From 7e923acc7135b8228ce3ff5f3c5ea6261758ad10 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 22 Oct 2024 18:15:34 +0200 Subject: [PATCH 01/10] Update RNA-seq single-end workflow --- .../transcriptomics/rnaseq-sr/CHANGELOG.md | 7 + .../rnaseq-sr/rnaseq-sr-tests.yml | 246 +- .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 2620 +++++++++++++---- 3 files changed, 2255 insertions(+), 618 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index 389e9e12d..92d1c363a 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.10] 2024-10-22 + +### Manual update +- Using a new subsampled test data from Zenodo record https://zenodo.org/records/13951092 +- Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, Picard reports +- Added DESeq2 step that uses tags to choose factors + ## [0.9] 2024-09-23 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 6be85c478..86c667abf 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -1,101 +1,211 @@ -- doc: Test outline for RNAseq_SR +- doc: Test outline for rnaseq-sr job: - gtf: + GTF file of annotation: class: File - location: https://zenodo.org/record/4541751/files/Drosophila_melanogaster.BDGP6.87.gtf + path: test-data/GTF file of annotation.gtf filetype: gtf - SR fastq input: + Sample table: + class: File + location: https://zenodo.org/records/13951092/files/chr4.gtf + filetype: gtf + Collection single-end FASTQ files: class: Collection collection_type: list elements: - class: File identifier: GSM461177 - location: https://zenodo.org/record/4541751/files/GSM461177_1_subsampled.fastqsanger - forward_adapter: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC - reference_genome: dm6 + location: https://zenodo.org/records/13951092/files/GSM461177_1.fastqsanger + - class: File + identifier: GSM461178 + location: https://zenodo.org/records/13951092/files/GSM461178_1.fastqsanger + - class: File + identifier: GSM461180 + location: https://zenodo.org/records/13951092/files/GSM461180_1.fastqsanger + - class: File + identifier: GSM461181 + location: https://zenodo.org/records/13951092/files/GSM461181_1.fastqsanger + Generate QC reports?: true + Reference genome: dm6 + Use featureCounts for generating count tables: true strandedness: unstranded - cufflinks_FPKM: true - stringtie_FPKM: true + Compute Cufflinks RPKM?: true + GTF with regions to exclude from RPKM normalization with Cufflinks: null + Compute StringTie RPKM?: true + DEseq2 batch factors: null outputs: - output_log: + MultiQC stats: + has_text_matching: + expression: "GSM461177\t0.04[0-9]*\t80.94[0-9]*\t0.61[0-9]*\t0.05[0-9]*\t0.04[0-9]*\t99.32[0-9]*\t0.04[0-9]*\t95.98\t0.00[0-9]*\t1.86[0-9]*" + expression: "GSM461177_forward\t\t\t\t\t\t\t\t\t\t\t27.95[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" + expression: "GSM461177_reverse\t\t\t\t\t\t\t\t\t\t\t28.22[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" + expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" + expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" + expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" + Differential Expression Analysis using DESeq2: + asserts: + has_text_matching: + expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" + expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" DESeq2 Plots: + has_size: + size: 33420 + delta: 1500 + Mapped Reads: element_tests: GSM461177: - asserts: - - that: "has_text" - text: "Number of input reads |\t1051466" - - that: "has_text" - text: "Uniquely mapped reads number |\t871202" - - that: "has_text" - text: "Number of reads mapped to multiple loci |\t91808" - mapped-reads: + has_size: + value: 3058282 + delta: 150000 + GSM461178: + has_size: + value: 3032322 + delta: 150000 + GSM461180: + has_size: + value: 3165439 + delta: 150000 + GSM461181: + has_size: + value: 3075214 + delta: 150000 + Transcripts Expression from Cufflinks: element_tests: GSM461177: asserts: - has_size: - value: 43037033 - delta: 4000000 - 'MultiQC on input dataset(s): Stats': - asserts: - has_line: - line: "Sample STAR_mqc_generalstats_star_total_reads_1 STAR_mqc_generalstats_star_mapped_1 STAR_mqc_generalstats_star_mapped_percent_1 STAR_mqc_generalstats_star_uniquely_mapped_1 STAR_mqc_generalstats_star_uniquely_mapped_percent_1 STAR_mqc_generalstats_star_multimapped_1 Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" - has_text_matching: - expression: "GSM461177\t1.0[0-9]*\t0.96[0-9]*\t91.[0-9]*\t0.8[0-9]*\t82.8[0-9]*\t0.091[0-9]*\t4.0[0-9]*" - MultiQC webpage: - asserts: - - that: "has_text" - text: "GSM461177" - - that: "has_text" - text: "Filtered Reads" - - that: "has_text" - text: "STAR" - reads_per_gene from STAR: - element_tests: - GSM461177: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + GSM461178: + asserts: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 370.382 128757 122145 135370 OK" + GSM461180: + asserts: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 366.172 122426 116120 128732 OK" + GSM461181: asserts: - - that: "has_text" - text: "N_ambiguous\t20961\t5272\t4705" - - that: "has_text" - text: "FBgn0010247\t14\t6\t8" - HTS count like output: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 404.198 115973 110059 121886 OK" + Genes Expression from Cufflinks: element_tests: GSM461177: asserts: - has_text: - text: "FBgn0010247\t14" - transcripts_expression_cufflinks: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + GSM461178: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 141422 134823 148020 OK" + GSM461180: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 134779 128494 141063 OK" + GSM461181: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 127880 121988 133772 OK" + Unstranded Coverage: element_tests: GSM461177: - asserts: - has_text: - text: "FBtr0078104\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t1583\t0.626702\t18.291\t9.78605\t26.796\tOK" - genes_expression_cufflinks: + has_size: + value: 445281 + delta: 20000 + GSM461178: + has_size: + value: 406443 + delta: 20000 + GSM461180: + has_size: + value: 423518 + delta: 20000 + GSM461181: + has_size: + value: 455334 + delta: 20000 + Stranded Coverage: + element_tests: + GSM461177_forward: + has_size: + value: 313382 + delta: 15000 + GSM461178_forward: + has_size: + value: 285608 + delta: 15000 + GSM461180_forward: + has_size: + value: 295650 + delta: 15000 + GSM461181_forward: + has_size: + value: 311698 + delta: 15000 + GSM461177_reverse: + has_size: + value: 313241 + delta: 15000 + GSM461178_reverse: + has_size: + value: 281153 + delta: 15000 + GSM461180_reverse: + has_size: + value: 292239 + delta: 15000 + GSM461181_reverse: + has_size: + value: 322248 + delta: 15000 + Gene Abundance Estimates from StringTie: element_tests: GSM461177: asserts: has_text_matching: - expression: "FBgn0031217\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t-\t-\t32.1016\t22.1771\t42.02[0-9]*\tOK" - genes_expression_stringtie: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + