From 598e5bbc3f1bf458bc0cc6e383cca181c3b7e614 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Thu, 24 Oct 2024 18:11:49 +0200 Subject: [PATCH 1/4] Add new ChIP-Seq WF that handles replicates and controls --- .../.dockstore.yml | 11 + .../.workflowhub.yml | 5 + .../CHANGELOG.md | 5 + .../README.md | 55 + ...pseq-pe-with-replicates-controls-tests.yml | 86 + .../chipseq-pe-with-replicates-controls.ga | 3692 +++++++++++++++++ .../test-data/test_sample_sheet.tsv | 4 + 7 files changed, 3858 insertions(+) create mode 100644 workflows/epigenetics/chipseq-pe-with-replicates-controls/.dockstore.yml create mode 100644 workflows/epigenetics/chipseq-pe-with-replicates-controls/.workflowhub.yml create mode 100644 workflows/epigenetics/chipseq-pe-with-replicates-controls/CHANGELOG.md create mode 100644 workflows/epigenetics/chipseq-pe-with-replicates-controls/README.md create mode 100644 workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml create mode 100644 workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls.ga create mode 100644 workflows/epigenetics/chipseq-pe-with-replicates-controls/test-data/test_sample_sheet.tsv diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/.dockstore.yml b/workflows/epigenetics/chipseq-pe-with-replicates-controls/.dockstore.yml new file mode 100644 index 000000000..9cf868614 --- /dev/null +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/.dockstore.yml @@ -0,0 +1,11 @@ +version: 1.2 +workflows: +- name: main + subclass: Galaxy + publish: true + primaryDescriptorPath: /chipseq-pe-with-replicates-controls.ga + testParameterFiles: + - /chipseq-pe-with-replicates-controls-tests.yml + authors: + - name: Wolfgang Maier + orcid: 0000-0002-9464-6640 diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/.workflowhub.yml b/workflows/epigenetics/chipseq-pe-with-replicates-controls/.workflowhub.yml new file mode 100644 index 000000000..64a998bcc --- /dev/null +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/.workflowhub.yml @@ -0,0 +1,5 @@ +version: '0.1' +registries: +- url: https://workflowhub.eu + project: iwc + workflow: chipseq-pe-with-replicates-controls/main diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/CHANGELOG.md b/workflows/epigenetics/chipseq-pe-with-replicates-controls/CHANGELOG.md new file mode 100644 index 000000000..c4efbee87 --- /dev/null +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/CHANGELOG.md @@ -0,0 +1,5 @@ +# Changelog + +## [0.1] 2024-10-22 + +Initial release diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/README.md b/workflows/epigenetics/chipseq-pe-with-replicates-controls/README.md new file mode 100644 index 000000000..0eaa7db29 --- /dev/null +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/README.md @@ -0,0 +1,55 @@ +# Quality control, mapping and peaks identification for ChIP-Seq replicates with controls + +This workflow is for analyzing batches of ChIP-Seq samples with controls and replicates from paired-end sequenced reads to called peaks. + +It uses: +- fastp for sequenced reads pre-processing, +- bowtie2 for mapping +- MACS2 for peak calling +- deeptools for cross-sample correlation and averaging + +The workflow provides quality control at the level of sequenced reads, mapping results and called peaks and visualizes correlation between samples. + +## Input datasets + +- Sequencing data: this must be provided as a single list collection of paired fastq datasets of all samples. +- Sample sheet: this is expected to be a 4-column tabular dataset that describes samples, their association with each other and with conditions and replicates. + + The first column of the file must list all samples with their names matching the element names in the Sequencing data collection. Samples can be listed in any order. + The second column is used to specify the specific experimental condition that each sample represents. There is no formal restriction on this column, but values should be kept short for readable reports. + The third column is used to specify the replicate that each sample belongs to. There is no formal restriction to replicate identifiers, but they should be kept as short as possible. At least two replicates are required per condition, but different conditions can have different numbers of replicates. + The fourth column must provide the name of the sample that serves as the control for the sample described on each line. Different samples can be associated with the same control sample. + Control samples must also be listed on their own lines just like regular samples, but must use . or - as the value of the fourth column. The value of the third column (replicate ID) is ignored for control sample lines so may also be set to . or -. + + Here's an example sample sheet: + + SRR5680995 input - - + SRR5680996 H3K4me3 rep1 SRR5680995 + SRR5680997 H3K27me3 rep1 SRR5680995 + SRR5681007 H3K27me3 rep2 SRR5681005 + SRR5681006 H3K4me3 rep2 SRR5681005 + SRR5680998 CTCF rep1 SRR5680995 + SRR5681008 CTCF rep2 SRR5681005 + SRR5681005 input - - + + This declares an experimental design with three conditions - H3K4me3, H3K27me3 and CTCF - with two replicates per condition and one input control per replicate. The control sample SRR5680995 is declared as the shared control for all samples from replicate rep1, SRR5681005 as the control for all samples from replicate rep2. + +## Input parameters + +- Reference genome: set this to the reference genome of your organism of interest; used at the read mapping step +- Sequencing adapter - forward (optional) +- Sequencing aadapter - reverse (optional) +- Effective genome size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes). +- Average size of sequenced fragments: used for deeptools-base QC + +## Outputs: + +- MultiQC analysis reports: +- Sample fingerprints: +- Between-samples correlation plot: +- Clustered heatmap of peaks across samples: +- Peak regions called by MACS2: +- Positions of summits of MACS2-called peaks: +- Peaks per replicate: +- Peaks averaged across replicates: + diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml b/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml new file mode 100644 index 000000000..8679b7874 --- /dev/null +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml @@ -0,0 +1,86 @@ +- doc: Test outline for ChIPseq-PE-with-replicates-controls workflow + job: + Sample sheet: + class: File + path: test-data/test_sample_sheet.tsv + filetype: tabular + Sequencing data: + class: Collection + collection_type: list:paired + elements: + - class: Collection + type: paired + identifier: SRR5204807 + elements: + - identifier: forward + class: File + location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204807_Spt5-ChIP_IP1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz + filetype: fastqsanger.gz + - identifier: reverse + class: File + location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204807_Spt5-ChIP_IP1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz + filetype: fastqsanger.gz + - class: Collection + type: paired + identifier: SRR5204808 + elements: + - identifier: forward + class: File + location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204808_Spt5-ChIP_IP2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz + filetype: fastqsanger.gz + - identifier: reverse + class: File + location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204808_Spt5-ChIP_IP2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz + filetype: fastqsanger.gz + - class: Collection + type: paired + identifier: SRR5204809 + elements: + - identifier: forward + class: File + location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz + filetype: fastqsanger.gz + - identifier: reverse + class: File + location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz + filetype: fastqsanger.gz + - class: Collection + type: paired + identifier: SRR5204810 + elements: + - identifier: forward + class: File + location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz + filetype: fastqsanger.gz + - identifier: reverse + class: File + location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz + filetype: fastqsanger.gz + Reference genome: "sacCer3" + Effective genome size: 12000000 + Average size of sequenced fragments: 200 + outputs: + multiqc_stats: + asserts: + has_n_lines: + n: 5 + has_text_matching: + expression: "SRR5204807_Spt5_rep1\t163.0\t0.0\t0.0\t844.+" + macs2_report: + element_tests: + wt_H3K4me3: + asserts: + - that: "has_text" + text: "# name = SRR5204807_Spt5_rep1" + - that: "has_text" + text: "# fragment size is determined as 163 bps" + - that: "has_text" + text: "# fragments after filtering in treatment: 86394" + mapping_stats: + element_tests: + SRR5204807_Spt5_rep1: + asserts: + - that: "has_text" + text: "3067 (3.14%) aligned concordantly 0 times" + - that: "has_text" + text: "80795 (82.60%) aligned concordantly exactly 1 time" diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls.ga b/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls.ga new file mode 100644 index 000000000..8984ff77c --- /dev/null +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls.ga @@ -0,0 +1,3692 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "A workflow for analyzing batches of ChIP-Seq samples with controls and replicates from paired-end sequenced reads to called peaks.", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "0000-0002-9464-6640", + "name": "Wolfgang Maier" + } + ], + "format-version": "0.1", + "license": "MIT", + "release": "0.1", + "name": "Quality control, mapping and peaks identification for ChIP-Seq replicates with controls", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "Four-column tabular dataset that describes the experimental design (see https://github.com/iwc-workflows/chipseq-pe-with-replicates-controls/blob/v0.1/README.md#input-datasets)", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Four-column tabular dataset that describes the experimental design (see https://github.com/iwc-workflows/chipseq-pe-with-replicates-controls/blob/v0.1/README.md#input-datasets)", + "name": "Sample sheet" + } + ], + "label": "Sample sheet", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 521.6343346071014 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "0b215137-17c5-4664-9146-29ab4f4aee98", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "List of pairs collection with outer IDs as specified in the sample sheet", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "List of pairs collection with outer IDs as specified in the sample sheet", + "name": "Sequencing data" + } + ], + "label": "Sequencing data", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 17.927373146289256, + "top": 776.0808460883304 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "5e044120-fe3e-4617-b2f9-ff2320eecb4e", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "Reference genome of organism of interest cached on the Galaxy server", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Reference genome of organism of interest cached on the Galaxy server", + "name": "Reference genome" + } + ], + "label": "Reference genome", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 995.0372542525865, + "top": 727.5163925231486 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "804c67ca-926d-485a-9e53-67a7aba494f7", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC ", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC ", + "name": "Sequencing adapter - forward" + } + ], + "label": "Sequencing adapter - forward", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 827.5595006162614, + "top": 1087.193451640713 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "cac41a72-6029-4df9-96a3-50f34e412101", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "name": "Sequencing adapter - reverse" + } + ], + "label": "Sequencing adapter - reverse", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 826.5021242474772, + "top": 1187.8400692669659 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "fbb01f6e-b7f4-42d1-8c58-76921b3553ab", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "Used by MACS2: H. