1", "id": 21 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"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": 32, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "22dad678-22d8-4d18-9a7d-682a0313fc94", "errors": null, "name": "Map with BWA", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 610, "left": 450 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "type": "tool" }, "33": { "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": 8 }, "input_type|fastq_input1": { "output_name": "out1", "id": 23 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"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": 33, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "89232b4a-4212-4a23-b272-cb182aec127e", "errors": null, "name": "Map with BWA", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 730, "left": 450 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "type": "tool" }, "34": { "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": 8 }, "input_type|fastq_input1": { "output_name": "out1", "id": 25 } }, "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"adv_se_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_se_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input1\\\": null, \\\"input_type_selector\\\": \\\"single\\\"}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"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": 34, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "01ac0a5fedc3", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "5adef389-fe74-46f1-bc47-dcea46487313", "errors": null, "name": "Map with BWA", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 850, "left": 450 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "type": "tool" }, "35": { "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": "bam_output", "id": 27 }, "gfffile": { "output_name": "output", "id": 9 } }, "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\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 35, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "f0a65002-0157-4f7e-8d5a-1f9e8583c7ef", "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" }, "36": { "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": "bam_output", "id": 28 }, "gfffile": { "output_name": "output", "id": 9 } }, "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\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 36, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "96d119ad-cfef-4b30-8b33-7bd2ab643669", "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" }, "37": { "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": "bam_output", "id": 29 }, "gfffile": { "output_name": "output", "id": 9 } }, "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\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 37, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "df4008f9-89ee-4e74-b8f6-3ae64b1683ab", "errors": null, "name": "htseq-count", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 370, "left": 670 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1", "type": "tool" }, "38": { "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": "bam_output", "id": 30 }, "gfffile": { "output_name": "output", "id": 9 } }, "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\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 38, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "9e5ad24b-daed-440b-ac49-d9fb0adf4c58", "errors": null, "name": "htseq-count", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 490, "left": 670 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1", "type": "tool" }, "39": { "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": "bam_output", "id": 31 }, "gfffile": { "output_name": "output", "id": 9 } }, "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\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 39, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "aa2d3dd5-eae1-4426-8091-d06bffe577a6", "errors": null, "name": "htseq-count", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 610, "left": 670 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1", "type": "tool" }, "40": { "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": "bam_output", "id": 32 }, "gfffile": { "output_name": "output", "id": 9 } }, "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\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 40, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "4f0272e9-b762-432c-affa-c7bdaa399dec", "errors": null, "name": "htseq-count", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 730, "left": 670 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1", "type": "tool" }, "41": { "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": "bam_output", "id": 33 }, "gfffile": { "output_name": "output", "id": 9 } }, "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\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 41, "tool_shed_repository": { "owner": "lparsons", "changeset_revision": "67b0b160903a", "name": "htseq_count", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "0e11890e-fa8d-4120-a61f-8724a1cb2a2a", "errors": null, "name": "htseq-count", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 850, "left": 670 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1", "type": "tool" }, "42": { "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1", "tool_version": "2.6.4.1", "outputs": [ { "type": "txt", "name": "output" } ], "workflow_outputs": [], "input_connections": { "input": { "output_name": "bam_output", "id": 34 }, "refgene": { "output_name": "outfile", "id": 26 } }, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"refgene\": \"null\", \"sample_size\": \"\\\"200000\\\"\", \"mapq\": \"\\\"0\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "id": 42, "tool_shed_repository": { "owner": "nilesh", "changeset_revision": "1a052c827e88", "name": "rseqc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "439d8d4e-3d05-44e9-94d0-579da0f745d3", "errors": null, "name": "Infer Experiment", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 10, "left": 670 }, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1", "type": "tool" }, "43": { "tool_id": "toolshed.g2.bx.psu.edu/repos/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": "bam_output", "id": 34 }, "gfffile": { "output_name": "output", "id": 9 } }, "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\\\"\", \"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": "6fc4d5b3-c053-4684-95e4-b44215774b34", "errors": null, "name": "htseq-count", "post_job_actions": {}, "label": null, "inputs": [], "position": { "top": 970, "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/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 }, { "output_name": "counts", "id": 41 }, { "output_name": "counts", "id": 40 }, { "output_name": "counts", "id": 39 } ], "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": [ { "output_name": "counts", "id": 38 }, { "output_name": "counts", "id": 37 }, { "output_name": "counts", "id": 36 }, { "output_name": "counts", "id": 35 } ] }, "tool_state": "{\"fit_type\": \"\\\"1\\\"\", \"__page__\": null, \"normVST\": \"\\\"false\\\"\", \"tximport\": \"{\\\"__current_case__\\\": 1, \\\"tximport_selector\\\": \\\"count\\\"}\", \"esf\": \"\\\"\\\"\", \"outlier_replace_off\": \"\\\"false\\\"\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"auto_mean_filter_off\": \"\\\"false\\\"\", \"header\": \"\\\"true\\\"\", \"normCounts\": \"\\\"false\\\"\", \"outlier_filter_off\": \"\\\"false\\\"\", \"many_contrasts\": \"\\\"false\\\"\", \"batch_factors\": \"null\", \"pdf\": \"\\\"true\\\"\", \"normRLog\": \"\\\"false\\\"\", \"select_data\": \"{\\\"__current_case__\\\": 1, \\\"how\\\": \\\"datasets_per_level\\\", \\\"rep_factorName\\\": [{\\\"__index__\\\": 0, \\\"factorName\\\": \\\"treatment\\\", \\\"rep_factorLevel\\\": [{\\\"__index__\\\": 0, \\\"countsFile\\\": null, \\\"factorLevel\\\": \\\"control\\\"}, {\\\"__index__\\\": 1, \\\"countsFile\\\": null, \\\"factorLevel\\\": \\\"treated\\\"}]}]}\"}", "id": 44, "tool_shed_repository": { "owner": "iuc", "changeset_revision": "0696db066a5b", "name": "deseq2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "uuid": "98591ab5-90fc-4c44-9f5e-5afaf00ee881", "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" }