GSM461178: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t286.68[0-9]*\t143296.84[0-9]*\t365993.15[0-9]*" + GSM461180: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t282.60[0-9]*\t138208.90[0-9]*\t367356.56[0-9]*" + GSM461181: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" + FeatureCounts Summary Table: element_tests: GSM461177: asserts: - has_text: - text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.067492\t36.649773\t74.784904" - both strands coverage: + has_line: + line: "Assigned 45715" + GSM461178: + asserts: + has_line: + line: "Assigned 38738" + GSM461180: + asserts: + has_line: + line: "Assigned 39998" + GSM461181: + asserts: + has_line: + line: "Assigned 44734" + Tagged Count Tables: element_tests: GSM461177: asserts: - has_size: - value: 6075761 - delta: 600000 - stranded coverage: - element_tests: - GSM461177_reverse: + has_line: + line: "FBgn0017545 6109" + GSM461178: asserts: - has_size: - value: 3103918 - delta: 300000 - GSM461177_forward: + has_line: + line: "FBgn0017545 5649" + GSM461180: + asserts: + has_line: + line: "FBgn0017545 5600" + GSM461181: asserts: - has_size: - value: 3103918 - delta: 300000 + has_line: + line: "FBgn0017545 5943" \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index 509d68a0d..952daa985 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -1,133 +1,249 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of single-reads fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.", - "comments": [], + "annotation": "This workflow takes as input a list of single-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. RPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", + "comments": [ + { + "child_steps": [ + 12, + 18, + 19 + ], + "color": "yellow", + "data": { + "title": "Additional quantification" + }, + "id": 1, + "position": [ + 1306.2, + 1413.8 + ], + "size": [ + 860, + 716 + ], + "type": "frame" + }, + { + "child_steps": [ + 13, + 14, + 15 + ], + "color": "lime", + "data": { + "title": "Map Strandedness parameter" + }, + "id": 0, + "position": [ + 770.5, + 1592.6 + ], + "size": [ + 251, + 558 + ], + "type": "frame" + }, + { + "child_steps": [ + 20, + 21 + ], + "color": "red", + "data": { + "title": "Coverage Files" + }, + "id": 2, + "position": [ + 2510.1, + 0 + ], + "size": [ + 375, + 538 + ], + "type": "frame" + } + ], "creator": [ { "class": "Person", - "identifier": "0000-0002-1964-4960", + "identifier": "https://orcid.org/0000-0002-1964-4960", "name": "Lucille Delisle" + }, + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-5192-126X", + "name": "Pavankumar Videm" } ], "format-version": "0.1", "license": "MIT", - "name": "RNAseq_SR", - "release": "0.9", + "release": "0.10", + "name": "rnaseq-sr", + "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": "Should be a list of single-read RNA-seq fastqs", + "annotation": "A list of single-end RNA-seq fastqs", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "Should be a list of single-read RNA-seq fastqs", - "name": "SR fastq input" + "description": "A list of single-end RNA-seq fastqs", + "name": "Collection single-end FASTQ files" } ], - "label": "SR fastq input", + "label": "Collection single-end FASTQ files", "name": "Input dataset collection", "outputs": [], "position": { "left": 0, - "top": 354 + "top": 1007.0008028213834 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "2fee2555-0a2f-4758-9011-3667db23f962", + "uuid": "d237002d-df52-4260-90c9-fffaf8c1816f", "when": null, "workflow_outputs": [] }, "1": { - "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "annotation": "Whether to report QC", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", - "name": "forward_adapter" + "description": "Whether to report QC", + "name": "Generate QC reports?" } ], - "label": "forward_adapter", + "label": "Generate QC reports?", "name": "Input parameter", "outputs": [], "position": { - "left": 42.45001220703125, - "top": 430.91668701171875 + "left": 40.67737161137343, + "top": 1117.6931018245803 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "124c7578-bdaa-445b-a756-326077f2567d", + "uuid": "6e56335f-7e1d-4268-ba1d-743f149a8f67", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f71c8f8f-3a3d-432e-a969-8cfe5c07f73b" + } + ] }, "2": { - "annotation": "reference_genome", + "annotation": "Select the reference genome", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "reference_genome", - "name": "reference_genome" + "description": "Select the reference genome", + "name": "Reference genome" } ], - "label": "reference_genome", + "label": "Reference genome", "name": "Input parameter", "outputs": [], "position": { - "left": 107.63336181640625, - "top": 522.134886401586 + "left": 70.67734212335759, + "top": 1229.3288050461836 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "39f1c435-1e7c-48d6-9149-37671b7b07da", + "uuid": "228cdc54-bca1-4237-a0b8-ec51e2ec29ec", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "6eee62e6-3ed0-410c-8cb6-50be2115625b" + } + ] }, "3": { - "annotation": "gtf compatible with the reference_genome. Mind the UCSC/Ensembl differences in chromosome naming", + "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "gtf compatible with the reference_genome. Mind the UCSC/Ensembl differences in chromosome naming", - "name": "gtf" + "description": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", + "name": "GTF file of annotation" } ], - "label": "gtf", + "label": "GTF file of annotation", "name": "Input dataset", "outputs": [], "position": { - "left": 125.60003662109375, - "top": 606.751585620336 + "left": 120.67736637119827, + "top": 1326.5006367761569 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "b32d0b73-c827-46f9-8279-697487cd3c4c", + "uuid": "f9a61edb-782b-4af5-a2c9-163168bee1b9", "when": null, "workflow_outputs": [] }, "4": { - "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "annotation": "Use featureCounts tool instead of RNA STAR?", "content_id": null, "errors": null, "id": 4, "input_connections": {}, + "inputs": [ + { + "description": "Use featureCounts tool instead of RNA STAR?", + "name": "Use featureCounts for generating count tables" + } + ], + "label": "Use featureCounts for generating count tables", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 160.33752190255188, + "top": 1435.2340383001115 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "0c6b0c89-1ee2-4de1-8ce5-31dbb24ee1e1", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "50dead7e-db45-40db-8734-6ed48f33dd8b" + } + ] + }, + "5": { + "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, "inputs": [ { "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", @@ -138,111 +254,191 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 156.25, - "top": 667.118284839086 + "left": 203.8828886044653, + "top": 1570.8860110851008 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "02b7890c-1d0d-493e-9943-3016f6594b46", + "uuid": "1f5b92ff-26f4-4c26-8e1b-f0e0c90f0608", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "de3792de-9587-459d-b8c4-8563f011510d" + } + ] }, - "5": { - "annotation": "Whether