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "Used by MACS2: H. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000", + "name": "Effective genome size" + } + ], + "label": "Effective genome size", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 880.9767764745772, + "top": 1306.8754214151072 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "5bb3b3df-60ab-4ec7-88e4-476be547ffbf", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "The approx. size that the genome has been fragmented into before sequencing.\nIf unsure the default of 500 bases is a reasonable guess in most situations.", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "The approx. size that the genome has been fragmented into before sequencing.\nIf unsure the default of 500 bases is a reasonable guess in most situations.", + "name": "Average size of sequenced fragments" + } + ], + "label": "Average size of sequenced fragments", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 1075.7813318055119, + "top": 1786.2927008908207 + }, + "tool_id": null, + "tool_state": "{\"default\": 500, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "d584c246-bf0a-4149-b393-ae9f430b98e1", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", + "errors": null, + "id": 7, + "input_connections": { + "infile": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": "Extended sample sheet", + "name": "Replace Text", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 264.85768736874513, + "top": 449.72044514833306 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^([^\\\\t]+)\\\\t([^\\\\t]+)\\\\t([^\\\\t]+)\\\\t([^\\\\t]+).*\", \"replace_pattern\": \"\\\\1\\\\t\\\\2\\\\t\\\\3\\\\t\\\\4\\\\t\\\\1_\\\\2_\\\\3\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "c9904710-f573-41aa-a24a-aec174c44222", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "errors": null, + "id": 8, + "input_connections": { + "in_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": "Times each control is used", + "name": "Datamash", + "outputs": [ + { + "name": "out_file", + "type": "input" + } + ], + "position": { + "left": 731.9419907206449, + "top": 646.8294730238549 + }, + "post_job_actions": { + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4c07ddedc198", + "name": "datamash_ops", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"grouping\": \"4\", \"header_in\": false, \"header_out\": false, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"count\", \"op_column\": \"1\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8+galaxy0", + "type": "tool", + "uuid": "b1abe732-30dd-4375-8f24-0392fa1def4a", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "errors": null, + "id": 9, + "input_connections": { + "input_collection": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Extract element identifiers", + "outputs": [ + { + "name": "output", + "type": "txt" + } + ], + "position": { + "left": 273.8575119333104, + "top": 661.2031907256822 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput": { + "action_arguments": { + "newtype": "tabular" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output" + }, + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "tool_shed_repository": { + "changeset_revision": "d3c07d270a50", + "name": "collection_element_identifiers", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.0.2", + "type": "tool", + "uuid": "d54d1d69-198c-46a5-bc1f-a9f4a9ae43c3", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "errors": null, + "id": 10, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 6, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 1322.255063702674, + "top": 1735.4406818912137 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"integer\", \"__current_case__\": 1, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": \"500\"}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", + "type": "tool", + "uuid": "a328900b-fa47-4d51-ab9a-8b86430b3507", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", + "errors": null, + "id": 11, + "input_connections": { + "infile": { + "id": 7, + "output_name": "outfile" + } + }, + "inputs": [], + "label": "Sorted extended sample sheet", + "name": "Sort", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 588.2721934241824, + "top": 322.27694778246416 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"3\", \"order\": \"\", \"style\": \"\"}, {\"__index__\": 1, \"column\": \"1\", \"order\": \"\", \"style\": \"V\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "88b7a534-a109-40c1-9c92-16f7ba0e7c15", + "when": null, + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 12, + "input_connections": { + "input": { + "id": 7, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 545.1399341423057, + "top": 781.7016976815331 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c1,c5\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "ae6dd67a-7374-4438-b997-d5baae7b21ad", + "when": null, + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 13, + "input_connections": { + "input": { + "id": 7, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1306.8618195584188, + "top": 642.9983147512831 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c5,c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "6e3bd74e-c68f-4e85-883f-ffab74305698", + "when": null, + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "join1", + "errors": null, + "id": 14, + "input_connections": { + "input1": { + "id": 9, + "output_name": "output" + }, + "input2": { + "id": 8, + "output_name": "out_file" + } + }, + "inputs": [], + "label": null, + "name": "Join two Datasets", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 966.0878668920052, + "top": 474.40108294302513 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "join1", + "tool_state": "{\"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"\", \"unmatched\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.1.3", + "type": "tool", + "uuid": "28965772-35a2-4ebb-abed-15d6084ec45b", + "when": null, + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "errors": null, + "id": 15, + "input_connections": { + "components_0|param_type|component_value": { + "id": 5, + "output_name": "output" + }, + "components_1|param_type|component_value": { + "id": 10, + "output_name": "integer_param" + } + }, + "inputs": [], + "label": null, + "name": "Calculate numeric parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 1349.9881681976492, + "top": 1395.0253368234305 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "tool_shed_repository": { + "changeset_revision": "0e586762f97b", + "name": "calculate_numeric_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"/\"}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"\"}], \"output_type\": \"integer\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "7370c82b-7b1a-46cd-a746-dcc6b07b2609", + "when": null, + "workflow_outputs": [] + }, + "16": { + "annotation": "", + "content_id": "Filter1", + "errors": null, + "id": 16, + "input_connections": { + "input": { + "id": 11, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 840.8899683615371, + "top": 320.8931025647788 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Filter1", + "tool_state": "{\"cond\": \"c4!='.' and c4 !='-'\", \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.1", + "type": "tool", + "uuid": "d2babe63-ac01-430f-812d-36f72c278360", + "when": null, + "workflow_outputs": [] + }, + "17": { + "annotation": "", + "content_id": "__RELABEL_FROM_FILE__", + "errors": null, + "id": 17, + "input_connections": { + "how|labels": { + "id": 12, + "output_name": "out_file1" + }, + "input": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Relabel identifiers", + "name": "how" + } + ], + "label": null, + "name": "Relabel identifiers", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 789.3249288889377, + "top": 881.9540173239981 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__RELABEL_FROM_FILE__", + "tool_state": "{\"how\": {\"how_select\": \"tabular\", \"__current_case__\": 1, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": true}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "0b02c063-17cd-48f7-93fb-77a8ed185ef7", + "when": null, + "workflow_outputs": [] + }, + "18": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 18, + "input_connections": { + "input": { + "id": 14, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1522.4113115404125, + "top": 504.3788813002956 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c3\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "819b3b0c-ebe6-4f87-84a5-78e31a157203", + "when": null, + "workflow_outputs": [] + }, + "19": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "errors": null, + "id": 19, + "input_connections": { + "components_0|param_type|component_value": { + "id": 15, + "output_name": "integer_param" + } + }, + "inputs": [], + "label": null, + "name": "Calculate numeric parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 1585.0225742456657, + "top": 1373.396403751527 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "tool_shed_repository": { + "changeset_revision": "0e586762f97b", + "name": "calculate_numeric_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"/\"}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": \"100000\"}, \"arith\": \"\"}], \"output_type\": \"integer\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "d52a247f-21aa-4ac1-b7a5-5b2e6aa4ee4a", + "when": null, + "workflow_outputs": [] + }, + "20": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", + "errors": null, + "id": 20, + "input_connections": { + "components_0|param_type|component_value": { + "id": 15, + "output_name": "integer_param" + } + }, + "inputs": [], + "label": null, + "name": "Compose text parameter value", + "outputs": [ + { + "name": "out1", + "type": "expression.json" + } + ], + "position": { + "left": 1618.186938289251, + "top": 1562.2890859128165 + }, + "post_job_actions": { + "HideDatasetActionout1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", + "tool_shed_repository": { + "changeset_revision": "e188c9826e0f", + "name": "compose_text_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.1", + "type": "tool", + "uuid": "2e881981-7e67-427a-b63f-c87694dd6d0b", + "when": null, + "workflow_outputs": [] + }, + "21": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", + "errors": null, + "id": 21, + "input_connections": { + "input": { + "id": 16, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Add column", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 980.3961008036761, + "top": 125.86588579144791 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", + "tool_shed_repository": { + "changeset_revision": "023f0a3760b3", + "name": "add_value", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.1", + "type": "tool", + "uuid": "67f20a9e-f5f5-4b89-bc9f-57f8cb6d8143", + "when": null, + "workflow_outputs": [] + }, + "22": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 22, + "input_connections": { + "input": { + "id": 16, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": "IDs to replicates association of IPed samples", + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1242.1656556688915, + "top": 155.60868928316074 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c1,c3\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "0dd5ab36-d43d-40a3-a04f-2c9f5f1cb81d", + "when": null, + "workflow_outputs": [] + }, + "23": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", + "errors": null, + "id": 23, + "input_connections": { + "single_paired|adapter_trimming_options|adapter_sequence1": { + "id": 3, + "output_name": "output" + }, + "single_paired|adapter_trimming_options|adapter_sequence2": { + "id": 4, + "output_name": "output" + }, + "single_paired|paired_input": { + "id": 17, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool fastp", + "name": "single_paired" + } + ], + "label": null, + "name": "fastp", + "outputs": [ + { + "name": "output_paired_coll", + "type": "input" + }, + { + "name": "report_html", + "type": "html" + }, + { + "name": "report_json", + "type": "json" + } + ], + "position": { + "left": 1104.3618353795332, + "top": 983.9513356433255 + }, + "post_job_actions": { + "HideDatasetActionreport_json": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "report_json" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", + "tool_shed_repository": { + "changeset_revision": "d60c3f704da0", + "name": "fastp", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": \"30\", \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": true, \"cut_window_size\": null, \"cut_mean_quality\": \"30\"}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_sequence2\": {\"__class__\": \"ConnectedValue\"}, \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.23.4+galaxy1", + "type": "tool", + "uuid": "37d83004-f627-4b68-808c-3b2bcb6f70ac", + "when": null, + "workflow_outputs": [ + { + "label": "report_html", + "output_name": "report_html", + "uuid": "58dd6572-c592-41c8-af6c-7ea445391426" + }, + { + "label": "output_paired_coll", + "output_name": "output_paired_coll", + "uuid": "590f893b-6188-4adc-9513-33ac2cabacb0" + } + ] + }, + "24": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", + "errors": null, + "id": 24, + "input_connections": { + "split_parms|input": { + "id": 18, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Split file", + "name": "split_parms" + } + ], + "label": null, + "name": "Split file", + "outputs": [ + { + "name": "list_output_tab", + "type": "input" + } + ], + "position": { + "left": 2317.6344412377093, + "top": 866.0422755242138 + }, + "post_job_actions": { + "HideDatasetActionlist_output_tab": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "list_output_tab" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", + "tool_shed_repository": { + "changeset_revision": "2dae863c8f42", + "name": "split_file_to_collection", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"split_parms\": {\"select_ftype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"top\": \"0\", \"split_by\": {\"select_split_by\": \"row\", \"__current_case__\": 1, \"select_mode\": {\"mode\": \"chunk\", \"__current_case__\": 0, \"chunksize\": \"1\"}, \"newfilenames\": \"repeat_times\", \"select_allocate\": {\"allocate\": \"byrow\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.5.2", + "type": "tool", + "uuid": "29a05f37-6cea-475a-af20-a97797efc29c", + "when": null, + "workflow_outputs": [] + }, + "25": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 25, + "input_connections": { + "input_param_type|input_param": { + "id": 19, + "output_name": "integer_param" + }, + "input_param_type|mappings_0|to": { + "id": 20, + "output_name": "out1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": null, + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_integer", + "type": "expression.json" + } + ], + "position": { + "left": 1844.569771108506, + "top": 1410.8865544094929 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_integer": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_integer" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"integer\", \"__current_case__\": 1, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"0\", \"to\": {\"__class__\": \"ConnectedValue\"}}]}, \"output_param_type\": \"integer\", \"unmapped\": {\"on_unmapped\": \"default\", \"__current_case__\": 2, \"default_value\": \"100000\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", + "type": "tool", + "uuid": "4747aad7-cd27-4690-b577-c62df03a30c2", + "when": null, + "workflow_outputs": [] + }, + "26": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 26, + "input_connections": { + "input": { + "id": 21, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": "Extended sample names mapped to conditions", + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1241.3099576196778, + "top": 0 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c5,c2,c6\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "330c6377-e8ab-4bf0-9b5e-8e7881d7326f", + "when": null, + "workflow_outputs": [] + }, + "27": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 27, + "input_connections": { + "input": { + "id": 21, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": "IDs to replicates associaction of matching controls", + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1240.51048330279, + "top": 296.7926761387355 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c4,c3,c6\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "1b79e171-ecc8-4202-91ed-24d68c3783a6", + "when": null, + "workflow_outputs": [] + }, + "28": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 28, + "input_connections": { + "input": { + "id": 22, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": "IDs of IPed samples", + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1795.0548103169126, + "top": 341.7169400274215 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "4709c8ea-3ca7-4613-9017-df4c50e72eb3", + "when": null, + "workflow_outputs": [] + }, + "29": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", + "errors": null, + "id": 29, + "input_connections": { + "library|input_1": { + "id": 23, + "output_name": "output_paired_coll" + }, + "reference_genome|index": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Bowtie2", + "name": "library" + }, + { + "description": "runtime parameter for tool Bowtie2", + "name": "reference_genome" + } + ], + "label": null, + "name": "Bowtie2", + "outputs": [ + { + "name": "output", + "type": "bam" + }, + { + "name": "mapping_stats", + "type": "txt" + } + ], + "position": { + "left": 1376.398809923191, + "top": 954.5764548042524 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "d5ceb9f3c25b", + "name": "bowtie2", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"set\", \"__current_case__\": 1, \"read_group_id_conditional\": {\"do_auto_name\": true, \"__current_case__\": 0}, \"read_group_sm_conditional\": {\"do_auto_name\": false, \"__current_case__\": 1, \"SM\": \"\"}, \"PL\": \"ILLUMINA\", \"read_group_lb_conditional\": {\"do_auto_name\": false, \"__current_case__\": 1, \"LB\": null}, \"CN\": null, \"DS\": null, \"DT\": null, \"FO\": null, \"KS\": null, \"PG\": null, \"PI\": null, \"PU\": null}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.5.3+galaxy1", + "type": "tool", + "uuid": "98ebcaae-3aa7-4b3c-8274-cb05b9286a58", + "when": null, + "workflow_outputs": [ + { + "label": "mapping_stats", + "output_name": "mapping_stats", + "uuid": "42dbd7d5-acfb-4432-abc9-f4341ded939a" + } + ] + }, + "30": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 30, + "input_connections": { + "input1": { + "id": 24, + "output_name": "list_output_tab" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 2558.35187957346, + "top": 872.8096430004058 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "c98a9b68-5a84-4162-8699-97daad6b04e5", + "when": null, + "workflow_outputs": [] + }, + "31": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", + "errors": null, + "id": 31, + "input_connections": { + "infile": { + "id": 26, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Replace Text", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 1789.4066406548234, + "top": 6.7480809547996365 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"(.+)\\\\t(.+)\\\\t(.+)\", \"replace_pattern\": \"\\\\1\\\\t\\\\2_\\\\3\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "44f85b6d-e4c4-4e6b-a4cf-c6c00c5d3c65", + "when": null, + "workflow_outputs": [] + }, + "32": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", + "errors": null, + "id": 32, + "input_connections": { + "infile": { + "id": 27, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Replace Text", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 2703.0942563792655, + "top": 1180.3701452209295 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"(.+)\\\\t(.+)\\\\t(.