FPKM values should be computed with cufflinks", + "6": { + "annotation": "Whether FPKM values should be computed with Cufflinks", "content_id": null, "errors": null, - "id": 5, + "id": 6, "input_connections": {}, "inputs": [ { - "description": "Whether FPKM values should be computed with cufflinks", - "name": "cufflinks_FPKM" + "description": "Whether FPKM values should be computed with Cufflinks", + "name": "Compute Cufflinks RPKM?" } ], - "label": "cufflinks_FPKM", + "label": "Compute Cufflinks RPKM?", "name": "Input parameter", "outputs": [], "position": { - "left": 177.6500244140625, - "top": 735.4800895070166 + "left": 228.7717684962176, + "top": 1666.0254709507822 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "a80fd45c-4164-4b94-847c-dcef5441b92a", + "uuid": "d7141054-23ac-40bf-abbb-6834251cf2ef", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1f3e3c7e-e42e-41b5-ab29-f4cc20170dc4" + } + ] + }, + "7": { + "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "name": "Sample table" + } + ], + "label": "Sample table", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 1462.1645523806205, + "top": 909.2581294996864 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "f7bf6134-db9e-4ae1-9454-689e9a54ddc8", "when": null, "workflow_outputs": [] }, - "6": { - "annotation": "Could be a gtf with for example one entry for the chrM forward and one entry for the chrM reverse", + "8": { + "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 6, + "id": 8, "input_connections": {}, "inputs": [ { - "description": "Could be a gtf with for example one entry for the chrM forward and one entry for the chrM reverse", - "name": "gtf with regions to exclude from FPKM normalization with Cufflinks" + "description": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", + "name": "GTF with regions to exclude from RPKM normalization with Cufflinks" } ], - "label": "gtf with regions to exclude from FPKM normalization with Cufflinks", + "label": "GTF with regions to exclude from RPKM normalization with Cufflinks", "name": "Input dataset", "outputs": [], "position": { - "left": 201.73333740234375, - "top": 809.5967887257666 + "left": 260.1137371795465, + "top": 1784.313630812311 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "54a833b6-bb4a-48c2-b8d7-4c8bb0172ce7", + "uuid": "ee50d135-7758-4bd9-a85d-176f3118b103", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "4ea1a61a-0c5b-4d51-a23a-187b6a381269" + } + ] }, - "7": { + "9": { "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 7, + "id": 9, "input_connections": {}, "inputs": [ { "description": "Whether FPKM values should be computed with StringTie", - "name": "stringtie_FPKM" + "name": "Compute StringTie RPKM?" } ], - "label": "stringtie_FPKM", + "label": "Compute StringTie RPKM?", "name": "Input parameter", "outputs": [], "position": { - "left": 245.88330078125, - "top": 926.4134391163916 + "left": 268.7808865853354, + "top": 1905.5010561327158 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "05bdc4bb-4988-42e6-b281-cbb826b96c7b", + "uuid": "dc096947-90a1-4ba3-9e90-22976d894ad2", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "3295d7f4-50f0-4c50-84ea-e0cfbf23671e" + } + ] }, - "8": { + "10": { + "annotation": "Tabular file with additional batch factors to include in the model", + "content_id": null, + "errors": null, + "id": 10, + "input_connections": {}, + "inputs": [ + { + "description": "Tabular file with additional batch factors to include in the model", + "name": "DEseq2 batch factors" + } + ], + "label": "DEseq2 batch factors", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 2203.102316887585, + "top": 1355.0225413410844 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "176298e5-b11c-4637-a4b8-034c9c1b418d", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "12faad0d-49ae-44d5-bad3-f8032dc01e4b" + } + ] + }, + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 8, + "id": 11, "input_connections": { "library|input_1": { "id": 0, "output_name": "output" - }, - "library|r1|adapters_0|adapter_source|adapter": { - "id": 1, - "output_name": "output" } }, "inputs": [ @@ -264,8 +460,8 @@ } ], "position": { - "left": 500.61669921875, - "top": 339.134886401586 + "left": 239.35765144976227, + "top": 494.46848655874044 }, "post_job_actions": { "HideDatasetActionout1": { @@ -291,18 +487,18 @@ "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.9+galaxy1", "type": "tool", - "uuid": "4d39b70d-c852-4c42-9e0d-f3641d632543", + "uuid": "8467e234-b99a-4f4e-9b6d-7bbea18da678", "when": null, "workflow_outputs": [] }, - "9": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, - "id": 9, + "id": 12, "input_connections": { "components_0|param_type|component_value": { "id": 2, @@ -319,8 +515,8 @@ } ], "position": { - "left": 979.0166015625, - "top": 1004.2468131398291 + "left": 1412.7865078407585, + "top": 1513.204961480357 }, "post_job_actions": { "HideDatasetActionout1": { @@ -339,18 +535,18 @@ "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.1", "type": "tool", - "uuid": "87e88a77-d412-4ed0-8bf1-9c23406d4a22", + "uuid": "3512ad84-2d57-44b5-a054-e01c2bf67e20", "when": null, "workflow_outputs": [] }, - "10": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 10, + "id": 13, "input_connections": { "input_param_type|input_param": { - "id": 4, + "id": 5, "output_name": "output" } }, @@ -360,7 +556,7 @@ "name": "input_param_type" } ], - "label": "awk command from strand", + "label": "Get featureCounts strandedness parameter", "name": "Map parameter value", "outputs": [ { @@ -369,8 +565,8 @@ } ], "position": { - "left": 1196.5, - "top": 814.2634757374854 + "left": 795.1082525210539, + "top": 1643.2637555172578 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -386,21 +582,21 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"NR>4{print $1\\\"\\\\t\\\"$3}\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"NR>4{print $1\\\"\\\\t\\\"$4}\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"NR>4{print $1\\\"\\\\t\\\"$2}\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"1\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"2\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"0\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "dc27749f-07ad-454d-8b8d-15612b31870c", + "uuid": "746d5413-b5a8-4a92-b661-f4654a409b67", "when": null, "workflow_outputs": [] }, - "11": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 11, + "id": 14, "input_connections": { "input_param_type|input_param": { - "id": 4, + "id": 5, "output_name": "output" } }, @@ -410,7 +606,7 @@ "name": "input_param_type" } ], - "label": "Get cufflinks strandess parameter", + "label": "Get cufflinks strandedness parameter", "name": "Map parameter value", "outputs": [ { @@ -419,8 +615,8 @@ } ], "position": { - "left": 1010.4833984375, - "top": 