+)\", \"replace_pattern\": \"\\\\1_\\\\3\\\\t\\\\2\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "2915992b-4cef-4f70-a978-92450fcb3036", + "when": null, + "workflow_outputs": [] + }, + "33": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", + "errors": null, + "id": 33, + "input_connections": { + "input": { + "id": 29, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Samtools view", + "outputs": [ + { + "name": "outputsam", + "type": "input" + } + ], + "position": { + "left": 1632.101587102184, + "top": 932.9832386429648 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", + "tool_shed_repository": { + "changeset_revision": "32dc5f781059", + "name": "samtools_view", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": \"30\", \"library\": null, \"cigarcons\": null, \"inclusive_filter\": [\"2\"], \"exclusive_filter\": [\"4\", \"8\"], \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": null}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", + "type": "tool", + "uuid": "bbe08c3f-bad6-46aa-87f8-8e0382a36c69", + "when": null, + "workflow_outputs": [ + { + "label": "outputsam", + "output_name": "outputsam", + "uuid": "585b9a5c-dcbd-45b7-88a6-11b689989c90" + } + ] + }, + "34": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 34, + "input_connections": { + "input": { + "id": 32, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 3279.8658049633555, + "top": 1343.3081517001117 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "79e787de-eb19-4596-b08e-25c611925b1c", + "when": null, + "workflow_outputs": [] + }, + "35": { + "annotation": "", + "content_id": "__RELABEL_FROM_FILE__", + "errors": null, + "id": 35, + "input_connections": { + "how|labels": { + "id": 13, + "output_name": "out_file1" + }, + "input": { + "id": 33, + "output_name": "outputsam" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Relabel identifiers", + "name": "how" + } + ], + "label": null, + "name": "Relabel identifiers", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 1872.5432264181763, + "top": 835.5329084162294 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__RELABEL_FROM_FILE__", + "tool_state": "{\"how\": {\"how_select\": \"tabular\", \"__current_case__\": 1, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": true}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "f6df4fc9-49c4-46ca-ba57-8c0657037c5e", + "when": null, + "workflow_outputs": [] + }, + "36": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0", + "errors": null, + "id": 36, + "input_connections": { + "advancedOpt|binSize": { + "id": 10, + "output_name": "integer_param" + }, + "advancedOpt|numberOfSamples": { + "id": 25, + "output_name": "output_param_integer" + }, + "multibam_conditional|bamfiles": { + "id": 33, + "output_name": "outputsam" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool plotFingerprint", + "name": "advancedOpt" + }, + { + "description": "runtime parameter for tool plotFingerprint", + "name": "advancedOpt" + }, + { + "description": "runtime parameter for tool plotFingerprint", + "name": "advancedOpt" + }, + { + "description": "runtime parameter for tool plotFingerprint", + "name": "multibam_conditional" + } + ], + "label": null, + "name": "plotFingerprint", + "outputs": [ + { + "name": "outFileName", + "type": "png" + } + ], + "position": { + "left": 2285.3674447155677, + "top": 1395.2896919166708 + }, + "post_job_actions": { + "RenameDatasetActionoutFileName": { + "action_arguments": { + "newname": "Sample Fingerprints" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFileName" + }, + "TagDatasetActionoutFileName": { + "action_arguments": { + "tags": "\ud83d\udd0d" + }, + "action_type": "TagDatasetAction", + "output_name": "outFileName" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4ed32329e0ed", + "name": "deeptools_plot_fingerprint", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": {\"__class__\": \"ConnectedValue\"}, \"numberOfSamples\": {\"__class__\": \"ConnectedValue\"}, \"doExtendCustom\": {\"doExtend\": \"no\", \"__current_case__\": 0}, \"ignoreDuplicates\": false, \"centerReads\": false, \"minMappingQuality\": \"1\", \"samFlagInclude\": null, \"samFlagExclude\": null, \"minFragmentLength\": \"0\", \"maxFragmentLength\": \"0\", \"skipZeros\": true, \"plotTitle\": \"\", \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"multibam_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bamfiles\": {\"__class__\": \"ConnectedValue\"}}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"region\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "0794697e-3653-4fdb-9362-7aafcee0a7c5", + "when": null, + "workflow_outputs": [ + { + "label": "fingerprints", + "output_name": "outFileName", + "uuid": "90ec9b14-a426-4cde-8fd4-9eda8f546c6c" + } + ] + }, + "37": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0", + "errors": null, + "id": 37, + "input_connections": { + "mode|binSize": { + "id": 10, + "output_name": "integer_param" + }, + "multibam_conditional|bamfiles": { + "id": 33, + "output_name": "outputsam" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool multiBamSummary", + "name": "mode" + }, + { + "description": "runtime parameter for tool multiBamSummary", + "name": "multibam_conditional" + } + ], + "label": null, + "name": "multiBamSummary", + "outputs": [ + { + "name": "outFile", + "type": "deeptools_coverage_matrix" + } + ], + "position": { + "left": 2292.240633135638, + "top": 1749.5475849533962 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "01fb6a7654e6", + "name": "deeptools_multi_bam_summary", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"mode\": {\"modeOpt\": \"bins\", \"__current_case__\": 0, \"binSize\": {\"__class__\": \"ConnectedValue\"}, \"distanceBetweenBins\": \"200\"}, \"multibam_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bamfiles\": {\"__class__\": \"ConnectedValue\"}}, \"outRawCounts\": false, \"region\": \"\", \"scalingFactors\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "b99feccd-72a9-4726-9537-e733621c16d9", + "when": null, + "workflow_outputs": [] + }, + "38": { + "annotation": "", + "content_id": "__FILTER_FROM_FILE__", + "errors": null, + "id": 38, + "input_connections": { + "how|filter_source": { + "id": 28, + "output_name": "out_file1" + }, + "input": { + "id": 35, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Filter collection", + "name": "how" + } + ], + "label": null, + "name": "Filter collection", + "outputs": [ + { + "name": "output_filtered", + "type": "input" + }, + { + "name": "output_discarded", + "type": "input" + } + ], + "position": { + "left": 2313.605995441952, + "top": 587.9874937180731 + }, + "post_job_actions": { + "HideDatasetActionoutput_discarded": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_discarded" + }, + "HideDatasetActionoutput_filtered": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_filtered" + } + }, + "tool_id": "__FILTER_FROM_FILE__", + "tool_state": "{\"how\": {\"how_filter\": \"remove_if_absent\", \"__current_case__\": 0, \"filter_source\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "f234484d-9b05-418f-b9dd-7da30887a88d", + "when": null, + "workflow_outputs": [] + }, + "39": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0", + "errors": null, + "id": 39, + "input_connections": { + "corData": { + "id": 37, + "output_name": "outFile" + } + }, + "inputs": [], + "label": null, + "name": "plotCorrelation", + "outputs": [ + { + "name": "outFileName", + "type": "png" + } + ], + "position": { + "left": 2544.385975396104, + "top": 1757.0696149631171 + }, + "post_job_actions": { + "RenameDatasetActionoutFileName": { + "action_arguments": { + "newname": "Between-samples correlation plot" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFileName" + }, + "TagDatasetActionoutFileName": { + "action_arguments": { + "tags": "\ud83d\udd0d" + }, + "action_type": "TagDatasetAction", + "output_name": "outFileName" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bad3ca889618", + "name": "deeptools_plot_correlation", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"corData\": {\"__class__\": \"ConnectedValue\"}, \"corMethod\": \"spearman\", \"outFileCorMatrix\": false, \"outFileFormat\": \"png\", \"plotting_type\": {\"whatToPlot\": \"heatmap\", \"__current_case__\": 0, \"zMin\": \"\", \"zMax\": \"\", \"colorMap\": \"RdYlBu\", \"plotTitle\": \"\", \"plotNumbers\": true, \"plotHeight\": \"9.5\", \"plotWidth\": \"11.0\"}, \"removeOutliers\": false, \"skipZeros\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "c2012389-0703-4c85-afe4-72a2a68308b7", + "when": null, + "workflow_outputs": [ + { + "label": "sample_correlation", + "output_name": "outFileName", + "uuid": "7285d4e5-803c-460d-a488-ccc1d62fe9b9" + } + ] + }, + "40": { + "annotation": "", + "content_id": "__SORTLIST__", + "errors": null, + "id": 40, + "input_connections": { + "input": { + "id": 38, + "output_name": "output_filtered" + }, + "sort_type|sort_file": { + "id": 28, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Sort collection", + "name": "sort_type" + } + ], + "label": null, + "name": "Sort collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 2782.0268972958656, + "top": 471.76721888258373 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__SORTLIST__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"sort_type\": {\"sort_type\": \"file\", \"__current_case__\": 2, \"sort_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "84a991d9-791b-41df-8a1e-c135f8e37a2c", + "when": null, + "workflow_outputs": [] + }, + "41": { + "annotation": "", + "content_id": "__DUPLICATE_FILE_TO_COLLECTION__", + "errors": null, + "id": 41, + "input_connections": { + "input": { + "id": 38, + "output_name": "output_discarded" + }, + "number": { + "id": 30, + "output_name": "integer_param" + } + }, + "inputs": [], + "label": null, + "name": "Duplicate file to collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 2953.9640182151957, + "top": 832.009632831452 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__DUPLICATE_FILE_TO_COLLECTION__", + "tool_state": "{\"element_identifier\": \"_\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"number\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "f75440bf-5cb7-4c6e-bc1a-fb2edbd1341e", + "when": null, + "workflow_outputs": [] + }, + "42": { + "annotation": "", + "content_id": "__TAG_FROM_FILE__", + "errors": null, + "id": 42, + "input_connections": { + "input": { + "id": 40, + "output_name": "output" + }, + "tags": { + "id": 22, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Tag elements", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3241.5932168576664, + "top": 355.58981740841716 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__TAG_FROM_FILE__", + "tool_state": "{\"how\": \"add\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"tags\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "28297280-7945-4795-a227-34ca2f72b9a8", + "when": null, + "workflow_outputs": [] + }, + "43": { + "annotation": "", + "content_id": "__APPLY_RULES__", + "errors": null, + "id": 43, + "input_connections": { + "input": { + "id": 41, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Apply rules", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3279.553432805206, + "top": 1153.628050156597 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__APPLY_RULES__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"rules\": {\"mapping\": [{\"columns\": [4], \"editing\": false, \"type\": \"list_identifiers\"}], \"rules\": [{\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier0\", \"warn\": null}, {\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier1\", \"warn\": null}, {\"error\": null, \"start\": 1, \"type\": \"add_column_rownum\", \"warn\": null}, {\"error\": null, \"expression\": \"(.