1180.2257433107284 + "left": 795.3259027398972, + "top": 1823.4515528952898 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -439,18 +635,18 @@ "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"fr-secondstrand\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"fr-firststrand\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"fr-unstranded\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "d2d1af99-7b7b-4ec1-b2dc-5997fd3d702b", + "uuid": "640cfa2b-f2e7-4b4b-8048-387bd0530d6a", "when": null, "workflow_outputs": [] }, - "12": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 12, + "id": 15, "input_connections": { "input_param_type|input_param": { - "id": 4, + "id": 5, "output_name": "output" } }, @@ -469,8 +665,8 @@ } ], "position": { - "left": 913.0522727953694, - "top": 1576.8436797276113 + "left": 790.5858684328869, + "top": 1993.6777444451404 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -489,15 +685,15 @@ "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"--fr\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"--rf\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "c04f4059-e125-46b4-9a85-446dd6f0a08b", + "uuid": "288968eb-fb08-437e-a60d-3e580c3e5305", "when": null, "workflow_outputs": [] }, - "13": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, - "id": 13, + "id": 16, "input_connections": { "refGenomeSource|GTFconditional|genomeDir": { "id": 2, @@ -508,7 +704,7 @@ "output_name": "output" }, "singlePaired|input1": { - "id": 8, + "id": 11, "output_name": "out1" } }, @@ -555,8 +751,8 @@ } ], "position": { - "left": 819.25, - "top": 335.9166717529297 + "left": 711.9721344157456, + "top": 703.9857277517348 }, "post_job_actions": { "HideDatasetActionsignal_unique_str1": { @@ -583,6 +779,20 @@ "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "splice_junctions" + }, + "RenameDatasetActionmapped_reads": { + "action_arguments": { + "newname": "Mapped Reads" + }, + "action_type": "RenameDatasetAction", + "output_name": "mapped_reads" + }, + "RenameDatasetActionreads_per_gene": { + "action_arguments": { + "newname": "Reads per gene from STAR" + }, + "action_type": "RenameDatasetAction", + "output_name": "reads_per_gene" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", @@ -592,126 +802,325 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"RuntimeValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"RuntimeValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.7.11a+galaxy1", "type": "tool", - "uuid": "8a26e154-29c0-426a-b0aa-215192f03596", + "uuid": "34f58f69-4107-4785-96df-f05d2d9f177c", "when": null, "workflow_outputs": [ { - "label": "output_log", - "output_name": "output_log", - "uuid": "4cb18b88-63ab-4881-afec-d6569dbd3533" - }, - { - "label": "reads_per_gene from STAR", - "output_name": "reads_per_gene", - "uuid": "056b9f4b-5208-4885-97e8-474f417537ee" - }, - { - "label": "mapped-reads", + "label": "Mapped Reads", "output_name": "mapped_reads", - "uuid": "94cb795a-4fa6-4323-af7d-99c346e83435" + "uuid": "8031b035-383e-4874-8f36-ee671b513a7e" } ] }, - "14": { + "17": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "errors": null, - "id": 14, + "id": 17, "input_connections": { - "results_0|software_cond|input": { - "id": 8, - "output_name": "report" + "alignment": { + "id": 16, + "output_name": "mapped_reads" }, - "results_1|software_cond|output_0|type|input": { - "id": 13, - "output_name": "output_log" + "anno|reference_gene_sets": { + "id": 3, + "output_name": "output" }, - "results_1|software_cond|output_1|type|input": { + "strand_specificity": { "id": 13, - "output_name": "reads_per_gene" + "output_name": "output_param_text" + }, + "when": { + "id": 4, + "output_name": "output" } }, - "inputs": [], - "label": "MultiQC", - "name": "MultiQC", - "outputs": [ + "inputs": [ { - "name": "plots", - "type": "input" + "description": "runtime parameter for tool featureCounts", + "name": "alignment" }, { - "name": "html_report", - "type": "html" + "description": "runtime parameter for tool featureCounts", + "name": "anno" + } + ], + "label": null, + "name": "featureCounts", + "outputs": [ + { + "name": "output_short", + "type": "tabular" }, { - "name": "stats", + "name": "output_summary", "type": "tabular" } ], "position": { - "left": 1195.211542597603, - "top": 0 - }, - "post_job_actions": { - "HideDatasetActionplots": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "plots" - } + "left": 1451.0321118801053, + "top": 1013.1160326850629 }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "f7e2f1eb3a16", - "name": "multiqc", + "changeset_revision": "f9d49f5cb597", + "name": "featurecounts", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.24.1+galaxy0", + "tool_state": "{\"alignment\": {\"__class__\": \"RuntimeValue\"}, \"anno\": {\"anno_select\": \"history\", \"__current_case__\": 2, \"reference_gene_sets\": {\"__class__\": \"RuntimeValue\"}, \"gff_feature_type\": \"exon\", \"gff_feature_attribute\": \"gene_id\", \"summarization_level\": false}, \"extended_parameters\": {\"multifeatures\": {\"multifeat\": \"\", \"__current_case__\": 0}, \"exon_exon_junction_read_counting_enabled\": {\"count_exon_exon_junction_reads\": \"\", \"__current_case__\": 1}, \"long_reads\": false, \"by_read_group\": false, \"largest_overlap\": false, \"min_overlap\": \"1\", \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"read_extension_5p\": \"0\", \"read_extension_3p\": \"0\", \"read_reduction\": \"\", \"R\": false}, \"format\": \"tabdel_short\", \"include_feature_length_file\": false, \"pe_parameters\": {\"paired_end_status\": \"single_end\", \"__current_case__\": 0}, \"read_filtering_parameters\": {\"mapping_quality\": \"0\", \"splitonly\": \"\", \"primary\": false, \"ignore_dup\": false}, \"strand_specificity\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.0.3+galaxy2", "type": "tool", - "uuid": "ba4d9ac2-f8b6-43bc-bc5f-e542c44441cd", - "when": null, - "workflow_outputs": [ - { - "label": "MultiQC webpage", - "output_name": "html_report", - "uuid": "24fe0860-563a-4938-b51d-6fdf10ec4175" - }, - { - "label": "MultiQC on input dataset(s): Stats", - "output_name": "stats", - "uuid": "4036a639-8e11-4de6-873f-a60183b789df" - } - ] + "uuid": "f2fd89e8-c03e-441a-a94c-6f8af0802299", + "when": "$(inputs.when)", + "workflow_outputs": [] }, - "15": { + "18": { "annotation": "", - "id": 15, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", + "errors": null, + "id": 18, "input_connections": { - "STAR BAM": { - "id": 13, - "input_subworkflow_step_id": 0, + "guide|guide_source|ref_hist": { + "id": 3, + "output_name": "output" + }, + "input_options|input_bam": { + "id": 16, "output_name": "mapped_reads" }, - "STAR log": { - "id": 13, - "input_subworkflow_step_id": 1, - "output_name": "output_log" + "rna_strandness": { + "id": 15, + "output_name": "output_param_text" + }, + "when": { + "id": 9, + "output_name": "output" } }, - "inputs": [], - "label": null, - "name": "Get Uniquely