+)\", \"group_count\": null, \"replacement\": \"_\\\\1\", \"target_column\": 2, \"type\": \"add_column_regex\", \"warn\": null}, {\"error\": null, \"target_column_0\": 0, \"target_column_1\": 3, \"type\": \"add_column_concatenate\", \"warn\": null}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0", + "type": "tool", + "uuid": "0b860ea0-f722-4a84-a5dc-2e5307ffae4f", + "when": null, + "workflow_outputs": [] + }, + "44": { + "annotation": "", + "content_id": "__RELABEL_FROM_FILE__", + "errors": null, + "id": 44, + "input_connections": { + "how|labels": { + "id": 12, + "output_name": "out_file1" + }, + "input": { + "id": 42, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Relabel identifiers", + "name": "how" + } + ], + "label": null, + "name": "Relabel identifiers", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3490.1173128420783, + "top": 246.44928205248672 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__RELABEL_FROM_FILE__", + "tool_state": "{\"how\": {\"how_select\": \"tabular\", \"__current_case__\": 1, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "c3fa7964-d4db-461e-8b88-b93b57fe3cc1", + "when": null, + "workflow_outputs": [] + }, + "45": { + "annotation": "", + "content_id": "__SORTLIST__", + "errors": null, + "id": 45, + "input_connections": { + "input": { + "id": 43, + "output_name": "output" + }, + "sort_type|sort_file": { + "id": 34, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Sort collection", + "name": "sort_type" + } + ], + "label": null, + "name": "Sort collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3724.324188083806, + "top": 1415.7620399621792 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__SORTLIST__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"sort_type\": {\"sort_type\": \"file\", \"__current_case__\": 2, \"sort_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "3bc49cc6-412c-4c51-ba89-b6a7257fc65d", + "when": null, + "workflow_outputs": [] + }, + "46": { + "annotation": "", + "content_id": "__APPLY_RULES__", + "errors": null, + "id": 46, + "input_connections": { + "input": { + "id": 44, + "output_name": "output" + } + }, + "inputs": [], + "label": "Per-replicate list of IPed sample data", + "name": "Apply rules", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3894.0699731774043, + "top": 669.1884364276625 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__APPLY_RULES__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"rules\": {\"mapping\": [{\"columns\": [1, 0], \"editing\": false, \"type\": \"list_identifiers\"}], \"rules\": [{\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier0\", \"warn\": null}, {\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"tags\", \"warn\": null}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0", + "type": "tool", + "uuid": "62ce7d38-d7f1-41f3-aae3-04f9e21d6a8f", + "when": null, + "workflow_outputs": [] + }, + "47": { + "annotation": "", + "content_id": "__TAG_FROM_FILE__", + "errors": null, + "id": 47, + "input_connections": { + "input": { + "id": 45, + "output_name": "output" + }, + "tags": { + "id": 32, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Tag elements", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3589.9859596505003, + "top": 1621.8916401244505 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__TAG_FROM_FILE__", + "tool_state": "{\"how\": \"add\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"tags\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "f83d3c2a-c857-4d18-937d-0111648fc08a", + "when": null, + "workflow_outputs": [] + }, + "48": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "errors": null, + "id": 48, + "input_connections": { + "input_collection": { + "id": 46, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Extract element identifiers", + "outputs": [ + { + "name": "output", + "type": "txt" + } + ], + "position": { + "left": 4230.8425725597335, + "top": 676.2845382917118 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "tool_shed_repository": { + "changeset_revision": "d3c07d270a50", + "name": "collection_element_identifiers", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.0.2", + "type": "tool", + "uuid": "d08d7a05-1578-4903-b986-be9eddf2e501", + "when": null, + "workflow_outputs": [] + }, + "49": { + "annotation": "", + "content_id": "__APPLY_RULES__", + "errors": null, + "id": 49, + "input_connections": { + "input": { + "id": 47, + "output_name": "output" + } + }, + "inputs": [], + "label": "Per-replicate list of control samples", + "name": "Apply rules", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 4008.752690864601, + "top": 1656.9030533546313 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__APPLY_RULES__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"rules\": {\"mapping\": [{\"columns\": [1, 0], \"editing\": false, \"type\": \"list_identifiers\"}], \"rules\": [{\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier0\", \"warn\": null}, {\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"tags\", \"warn\": null}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0", + "type": "tool", + "uuid": "ee8cb05d-3642-4109-aec0-5f002070cf3c", + "when": null, + "workflow_outputs": [] + }, + "50": { + "annotation": "", + "content_id": "wc_gnu", + "errors": null, + "id": 50, + "input_connections": { + "input1": { + "id": 48, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Line/Word/Character count", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 4551.65577744577, + "top": 626.0141158113014 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "wc_gnu", + "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "a7b1293a-c57d-4d33-a5ab-dbc8b1cd6a62", + "when": null, + "workflow_outputs": [] + }, + "51": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", + "errors": null, + "id": 51, + "input_connections": { + "control|c_multiple|input_control_file": { + "id": 49, + "output_name": "output" + }, + "effective_genome_size_options|gsize": { + "id": 5, + "output_name": "output" + }, + "treatment|input_treatment_file": { + "id": 46, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool MACS2 callpeak", + "name": "effective_genome_size_options" + }, + { + "description": "runtime parameter for tool MACS2 callpeak", + "name": "treatment" + } + ], + "label": "Call Peaks with MACS2", + "name": "MACS2 callpeak", + "outputs": [ + { + "name": "output_tabular", + "type": "tabular" + }, + { + "name": "output_narrowpeaks", + "type": "bed" + }, + { + "name": "output_summits", + "type": "bed" + }, + { + "name": "output_treat_pileup", + "type": "bedgraph" + }, + { + "name": "output_control_lambda", + "type": "bedgraph" + } + ], + "position": { + "left": 4464.50389169328, + "top": 1163.6764259639986 + }, + "post_job_actions": { + "HideDatasetActionoutput_control_lambda": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_control_lambda" + }, + "HideDatasetActionoutput_extra_files": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_extra_files" + }, + "HideDatasetActionoutput_treat_pileup": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_treat_pileup" + }, + "RenameDatasetActionoutput_control_lambda": { + "action_arguments": { + "newname": "MACS2 control coverage" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_control_lambda" + }, + "RenameDatasetActionoutput_narrowpeaks": { + "action_arguments": { + "newname": "Peak regions called by MACS2" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_narrowpeaks" + }, + "RenameDatasetActionoutput_summits": { + "action_arguments": { + "newname": "Positions of summits of MACS2-called peaks" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_summits" + }, + "RenameDatasetActionoutput_treat_pileup": { + "action_arguments": { + "newname": "MACS2 treatment coverage" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_treat_pileup" + }, + "TagDatasetActionoutput_narrowpeaks": { + "action_arguments": { + "tags": "\ud83c\udf1f" + }, + "action_type": "TagDatasetAction", + "output_name": "output_narrowpeaks" + }, + "TagDatasetActionoutput_summits": { + "action_arguments": { + "tags": "\ud83c\udf1f" + }, + "action_type": "TagDatasetAction", + "output_name": "output_summits" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", + "tool_shed_repository": { + "changeset_revision": "86e2413cf3f8", + "name": "macs2", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": true, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": true}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"control\": {\"c_select\": \"Yes\", \"__current_case__\": 0, \"c_multiple\": {\"c_multi_select\": \"No\", \"__current_case__\": 0, \"input_control_file\": {\"__class__\": \"ConnectedValue\"}}}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 4, \"gsize\": {\"__class__\": \"ConnectedValue\"}}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"peaks_tabular\", \"summits\", \"bdg\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2.9.1+galaxy0", + "type": "tool", + "uuid": "06ca906e-c512-4376-9ffc-8eb2b5774af1", + "when": null, + "workflow_outputs": [ + { + "label": "peak_summits", + "output_name": "output_summits", + "uuid": "a10f9de1-eafd-4d68-bf8f-a331d111f272" + }, + { + "label": "peak_regions", + "output_name": "output_narrowpeaks", + "uuid": "feac3ce1-00ff-4065-9279-eea3ddc58191" + } + ] + }, + "52": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0", + "errors": null, + "id": 52, + "input_connections": { + "bamFile1": { + "id": 46, + "output_name": "output" + }, + "bamFile2": { + "id": 49, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool bamCompare", + "name": "advancedOpt" + } + ], + "label": null, + "name": "bamCompare", + "outputs": [ + { + "name": "outFileName", + "type": "bigwig" + } + ], + "position": { + "left": 4647.906234356017, + "top": 1970.5531892679364 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "c929a006727f", + "name": "deeptools_bam_compare", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"smoothLength\": null, \"doExtendCustom\": {\"doExtend\": \"no\", \"__current_case__\": 0}, \"ignoreDuplicates\": false, \"centerReads\": false, \"minMappingQuality\": \"1\", \"samFlagInclude\": null, \"samFlagExclude\": null, \"minFragmentLength\": \"0\", \"maxFragmentLength\": \"0\", \"skipNAs\": false, \"skipZeroOverZero\": \"--skipZeroOverZero\", \"ignoreForNormalization\": \"\", \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "3f1782e6-2fa5-44fa-9492-5754df8db988", + "when": null, + "workflow_outputs": [] + }, + "53": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 53, + "input_connections": { + "input1": { + "id": 50, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 4961.0048130551595, + "top": 619.5695622494998 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "8eeff7e3-dab2-40fd-9d2a-45ed37e65dc4", + "when": null, + "workflow_outputs": [] + }, + "54": { + "annotation": "", + "content_id": "__FLATTEN__", + "errors": null, + "id": 54, + "input_connections": { + "input": { + "id": 51, + "output_name": "output_tabular" + } + }, + "inputs": [], + "label": null, + "name": "Flatten collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 4812.33347874683, + "top": 987.3303206340295 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__FLATTEN__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"join_identifier\": \"_\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "e28b32fa-bfff-4317-a852-c43c76c29778", + "when": null, + "workflow_outputs": [] + }, + "55": { + "annotation": "summary of MACS2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", + "errors": null, + "id": 55, + "input_connections": { + "infile": { + "id": 51, + "output_name": "output_tabular" + } + }, + "inputs": [], + "label": "summary of MACS2", + "name": "Search in textfiles", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 