mapped unstranded coverage", - "outputs": [], - "position": { - "left": 1134, - "top": 420 - }, - "subworkflow": { - "a_galaxy_workflow": "true", + "inputs": [ + { + "description": "runtime parameter for tool StringTie", + "name": "adv" + }, + { + "description": "runtime parameter for tool StringTie", + "name": "input_options" + } + ], + "label": "Compute RPKM with StringTie", + "name": "StringTie", + "outputs": [ + { + "name": "output_gtf", + "type": "gtf" + }, + { + "name": "gene_abundance_estimation", + "type": "tabular" + } + ], + "position": { + "left": 1646.7273564460595, + "top": 1764.3142641508387 + }, + "post_job_actions": { + "HideDatasetActionoutput_gtf": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_gtf" + }, + "RenameDatasetActiongene_abundance_estimation": { + "action_arguments": { + "newname": "Gene abundance estimates from StringTie" + }, + "action_type": "RenameDatasetAction", + "output_name": "gene_abundance_estimation" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "cbf488da3b2c", + "name": "stringtie", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"adv\": {\"abundance_estimation\": true, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": true, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"rna_strandness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2.3+galaxy0", + "type": "tool", + "uuid": "b5bf2f84-4b28-48ae-90f6-beb477781643", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "Gene Abundance Estimates from StringTie", + "output_name": "gene_abundance_estimation", + "uuid": "f74d4707-f37b-4bb4-97a7-1ebf95cf5009" + } + ] + }, + "19": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", + "errors": null, + "id": 19, + "input_connections": { + "advanced_settings|library_type": { + "id": 14, + "output_name": "output_param_text" + }, + "advanced_settings|mask_file": { + "id": 8, + "output_name": "output" + }, + "bias_correction|seq_source|index": { + "id": 12, + "output_name": "out1" + }, + "input": { + "id": 16, + "output_name": "mapped_reads" + }, + "reference_annotation|reference_annotation_file": { + "id": 3, + "output_name": "output" + }, + "when": { + "id": 6, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Cufflinks", + "name": "advanced_settings" + }, + { + "description": "runtime parameter for tool Cufflinks", + "name": "advanced_settings" + }, + { + "description": "runtime parameter for tool Cufflinks", + "name": "reference_annotation" + } + ], + "label": "Compute RPKM with cufflinks", + "name": "Cufflinks", + "outputs": [ + { + "name": "genes_expression", + "type": "tabular" + }, + { + "name": "transcripts_expression", + "type": "tabular" + }, + { + "name": "assembled_isoforms", + "type": "gtf" + }, + { + "name": "total_map_mass", + "type": "txt" + }, + { + "name": "skipped", + "type": "gtf" + } + ], + "position": { + "left": 1912.2865371888552, + "top": 1491.4458958341904 + }, + "post_job_actions": { + "HideDatasetActionassembled_isoforms": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "assembled_isoforms" + }, + "HideDatasetActionskipped": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "skipped" + }, + "HideDatasetActiontotal_map_mass": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "total_map_mass" + }, + "RenameDatasetActiongenes_expression": { + "action_arguments": { + "newname": "Genes Expression from Cufflinks" + }, + "action_type": "RenameDatasetAction", + "output_name": "genes_expression" + }, + "RenameDatasetActiontranscripts_expression": { + "action_arguments": { + "newname": "Transcripts Expression from Cufflinks" + }, + "action_type": "RenameDatasetAction", + "output_name": "transcripts_expression" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", + "tool_shed_repository": { + "changeset_revision": "d080005cffe1", + "name": "cufflinks", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2.1.3", + "type": "tool", + "uuid": "5f38ce95-689a-4c5e-904c-0aaa219c4252", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "Transcripts Expression from Cufflinks", + "output_name": "transcripts_expression", + "uuid": "30246471-43f3-49ec-b0f3-ee9555c35a79" + }, + { + "label": "Genes Expression from Cufflinks", + "output_name": "genes_expression", + "uuid": "afa8e60c-8ce1-48e7-b404-9a96df9c9715" + } + ] + }, + "20": { + "annotation": "", + "id": 20, + "input_connections": { + "STAR BAM": { + "id": 16, + "input_subworkflow_step_id": 1, + "output_name": "mapped_reads" + }, + "STAR log": { + "id": 16, + "input_subworkflow_step_id": 0, + "output_name": "output_log" + } + }, + "inputs": [ + { + "description": "", + "name": "Generate Unstranded Coverage" + } + ], + "label": "Generate Unstranded Coverage", + "name": "Get Uniquely mapped unstranded coverage", + "outputs": [], + "position": { + "left": 2589.7316316136303, + "top": 86.74550095753672 + }, + "subworkflow": { + "a_galaxy_workflow": "true", "annotation": "", "comments": [], "creator": [ @@ -724,73 +1133,121 @@ "format-version": "0.1", "license": "MIT", "name": "Get Uniquely mapped unstranded coverage", + "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": "", + "annotation": "RNA STAR log files", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "", - "name": "STAR BAM" + "description": "RNA STAR log files", + "name": "STAR log" } ], - "label": "STAR BAM", + "label": "STAR log", "name": "Input dataset collection", "outputs": [], "position": { "left": 0, - "top": 45.91668701171875 + "top": 46 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "8688442b-cd63-46b3-8f36-a02e11091e4c", + "uuid": "3e3f7463-a635-44a2-a1f4-7e12aae3d25b", "when": null, "workflow_outputs": [] }, "1": { - "annotation": "", + "annotation": "Mapped BAM files generate from RNA STAR", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "", - "name": "STAR log" + "description": "Mapped BAM files generate from RNA STAR", + "name": "STAR BAM" } ], - "label": "STAR log", + "label": "STAR BAM", "name": "Input dataset collection", "outputs": [], "position": { - "left": 40, - "top": 259.91668701171875 + "left": 280, + "top": 209 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "e97ce94f-3ccb-4abf-ab75-8b76c7cb1762", + "uuid": "10dddc85-d3fc-4cba-a637-0c40153d284f", "when": null, "workflow_outputs": [] }, "2": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, "id": 2, "input_connections": { - "input_bam": { + "infile": { "id": 0, "output_name": "output" } }, "inputs": [], + "label": "get scaling factor", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 280, + "top": 20 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"code\": \"$0~\\\"Uniquely mapped reads number\\\"{print 1000000/$NF}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "77cf2304-36bf-4337-bc2d-bc4d8b831668", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2", + "errors": null, + "id": 3, + "input_connections": { + "input_bam": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], "label": "keep uniquely mapped reads", "name": "Filter