4809.930234624945, + "top": 1115.5899113520873 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput": { + "action_arguments": { + "newtype": "txt" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output" + }, + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "MACS2 report" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"^#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "95832fa1-e96e-4867-8162-d1e39cb1dc46", + "when": null, + "workflow_outputs": [ + { + "label": "macs2_report", + "output_name": "output", + "uuid": "dc081d2e-e155-4ff3-98c5-45ee266a5e34" + } + ] + }, + "56": { + "annotation": "", + "content_id": "__APPLY_RULES__", + "errors": null, + "id": 56, + "input_connections": { + "input": { + "id": 51, + "output_name": "output_narrowpeaks" + } + }, + "inputs": [], + "label": null, + "name": "Apply rules", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 4697.796238588279, + "top": 1590.6968405266741 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__APPLY_RULES__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"rules\": {\"mapping\": [{\"columns\": [1], \"editing\": false, \"type\": \"list_identifiers\"}], \"rules\": [{\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier0\", \"warn\": null}, {\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier1\", \"warn\": null}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0", + "type": "tool", + "uuid": "53d75717-943d-4273-89ad-875890803997", + "when": null, + "workflow_outputs": [] + }, + "57": { + "annotation": "", + "content_id": "wig_to_bigWig", + "errors": null, + "id": 57, + "input_connections": { + "input1": { + "id": 51, + "output_name": "output_treat_pileup" + } + }, + "inputs": [], + "label": "Bigwig from MACS2", + "name": "Wig/BedGraph-to-bigWig", + "outputs": [ + { + "name": "out_file1", + "type": "bigwig" + } + ], + "position": { + "left": 4808.151849816254, + "top": 1251.996347388883 + }, + "post_job_actions": { + "RenameDatasetActionout_file1": { + "action_arguments": { + "newname": "Peaks per replicate" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file1" + }, + "TagDatasetActionout_file1": { + "action_arguments": { + "tags": "\ud83c\udf1f" + }, + "action_type": "TagDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "wig_to_bigWig", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"settingsType\": \"preset\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.1", + "type": "tool", + "uuid": "0fe57c5d-00a0-4cb6-9bac-97e6d03c6b76", + "when": null, + "workflow_outputs": [ + { + "label": "peaks_per_replicate", + "output_name": "out_file1", + "uuid": "23ab8786-c4d4-40ed-bef4-acedc42be197" + } + ] + }, + "58": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", + "errors": null, + "id": 58, + "input_connections": { + "inputs": { + "id": 51, + "output_name": "output_narrowpeaks" + } + }, + "inputs": [], + "label": null, + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 4790.608440552391, + "top": 1468.3010704169935 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "d2f57b39-897d-4cf3-87f4-fdef2bba9a34", + "when": null, + "workflow_outputs": [] + }, + "59": { + "annotation": "", + "content_id": "__APPLY_RULES__", + "errors": null, + "id": 59, + "input_connections": { + "input": { + "id": 52, + "output_name": "outFileName" + } + }, + "inputs": [], + "label": null, + "name": "Apply rules", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 4993.266797305287, + "top": 2216.028845870027 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__APPLY_RULES__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"rules\": {\"mapping\": [{\"columns\": [1], \"editing\": false, \"type\": \"list_identifiers\"}], \"rules\": [{\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier0\", \"warn\": null}, {\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier1\", \"warn\": null}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0", + "type": "tool", + "uuid": "d2cc1859-dd0f-47dd-a491-507202d83bd1", + "when": null, + "workflow_outputs": [] + }, + "60": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "errors": null, + "id": 60, + "input_connections": { + "components_0|param_type|component_value": { + "id": 53, + "output_name": "integer_param" + } + }, + "inputs": [], + "label": null, + "name": "Calculate numeric parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 5414.434887704011, + "top": 674.0866656183726 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "tool_shed_repository": { + "changeset_revision": "0e586762f97b", + "name": "calculate_numeric_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"+\"}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": \"1\"}, \"arith\": \"\"}], \"output_type\": \"integer\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "70ecbc61-0e0f-4b36-976d-c275b0367af4", + "when": null, + "workflow_outputs": [] + }, + "61": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", + "errors": null, + "id": 61, + "input_connections": { + "results_0|software_cond|input": { + "id": 23, + "output_name": "report_json" + }, + "results_1|software_cond|input": { + "id": 29, + "output_name": "mapping_stats" + }, + "results_2|software_cond|input": { + "id": 54, + "output_name": "output" + } + }, + "inputs": [], + "label": "MultiQC", + "name": "MultiQC", + "outputs": [ + { + "name": "plots", + "type": "input" + }, + { + "name": "html_report", + "type": "html" + }, + { + "name": "stats", + "type": "tabular" + } + ], + "position": { + "left": 5055.562870683207, + "top": 831.7856227940173 + }, + "post_job_actions": { + "HideDatasetActionplots": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "plots" + }, + "RenameDatasetActionhtml_report": { + "action_arguments": { + "newname": "MultiQC analysis reports" + }, + "action_type": "RenameDatasetAction", + "output_name": "html_report" + }, + "TagDatasetActionhtml_report": { + "action_arguments": { + "tags": "\ud83d\udd0d" + }, + "action_type": "TagDatasetAction", + "output_name": "html_report" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", + "tool_shed_repository": { + "changeset_revision": "f7e2f1eb3a16", + "name": "multiqc", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", + "type": "tool", + "uuid": "fb066848-43df-412a-9767-9613bac7d961", + "when": null, + "workflow_outputs": [ + { + "label": "multiqc_stats", + "output_name": "stats", + "uuid": "2b8cbf83-886d-438e-887e-82e2deba114e" + }, + { + "label": "multiqc_html", + "output_name": "html_report", + "uuid": "d1b408d8-842b-45da-85d5-7e67d2c17a87" + } + ] + }, + "62": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", + "errors": null, + "id": 62, + "input_connections": { + "inputs": { + "id": 56, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 4921.295213664614, + "top": 1708.9590342670465 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "85dd9ee4-d2a0-4c9c-b280-913a751d20ac", + "when": null, + "workflow_outputs": [] + }, + "63": { + "annotation": "", + "content_id": "__APPLY_RULES__", + "errors": null, + "id": 63, + "input_connections": { + "input": { + "id": 57, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Apply rules", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 5025.234311821274, + "top": 1383.635801779973 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__APPLY_RULES__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"rules\": {\"mapping\": [{\"columns\": [1], \"editing\": false, \"type\": \"list_identifiers\"}], \"rules\": [{\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier0\", \"warn\": null}, {\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier1\", \"warn\": null}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0", + "type": "tool", + "uuid": "5a756cf1-34d2-423d-b570-d90a75d3455f", + "when": null, + "workflow_outputs": [] + }, + "64": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0", + "errors": null, + "id": 64, + "input_connections": { + "input": { + "id": 58, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "bedtools SortBED", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 5010.262154627027, + "top": 1522.1090700056002 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0", + "tool_shed_repository": { + "changeset_revision": "64e2edfe7a2c", + "name": "bedtools", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"genome_file_opts\": {\"genome_file_opts_selector\": \"loc\", \"__current_case__\": 0, \"genome\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.31.1+galaxy0", + "type": "tool", + "uuid": "a2cf62b4-95d9-49af-9c4e-9fbc934b5956", + "when": null, + "workflow_outputs": [] + }, + "65": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "errors": null, + "id": 65, + "input_connections": { + "input_collection": { + "id": 59, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Extract element identifiers", + "outputs": [ + { + "name": "output", + "type": "txt" + } + ], + "position": { + "left": 5334.367004120032, + "top": 2262.7786204080885 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "tool_shed_repository": { + "changeset_revision": "d3c07d270a50", + "name": "collection_element_identifiers", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.0.2", + "type": "tool", + "uuid": "4bc92cf8-76d0-478c-929a-893a92625df3", + "when": null, + "workflow_outputs": [] + }, + "66": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0", + "errors": null, + "id": 66, + "input_connections": { + "input": { + "id": 62, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "bedtools SortBED", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 5146.236117612409, + "top": 1757.9605896160601 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0", + "tool_shed_repository": { + "changeset_revision": "64e2edfe7a2c", + "name": "bedtools", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"genome_file_opts\": {\"genome_file_opts_selector\": \"loc\", \"__current_case__\": 0, \"genome\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.31.1+galaxy0", + "type": "tool", + "uuid": "ba5f7bfb-c3bc-4e45-b493-297b4501d514", + "when": null, + "workflow_outputs": [] + }, + "67": { + "annotation": "", + "content_id": "__RELABEL_FROM_FILE__", + "errors": null, + "id": 67, + "input_connections": { + "how|labels": { + "id": 31, + "output_name": "outfile" + }, + "input": { + "id": 63, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Relabel identifiers", + "name": "how" + } + ], + "label": null, + "name": "Relabel identifiers", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 5092.64448656204, + "top": 1185.0581963017723 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__RELABEL_FROM_FILE__", + "tool_state": "{\"how\": {\"how_select\": \"tabular\", \"__current_case__\": 1, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "f35e5d52-4d41-4aa4-b8c8-b33a6be98afb", + "when": null, + "workflow_outputs": [] + }, + "68": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1", + "errors": null, + "id": 68, + "input_connections": { + "input": { + "id": 64, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "bedtools MergeBED", + "outputs": [ + { + "name": "output", + "type": "bed" + } + ], + "position": { + "left": 