BAM", "outputs": [ @@ -804,8 +1261,8 @@ } ], "position": { - "left": 260.4666748046875, - "top": 0 + "left": 560, + "top": 195 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -829,64 +1286,19 @@ "tool_state": "{\"conditions\": [{\"__index__\": 0, \"filters\": [{\"__index__\": 0, \"bam_property\": {\"bam_property_selector\": \"tag\", \"__current_case__\": 21, \"bam_property_value\": \"NH=1\"}}]}], \"input_bam\": {\"__class__\": \"ConnectedValue\"}, \"rule_configuration\": {\"rules_selector\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.5.2+galaxy2", "type": "tool", - "uuid": "8b2522f8-237b-4bb0-8429-94c029a1c9d8", + "uuid": "59db7088-85bf-42ba-9dcd-76836f9d6310", "when": null, "workflow_outputs": [] }, - "3": { + "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", + "content_id": "param_value_from_file", "errors": null, - "id": 3, + "id": 4, "input_connections": { - "infile": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": "get scaling factor", - "name": "Text reformatting", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 319.4666748046875, - "top": 300 - }, - "post_job_actions": { - "HideDatasetActionoutfile": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", - "tool_shed_repository": { - "changeset_revision": "86755160afbf", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"code\": \"$0~\\\"Uniquely mapped reads number\\\"{print 1000000/$NF}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", - "type": "tool", - "uuid": "12b386f6-5254-4389-9400-4fe5381b3336", - "when": null, - "workflow_outputs": [] - }, - "4": { - "annotation": "", - "content_id": "param_value_from_file", - "errors": null, - "id": 4, - "input_connections": { - "input1": { - "id": 3, - "output_name": "outfile" + "input1": { + "id": 2, + "output_name": "outfile" } }, "inputs": [], @@ -899,8 +1311,8 @@ } ], "position": { - "left": 584.4666748046875, - "top": 327 + "left": 560, + "top": 0 }, "post_job_actions": { "HideDatasetActionfloat_param": { @@ -913,7 +1325,7 @@ "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"float\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.0", "type": "tool", - "uuid": "2c5c3ff1-a96f-4002-937c-d0560c1b190f", + "uuid": "83e6d856-5809-419a-b4bc-639662a95751", "when": null, "workflow_outputs": [] }, @@ -924,7 +1336,7 @@ "id": 5, "input_connections": { "input_type|input": { - "id": 2, + "id": 3, "output_name": "out_file1" }, "report|scale": { @@ -951,8 +1363,8 @@ } ], "position": { - "left": 855.418361599966, - "top": 226.99244090393722 + "left": 840, + "top": 12 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -971,7 +1383,7 @@ "tool_state": "{\"d\": false, \"dz\": false, \"five\": false, \"input_type\": {\"input_type_select\": \"bam\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"report\": {\"report_select\": \"bg\", \"__current_case__\": 0, \"zero_regions\": false, \"scale\": {\"__class__\": \"ConnectedValue\"}}, \"split\": true, \"strand\": \"\", \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.31.1", "type": "tool", - "uuid": "6a733bff-0f07-454f-9e07-1abd649f8ab6", + "uuid": "df53e789-be2d-4b09-be8d-a07a35c14913", "when": null, "workflow_outputs": [] }, @@ -996,13 +1408,13 @@ } ], "position": { - "left": 1104.4183615999664, - "top": 298.7166748046875 + "left": 1120, + "top": 67 }, "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { - "newname": "both strands coverage" + "newname": "Both Strands Coverage" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" @@ -1012,59 +1424,64 @@ "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": "518f3e4f-cef7-4c50-936f-661873aee1d4", + "uuid": "62d76728-f614-48c0-9560-3abd05b8366d", "when": null, "workflow_outputs": [ { - "label": "both strands coverage", + "label": "Both Strands Coverage", "output_name": "out_file1", - "uuid": "69f8c8e8-85d2-42c5-8b28-f7ba79dbcfa7" + "uuid": "73763ad9-c132-4764-ada6-eece0c30e74f" } ] } }, "tags": [], - "uuid": "d629f889-14c9-4a3f-bf9f-1b31117e3191" + "uuid": "451bba09-1c21-4978-b693-4e64402c5787" }, "tool_id": null, "type": "subworkflow", - "uuid": "093c0e8d-69f6-4bf9-9277-3e4183be1988", + "uuid": "c472b674-81d0-4430-af81-3c15dfd5304d", "when": null, "workflow_outputs": [ { - "label": "both strands coverage", - "output_name": "both strands coverage", - "uuid": "0ee924f9-48e4-406a-b7e2-dd14a8e1640f" + "label": "Unstranded Coverage", + "output_name": "Both Strands Coverage", + "uuid": "db62edb2-0797-4b07-9325-37f8a0ad5d8f" } ] }, - "16": { + "21": { "annotation": "", - "id": 16, + "id": 21, "input_connections": { "Bedgraph strand 1": { - "id": 13, + "id": 16, "input_subworkflow_step_id": 1, "output_name": "signal_unique_str1" }, "Bedgraph strand 2": { - "id": 13, + "id": 16, "input_subworkflow_step_id": 2, "output_name": "signal_unique_str2" }, "strandedness": { - "id": 4, + "id": 5, "input_subworkflow_step_id": 0, "output_name": "output" } }, - "inputs": [], - "label": null, + "inputs": [ + { + "description": "", + "name": "Generate Stranded Coverage" + } + ], + "label": "Generate Stranded Coverage", "name": "Re-arrange Stranded RNA-seq coverage", "outputs": [], "position": { - "left": 1144, - "top": 591 + "left": 2598.7389363604525, + "top": 282.08680861650623 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1080,6 +1497,9 @@ "format-version": "0.1", "license": "MIT", "name": "Re-arrange Stranded RNA-seq coverage", + "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": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", @@ -1098,31 +1518,31 @@ "outputs": [], "position": { "left": 0, - "top": 86.19999694824209 + "top": 370 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "1865e89f-6f75-4bef-a34f-65c44f68eb83", + "uuid": "56955f25-7e9e-4201-a056-b61f47359c84", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "d9eef145-06bd-44e9-b2e5-ba276897fd0f" + "uuid": "d363c181-7f37-45ef-9732-86aaf879478a" } ] }, "1": { - "annotation": "", + "annotation": "From STAR strand 1", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "", + "description": "From STAR strand 1", "name": "Bedgraph strand 1" } ], @@ -1130,14 +1550,14 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 62.75, - "top": 182.01666259765614 + "left": 0, + "top": 472 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bedgraph\"], \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "480154cb-4343-4ed2-b106-9c20032aca7f", + "uuid": "7919f2ed-554a-4e08-93eb-6896a2195293", "when": null, "workflow_outputs": [] }, @@ -1157,14 +1577,14 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 124.7500000000002, - "top": 291.0166625976562 + "left": 569.999952609169, + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bedgraph\"], \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "99862f93-3061-4074-bb86-486b8bbf6009", + "uuid": "9318223c-4443-4341-8448-11df606ccfdf", "when": null, "workflow_outputs": [] }, @@ -1185,7 +1605,7 @@ "name": "input_param_type" } ], - "label": "Get replacement for