5250.271320891606, + "top": 1579.3295935194308 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1", + "tool_shed_repository": { + "changeset_revision": "64e2edfe7a2c", + "name": "bedtools", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"c_and_o_argument_repeat\": [], \"distance\": \"0\", \"header\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.31.1", + "type": "tool", + "uuid": "fae4cb88-ee87-4423-b0b9-079965cb6c0a", + "when": null, + "workflow_outputs": [] + }, + "69": { + "annotation": "", + "content_id": "wc_gnu", + "errors": null, + "id": 69, + "input_connections": { + "input1": { + "id": 65, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Line/Word/Character count", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 5568.11587681034, + "top": 2253.0534566256933 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "wc_gnu", + "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "5d5d6821-2eea-4b54-9490-7ef22ead73e4", + "when": null, + "workflow_outputs": [] + }, + "70": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1", + "errors": null, + "id": 70, + "input_connections": { + "input": { + "id": 66, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "bedtools MergeBED", + "outputs": [ + { + "name": "output", + "type": "bed" + } + ], + "position": { + "left": 5368.293163817283, + "top": 1915.8758273215888 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1", + "tool_shed_repository": { + "changeset_revision": "64e2edfe7a2c", + "name": "bedtools", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"c_and_o_argument_repeat\": [], \"distance\": \"0\", \"header\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.31.1", + "type": "tool", + "uuid": "355fca3e-6cc0-454a-aab9-3fe381075940", + "when": null, + "workflow_outputs": [] + }, + "71": { + "annotation": "", + "content_id": "__APPLY_RULES__", + "errors": null, + "id": 71, + "input_connections": { + "input": { + "id": 67, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Apply rules", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 5321.767019440411, + "top": 1425.4757653329539 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__APPLY_RULES__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"rules\": {\"mapping\": [{\"columns\": [1, 2], \"editing\": false, \"type\": \"list_identifiers\"}], \"rules\": [{\"error\": null, \"type\": \"add_column_metadata\", \"value\": \"identifier0\", \"warn\": null}, {\"error\": null, \"expression\": \"(.+)_(\\\\d+)\", \"group_count\": 2, \"replacement\": null, \"target_column\": 0, \"type\": \"add_column_regex\", \"warn\": null}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0", + "type": "tool", + "uuid": "ae68e55b-1f4f-40d5-bc92-0ece04a8963e", + "when": null, + "workflow_outputs": [] + }, + "72": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0", + "errors": null, + "id": 72, + "input_connections": { + "multibigwig_conditional|bigwigfiles": { + "id": 52, + "output_name": "outFileName" + }, + "regionsFiles_0|regionsFile": { + "id": 68, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool computeMatrix", + "name": "advancedOpt" + }, + { + "description": "runtime parameter for tool computeMatrix", + "name": "multibigwig_conditional" + } + ], + "label": null, + "name": "computeMatrix", + "outputs": [ + { + "name": "outFileName", + "type": "deeptools_compute_matrix_archive" + } + ], + "position": { + "left": 5551.394104212098, + "top": 1633.9066101050357 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a60c359ec43c", + "name": "deeptools_compute_matrix", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": \"50\", \"sortRegions\": \"keep\", \"sortUsing\": \"mean\", \"averageTypeBins\": \"mean\", \"missingDataAsZero\": true, \"skipZeros\": true, \"minThreshold\": null, \"maxThreshold\": null, \"scale\": null, \"metagene\": false, \"transcriptID\": \"transcript\", \"exonID\": \"exon\", \"transcript_id_designator\": \"transcript_id\", \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"mode\": {\"mode_select\": \"reference-point\", \"__current_case__\": 1, \"referencePoint\": \"center\", \"nanAfterEnd\": false, \"beforeRegionStartLength\": \"3000\", \"afterRegionStartLength\": \"3000\"}, \"multibigwig_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bigwigfiles\": {\"__class__\": \"ConnectedValue\"}}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"regionsFiles\": [{\"__index__\": 0, \"regionsFile\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "16eeab2c-fdb0-4217-9ef4-d65d4a092b8a", + "when": null, + "workflow_outputs": [] + }, + "73": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 73, + "input_connections": { + "input1": { + "id": 69, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 5796.6703301075295, + "top": 2214.845644382288 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "81751af5-8e85-49ef-8698-7afe580894d0", + "when": null, + "workflow_outputs": [] + }, + "74": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0", + "errors": null, + "id": 74, + "input_connections": { + "multibigwig_conditional|bigwigfiles": { + "id": 59, + "output_name": "output" + }, + "regionsFiles_0|regionsFile": { + "id": 70, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool computeMatrix", + "name": "advancedOpt" + }, + { + "description": "runtime parameter for tool computeMatrix", + "name": "multibigwig_conditional" + } + ], + "label": null, + "name": "computeMatrix", + "outputs": [ + { + "name": "outFileName", + "type": "deeptools_compute_matrix_archive" + } + ], + "position": { + "left": 5641.443721637562, + "top": 1952.614017550237 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a60c359ec43c", + "name": "deeptools_compute_matrix", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": \"50\", \"sortRegions\": \"keep\", \"sortUsing\": \"mean\", \"averageTypeBins\": \"mean\", \"missingDataAsZero\": true, \"skipZeros\": true, \"minThreshold\": null, \"maxThreshold\": null, \"scale\": null, \"metagene\": false, \"transcriptID\": \"transcript\", \"exonID\": \"exon\", \"transcript_id_designator\": \"transcript_id\", \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"mode\": {\"mode_select\": \"reference-point\", \"__current_case__\": 1, \"referencePoint\": \"center\", \"nanAfterEnd\": false, \"beforeRegionStartLength\": \"3000\", \"afterRegionStartLength\": \"3000\"}, \"multibigwig_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bigwigfiles\": {\"__class__\": \"ConnectedValue\"}}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"regionsFiles\": [{\"__index__\": 0, \"regionsFile\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "a353aee5-7309-41d2-99a1-2d24a71560c6", + "when": null, + "workflow_outputs": [] + }, + "75": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", + "errors": null, + "id": 75, + "input_connections": { + "bigwigs": { + "id": 71, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "bigwigAverage", + "outputs": [ + { + "name": "outFileName", + "type": "bigwig" + } + ], + "position": { + "left": 5376.223772610315, + "top": 1177.6322714145876 + }, + "post_job_actions": { + "RenameDatasetActionoutFileName": { + "action_arguments": { + "newname": "Peaks averaged across replicates" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFileName" + }, + "TagDatasetActionoutFileName": { + "action_arguments": { + "tags": "\ud83c\udf1f" + }, + "action_type": "TagDatasetAction", + "output_name": "outFileName" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4a53856a5b85", + "name": "deeptools_bigwig_average", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bigwigs\": {\"__class__\": \"ConnectedValue\"}, \"outFileFormat\": \"bigwig\", \"region\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "4d5765f4-a5a5-4aa8-b432-f374261acff7", + "when": null, + "workflow_outputs": [ + { + "label": "peaks_averaged_across_replicates", + "output_name": "outFileName", + "uuid": "42af7412-853b-4b96-8570-790bdb587f81" + } + ] + }, + "76": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0", + "errors": null, + "id": 76, + "input_connections": { + "advancedOpt|used_multiple_regions|clustering|k_kmeans": { + "id": 60, + "output_name": "integer_param" + }, + "matrixFile": { + "id": 72, + "output_name": "outFileName" + } + }, + "inputs": [], + "label": null, + "name": "plotHeatmap", + "outputs": [ + { + "name": "outFileName", + "type": "png" + } + ], + "position": { + "left": 5790.249568964471, + "top": 1179.410656223279 + }, + "post_job_actions": { + "RenameDatasetActionoutFileName": { + "action_arguments": { + "newname": "Per-replicate clustered heatmaps of peaks" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFileName" + }, + "TagDatasetActionoutFileName": { + "action_arguments": { + "tags": "\ud83d\udd0d" + }, + "action_type": "TagDatasetAction", + "output_name": "outFileName" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "e4c7985d4585", + "name": "deeptools_plot_heatmap", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"sortRegions\": \"descend\", \"sortUsing\": \"mean\", \"sortUsingSamples\": null, \"linesAtTickMarks\": false, \"averageTypeSummaryPlot\": \"mean\", \"plotType\": \"lines\", \"missingDataColor\": \"black\", \"colorMapRepeat\": [], \"alpha\": \"1.0\", \"colorList\": \"\", \"zMin\": \"\", \"zMax\": \"\", \"yMin\": null, \"yMax\": null, \"xAxisLabel\": \"distance from region center (bp)\", \"yAxisLabel\": \"peak regions\", \"heatmapWidth\": \"7.5\", \"heatmapHeight\": \"25.0\", \"whatToShow\": \"plot, heatmap and colorbar\", \"startLabel\": \"peak start\", \"endLabel\": \"peak end\", \"referencePointLabel\": \"peak center\", \"samplesLabel\": null, \"regionsLabel\": null, \"plotTitle\": \"\", \"legendLocation\": \"best\", \"labelRotation\": \"0\", \"perGroup\": false, \"used_multiple_regions\": {\"used_multiple_regions_options\": \"no\", \"__current_case__\": 0, \"clustering\": {\"clustering_options\": \"kmeans\", \"__current_case__\": 0, \"k_kmeans\": {\"__class__\": \"ConnectedValue\"}}, \"silhouette\": false}, \"clusterUsingSamples\": null}, \"matrixFile\": {\"__class__\": \"ConnectedValue\"}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "ff8a6416-3798-4a34-92ab-d4091a240830", + "when": null, + "workflow_outputs": [ + { + "label": "peaks_heatmap_per_replicate", + "output_name": "outFileName", + "uuid": "b956cbd5-d609-4476-99ca-14b79afb2a05" + } + ] + }, + "77": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "errors": null, + "id": 77, + "input_connections": { + "components_0|param_type|component_value": { + "id": 73, + "output_name": "integer_param" + } + }, + "inputs": [], + "label": null, + "name": "Calculate numeric parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 6021.761837142641, + "top": 2031.3094924921204 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "tool_shed_repository": { + "changeset_revision": "0e586762f97b", + "name": "calculate_numeric_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"+\"}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": \"1\"}, \"arith\": \"\"}], \"output_type\": \"integer\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "cdd2f146-6086-4bec-b1c1-9f273ed951ce", + "when": null, + "workflow_outputs": [] + }, + "78": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0", + "errors": null, + "id": 