strand1", + "label": "Get replacement for strand2", "name": "Map parameter value", "outputs": [ { @@ -1194,8 +1614,8 @@ } ], "position": { - "left": 445, - "top": 105 + "left": 289.9999763045845, + "top": 51 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -1216,10 +1636,10 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"$1_forward\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"$1_reverse\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"$1_forward\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"$1_reverse\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"$1_forward\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"$1_reverse\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "22cf84f4-9cc7-49aa-a568-39b8716311a5", + "uuid": "2ec50fce-ef76-4f56-9fc6-5c6b34c6593e", "when": null, "workflow_outputs": [] }, @@ -1240,7 +1660,7 @@ "name": "input_param_type" } ], - "label": "Get replacement for strand2", + "label": "Get replacement for strand1", "name": "Map parameter value", "outputs": [ { @@ -1249,8 +1669,8 @@ } ], "position": { - "left": 491, - "top": 283 + "left": 289.9999763045845, + "top": 359 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -1271,10 +1691,10 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"$1_reverse\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"$1_forward\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"$1_reverse\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"$1_forward\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"$1_reverse\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"$1_forward\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "d6c2ce80-2927-4a4f-beab-2afd85b899f0", + "uuid": "b7e2cedf-e846-4553-9e48-4aa9a93d40b2", "when": null, "workflow_outputs": [] }, @@ -1299,8 +1719,8 @@ } ], "position": { - "left": 351.00000000000017, - "top": 0 + "left": 289.9999763045845, + "top": 225 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", @@ -1313,7 +1733,7 @@ "tool_state": "{\"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.2", "type": "tool", - "uuid": "1fd86b13-3273-4a95-9b38-657ede0cb1a5", + "uuid": "7d866aad-dd6c-4d17-bf6d-8f0026652265", "when": null, "workflow_outputs": [] }, @@ -1333,7 +1753,7 @@ } }, "inputs": [], - "label": "New labels strand 1", + "label": "New labels strand 2", "name": "Replace", "outputs": [ { @@ -1342,8 +1762,8 @@ } ], "position": { - "left": 782, - "top": 76 + "left": 569.999952609169, + "top": 123 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1362,7 +1782,7 @@ "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"^(.+)$\", \"replace_pattern\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "9.3+galaxy1", "type": "tool", - "uuid": "930e865a-bafd-4f20-81fd-c008d781b7d2", + "uuid": "ec10a98b-adb9-4037-9137-1717068d7157", "when": null, "workflow_outputs": [] }, @@ -1382,7 +1802,7 @@ } }, "inputs": [], - "label": "New labels strand 2", + "label": "New labels strand 1", "name": "Replace", "outputs": [ { @@ -1391,8 +1811,8 @@ } ], "position": { - "left": 821, - "top": 276 + "left": 569.999952609169, + "top": 328 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1411,7 +1831,7 @@ "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"^(.+)$\", \"replace_pattern\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "9.3+galaxy1", "type": "tool", - "uuid": "7f9c10e6-8f19-4467-9549-641668c84812", + "uuid": "4eb0d67c-f53c-4f84-90fc-3db41e4f0aa7", "when": null, "workflow_outputs": [] }, @@ -1426,7 +1846,7 @@ "output_name": "outfile" }, "input": { - "id": 1, + "id": 2, "output_name": "output" } }, @@ -1436,7 +1856,7 @@ "name": "how" } ], - "label": "Relabelled strand 1", + "label": "Relabelled strand 2", "name": "Relabel identifiers", "outputs": [ { @@ -1445,8 +1865,8 @@ } ], "position": { - "left": 1056, - "top": 176.99999999999994 + "left": 849.9998437853558, + "top": 106 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1459,7 +1879,7 @@ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "89b5768c-6f33-403a-98ca-efcdb302e65a", + "uuid": "147ccbb0-b951-4851-9bf5-2c6b439ac1b6", "when": null, "workflow_outputs": [] }, @@ -1474,7 +1894,7 @@ "output_name": "outfile" }, "input": { - "id": 2, + "id": 1, "output_name": "output" } }, @@ -1484,7 +1904,7 @@ "name": "how" } ], - "label": "Relabelled strand 2", + "label": "Relabelled strand 1", "name": "Relabel identifiers", "outputs": [ { @@ -1493,8 +1913,8 @@ } ], "position": { - "left": 1077, - "top": 324.99999999999994 + "left": 849.9999005376209, + "top": 365 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1507,7 +1927,7 @@ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "554d85f6-7c54-44f7-a9f4-9b0d2d9737f6", + "uuid": "e9dcd2df-2834-4e9a-bef2-7666de012b8a", "when": null, "workflow_outputs": [] }, @@ -1518,11 +1938,11 @@ "id": 10, "input_connections": { "inputs_0|input": { - "id": 8, + "id": 9, "output_name": "output" }, "inputs_1|input": { - "id": 9, + "id": 8, "output_name": "output" } }, @@ -1536,8 +1956,8 @@ } ], "position": { - "left": 1360.7832000000906, - "top": 265.99999999999994 + "left": 1129.9999903467356, + "top": 120 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1550,7 +1970,7 @@ "tool_state": "{\"advanced\": {\"conflict\": {\"duplicate_options\": \"keep_first\", \"__current_case__\": 3}}, \"inputs\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "e3c1b832-2f79-4ce4-94d2-4e6396e569e3", + "uuid": "f47d7381-13b2-4615-b947-17a0ac2ad500", "when": null, "workflow_outputs": [] }, @@ -1575,8 +1995,8 @@ } ], "position": { - "left": 1624.7832000000903, - "top": 317.99999999999994 + "left": 1410.000136908115, + "top": 171 }, "post_job_actions": { "RenameDatasetActionout_file1": { @@ -1591,277 +2011,1377 @@ "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": "f9b2dbd6-c547-4c2e-be60-1423e06710a4", + "uuid": "852f2d23-b48e-44d0-aaf2-aed33532d98a", "when": null, "workflow_outputs": [ { - "label": "stranded coverage", + "label": "Uniquely Mapped Stranded Coverage", "output_name": "out_file1", - "uuid": "b747244f-fc40-4f20-b713-882715921a5b" + "uuid": "0a31ff80-b3d1-4959-869f-1a6a3c627dde" } ] } }, "tags": [], - "uuid": "f97bb6df-6f4c-4ccd-8108-6b2d88f35ff4" + "uuid": "f5bde9df-1387-4d76-a90c-1043c93e8de5" }, "tool_id": null, "type": "subworkflow", - "uuid": "3dbdc02e-6875-495d-841a-aae50c3b5f96", + "uuid": "be76fba3-55f5-4907-8f56-1de05fe3cf8d", "when": null, "workflow_outputs": [ { - "label": "stranded coverage", - "output_name": "stranded coverage", - "uuid": "7302e44f-8cce-466e-9672-3b510b55072b" + "label": "Stranded Coverage", + "output_name": "Uniquely Mapped Stranded Coverage", + "uuid": "bb9eec4c-9d26-4f9b-8ee3-58d6bd3a71fa" + }, + { + "label": null, + "output_name": "0:output", + "uuid": "dc44e70a-0705-48bf-a99d-33f354e00957" } ] }, - "17": { + "22": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", - "errors": null, - "id": 17, + "id": 22, "input_connections": { - "advanced_settings|library_type": { - "id": 