78, + "input_connections": { + "advancedOpt|used_multiple_regions|clustering|k_kmeans": { + "id": 77, + "output_name": "integer_param" + }, + "matrixFile": { + "id": 74, + "output_name": "outFileName" + } + }, + "inputs": [], + "label": null, + "name": "plotHeatmap", + "outputs": [ + { + "name": "outFileName", + "type": "png" + } + ], + "position": { + "left": 6062.768920644284, + "top": 1445.8118637992488 + }, + "post_job_actions": { + "RenameDatasetActionoutFileName": { + "action_arguments": { + "newname": "Clustered heatmap of peaks across all samples" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFileName" + }, + "TagDatasetActionoutFileName": { + "action_arguments": { + "tags": "\ud83d\udd0d" + }, + "action_type": "TagDatasetAction", + "output_name": "outFileName" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "e4c7985d4585", + "name": "deeptools_plot_heatmap", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"sortRegions\": \"descend\", \"sortUsing\": \"mean\", \"sortUsingSamples\": null, \"linesAtTickMarks\": false, \"averageTypeSummaryPlot\": \"mean\", \"plotType\": \"lines\", \"missingDataColor\": \"black\", \"colorMapRepeat\": [], \"alpha\": \"1.0\", \"colorList\": \"\", \"zMin\": \"\", \"zMax\": \"\", \"yMin\": null, \"yMax\": null, \"xAxisLabel\": \"distance from region center (bp)\", \"yAxisLabel\": \"peak regions\", \"heatmapWidth\": \"7.5\", \"heatmapHeight\": \"25.0\", \"whatToShow\": \"plot, heatmap and colorbar\", \"startLabel\": \"peak start\", \"endLabel\": \"peak end\", \"referencePointLabel\": \"peak center\", \"samplesLabel\": null, \"regionsLabel\": null, \"plotTitle\": \"\", \"legendLocation\": \"best\", \"labelRotation\": \"0\", \"perGroup\": false, \"used_multiple_regions\": {\"used_multiple_regions_options\": \"no\", \"__current_case__\": 0, \"clustering\": {\"clustering_options\": \"kmeans\", \"__current_case__\": 0, \"k_kmeans\": {\"__class__\": \"ConnectedValue\"}}, \"silhouette\": false}, \"clusterUsingSamples\": null}, \"matrixFile\": {\"__class__\": \"ConnectedValue\"}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", + "type": "tool", + "uuid": "43e6e642-909f-411a-8a8d-b4d1dd1edf82", + "when": null, + "workflow_outputs": [ + { + "label": "peaks_heatmap", + "output_name": "outFileName", + "uuid": "121c315b-a034-45c3-b625-5be54466b680" + } + ] + } + }, + "tags": [ + "ChIP-Seq" + ] +} diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/test-data/test_sample_sheet.tsv b/workflows/epigenetics/chipseq-pe-with-replicates-controls/test-data/test_sample_sheet.tsv new file mode 100644 index 000000000..096b58c0a --- /dev/null +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/test-data/test_sample_sheet.tsv @@ -0,0 +1,4 @@ +SRR5204807 Spt5 rep1 SRR5204809 +SRR5204808 Spt5 rep2 SRR5204810 +SRR5204809 input rep1 . +SRR5204810 input rep2 . From 605f7232fc64e2dd71e39b5ff911d40d552e9da3 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Fri, 25 Oct 2024 12:12:19 +0200 Subject: [PATCH 2/4] Declare optional params as null in test instead of omitting them --- .../chipseq-pe-with-replicates-controls-tests.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml b/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml index 8679b7874..4b4a05ca9 100644 --- a/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml @@ -57,6 +57,8 @@ location: https://github.com/nf-core/test-datasets/raw/refs/heads/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz filetype: fastqsanger.gz Reference genome: "sacCer3" + Sequencing adapter - forward: null + Sequencing adapter - reverse: null Effective genome size: 12000000 Average size of sequenced fragments: 200 outputs: From 99e50981a4812eddc503780efc4c369f13b2bb11 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Fri, 25 Oct 2024 13:34:34 +0200 Subject: [PATCH 3/4] Fix macs2_report check --- ...ipseq-pe-with-replicates-controls-tests.yml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml b/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml index 4b4a05ca9..e315f5642 100644 --- a/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/chipseq-pe-with-replicates-controls-tests.yml @@ -70,14 +70,16 @@ expression: "SRR5204807_Spt5_rep1\t163.0\t0.0\t0.0\t844.+" macs2_report: element_tests: - wt_H3K4me3: - asserts: - - that: "has_text" - text: "# name = SRR5204807_Spt5_rep1" - - that: "has_text" - text: "# fragment size is determined as 163 bps" - - that: "has_text" - text: "# fragments after filtering in treatment: 86394" + rep1: + elements: + SRR5204807_Spt5_rep1: + asserts: + - that: "has_text" + text: "# name = SRR5204807_Spt5_rep1" + - that: "has_text" + text: "# fragment size is determined as 163 bps" + - that: "has_text" + text: "# fragments after filtering in treatment: 86394" mapping_stats: element_tests: SRR5204807_Spt5_rep1: From 0c04063737a8be27fecc4838b31d7b424f22a6a1 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 29 Oct 2024 17:42:51 +0100 Subject: [PATCH 4/4] Finish WF README --- .../README.md | 47 +++++++++++-------- 1 file changed, 27 insertions(+), 20 deletions(-) diff --git a/workflows/epigenetics/chipseq-pe-with-replicates-controls/README.md b/workflows/epigenetics/chipseq-pe-with-replicates-controls/README.md index 0eaa7db29..31f97c2b7 100644 --- a/workflows/epigenetics/chipseq-pe-with-replicates-controls/README.md +++ b/workflows/epigenetics/chipseq-pe-with-replicates-controls/README.md @@ -3,17 +3,17 @@ This workflow is for analyzing batches of ChIP-Seq samples with controls and replicates from paired-end sequenced reads to called peaks. It uses: -- fastp for sequenced reads pre-processing, -- bowtie2 for mapping -- MACS2 for peak calling -- deeptools for cross-sample correlation and averaging +- **fastp** for sequenced reads pre-processing, +- **bowtie2** for mapping +- **MACS2** for peak calling +- **deeptools** for cross-sample correlation and averaging -The workflow provides quality control at the level of sequenced reads, mapping results and called peaks and visualizes correlation between samples. +The workflow provides quality control at the level of sequenced reads, mapping results and called peaks, and visualizes correlation between samples. ## Input datasets -- Sequencing data: this must be provided as a single list collection of paired fastq datasets of all samples. -- Sample sheet: this is expected to be a 4-column tabular dataset that describes samples, their association with each other and with conditions and replicates. +- **Sequencing data**: this must be provided as a single list collection of paired fastq datasets of all samples. +- **Sample sheet**: this is expected to be a 4-column tabular dataset that describes samples, their association with each other and with conditions and replicates. The first column of the file must list all samples with their names matching the element names in the Sequencing data collection. Samples can be listed in any order. The second column is used to specify the specific experimental condition that each sample represents. There is no formal restriction on this column, but values should be kept short for readable reports. @@ -34,22 +34,29 @@ The workflow provides quality control at the level of sequenced reads, mapping r This declares an experimental design with three conditions - H3K4me3, H3K27me3 and CTCF - with two replicates per condition and one input control per replicate. The control sample SRR5680995 is declared as the shared control for all samples from replicate rep1, SRR5681005 as the control for all samples from replicate rep2. + When importing the sample sheet into Galaxy make sure you are using Tab characters as the column separators. + ## Input parameters -- Reference genome: set this to the reference genome of your organism of interest; used at the read mapping step -- Sequencing adapter - forward (optional) -- Sequencing aadapter - reverse (optional) -- Effective genome size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes). -- Average size of sequenced fragments: used for deeptools-base QC +- **Reference genome**: set this to the reference genome of your organism of interest; used at the read mapping step +- **Sequencing adapter - forward** (optional) +- **Sequencing adapter - reverse** (optional) +- **Effective genome size**: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes). +- **Average size of sequenced fragments**: used for deeptools-based QC ## Outputs: -- MultiQC analysis reports: -- Sample fingerprints: -- Between-samples correlation plot: -- Clustered heatmap of peaks across samples: -- Peak regions called by MACS2: -- Positions of summits of MACS2-called peaks: -- Peaks per replicate: -- Peaks averaged across replicates: +- **MultiQC analysis reports**: contains key quality metrics from the fastp, bowtie2 and MACS2 steps of the workflow +- **Sample fingerprints**: plot comparing IP strengths for all samples + (see https://deeptools.readthedocs.io/en/latest/content/tools/plotFingerprint.html#background) +- **Between-samples correlation plot**: plot comparing the similarity between all samples in terms of read coverage across genomic regions (see https://deeptools.readthedocs.io/en/latest/content/tools/plotCorrelation.html#background) +- **Per-replicate clustered heatmaps of peaks**: Clustered heatmap plots of IP read coverage (relative to control) around peaks called by MACS2; collection with one plot per replicate; the WF produces one more cluster per plot than there are samples in the replicate, but you can experiment with different cluster numbers by rerunning the tool with a different setting for *"Number of clusters to compute"* in the *"Clustering algorithm"* section near the bottom of the tool interface. +- **Clustered heatmap of peaks across all samples**: Clustered heatmap like above but as a single plot including all samples from all replicates; the WF produces one more cluster per plot than there are total samples across all replicates, but you can experiment with different cluster numbers by rerunning the tool with a different setting for *"Number of clusters to compute"* in the *"Clustering algorithm"* section near the bottom of the tool interface. +- **Peak regions called by MACS2**: collection of bed files describing the peak regions called by MACS2 and organized by replicate and IP condition +- **Positions of summits of MACS2-called peaks**: collection of bed files describing just the summits of the peaks called by MACS2, again organized by replicate and IP condition +- **Peaks per replicate**: collection of MACS2 treatment pileup output converted to bigWig format, organized by replicate and IP condition +- **Peaks averaged across replicates**: the Peaks per replicate output averaged across replicates with bigwigAverage from the deeptools suite; collection organized by IP condition + +## Related training material +https://gxy.io/GTN:T00140 guides you through manual execution of all the key steps of this workflow with more detailed explanations.