11, - "output_name": "output_param_text" - }, - "advanced_settings|mask_file": { - "id": 6, - "output_name": "output" - }, - "bias_correction|seq_source|index": { - "id": 9, - "output_name": "out1" - }, - "input": { - "id": 13, - "output_name": "mapped_reads" + "RNA STAR count tables": { + "id": 16, + "input_subworkflow_step_id": 4, + "output_name": "reads_per_gene" }, - "reference_annotation|reference_annotation_file": { - "id": 3, + "Sample table to add tags": { + "id": 7, + "input_subworkflow_step_id": 2, "output_name": "output" }, - "when": { + "Strandness param": { "id": 5, + "input_subworkflow_step_id": 3, "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Cufflinks", - "name": "advanced_settings" - }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "advanced_settings" - }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "reference_annotation" - } - ], - "label": "Compute FPKM with cufflinks", - "name": "Cufflinks", - "outputs": [ - { - "name": "genes_expression", - "type": "tabular" - }, - { - "name": "transcripts_expression", - "type": "tabular" - }, - { - "name": "assembled_isoforms", - "type": "gtf" - }, - { - "name": "total_map_mass", - "type": "txt" - }, - { - "name": "skipped", - "type": "gtf" - } - ], - "position": { - "left": 1266.433349609375, - "top": 1002.5131353932526 - }, - "post_job_actions": { - "HideDatasetActionassembled_isoforms": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "assembled_isoforms" - }, - "HideDatasetActionskipped": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "skipped" - }, - "HideDatasetActiontotal_map_mass": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "total_map_mass" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", - "tool_shed_repository": { - "changeset_revision": "d080005cffe1", - "name": "cufflinks", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.1.3", - "type": "tool", - "uuid": "351d3b94-214e-496d-8eae-ef61174b6809", - "when": "$(inputs.when)", - "workflow_outputs": [ - { - "label": "genes_expression_cufflinks", - "output_name": "genes_expression", - "uuid": "3ca1813f-0dcd-48b3-9075-15fa3b4a2ef3" }, - { - "label": "transcripts_expression_cufflinks", - "output_name": "transcripts_expression", - "uuid": "37c571b6-cd9a-42a2-ae3e-d167daf8ef47" - } - ] - }, - "18": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", - "errors": null, - "id": 18, - "input_connections": { - "code": { - "id": 10, - "output_name": "output_param_text" + "featureCounts count table": { + "id": 17, + "input_subworkflow_step_id": 5, + "output_name": "output_short" }, - "infile": { - "id": 13, - "output_name": "reads_per_gene" + "featureCounts summaries collection": { + "id": 17, + "input_subworkflow_step_id": 1, + "output_name": "output_summary" } }, "inputs": [], - "label": "Extract gene counts", - "name": "Text reformatting", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], + "label": null, + "name": "Process Count files", + "outputs": [], "position": { - "left": 1438.3449044140093, - "top": 809.4166412353516 + "left": 1875.6228149071408, + "top": 962.4763887841759 }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "HTS count like output" + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-1964-4960", + "name": "Lucille Delisle" }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", - "tool_shed_repository": { - "changeset_revision": "86755160afbf", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"code\": {\"__class__\": \"ConnectedValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", - "type": "tool", - "uuid": "bae7a5b1-a9a1-4d45-9e8b-e375bfc27942", - "when": null, - "workflow_outputs": [ - { - "label": "HTS count like output", - "output_name": "outfile", - "uuid": "87baa6e9-1455-4537-bf0b-42d4beeba4c0" - } - ] - }, - "19": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", - "errors": null, - "id": 19, - "input_connections": { - "guide|guide_source|ref_hist": { - "id": 3, - "output_name": "output" - }, - "input_options|input_bam": { - "id": 13, - "output_name": "mapped_reads" - }, - "rna_strandness": { - "id": 12, - "output_name": "output_param_text" + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-5192-126X", + "name": "Pavankumar Videm" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "Process Count files", + "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" }, - "when": { - "id": 7, - "output_name": "output" - } + "steps": { + "0": { + "annotation": "This file will be used in MultiQC if the user opts out of featureCounts to generate count files. ", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [], + "label": "A dummy featureCounts summary file", + "name": "Create text file", + "outputs": [ + { + "name": "outfile", + "type": "txt" + } + ], + "position": { + "left": 2.142187583634133, + "top": 16 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": \"Status\\tFeaturecounts_was_not_used\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}, {\"__index__\": 1, \"line\": \"Assigned\\t0\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}, {\"__index__\": 2, \"line\": \"Unassigned_Unmapped\\t0\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "be0268be-a3ec-4d75-854b-d8eecf4b4521", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "Collection from featureCounts summaries", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Collection from featureCounts summaries", + "name": "featureCounts summaries collection" + } + ], + "label": "featureCounts summaries collection", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 4.490321414251932, + "top": 215.26828327443155 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "9ca62bd8-0272-41e2-9e4b-e8f45c4e0c19", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "name": "Sample table to add tags" + } + ], + "label": "Sample table to add tags", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 320.17684220773725 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "9b903f17-a37b-48d9-a214-bcdf393a7574", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "name": "Strandness param" + } + ], + "label": "Strandness param", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 2.142204774107931, + "top": 433.85391433745605 + }, + "tool_id": null, + "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "180fc8bd-b8f4-486b-b300-e503bf379373", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f2007283-e5e7-47e6-b922-ef6b95e50354" + } + ] + }, + "4": { + "annotation": "Count tables collection from RNA STAR", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "Count tables collection from RNA STAR", + "name": "RNA STAR count tables" + } + ], + "label": "RNA STAR count tables", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 7.511091326709437, + "top": 589.5341644488473 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "d94c5c03-7bad-493f-9f5d-c5b6f33157ae", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "Count tables collection from featureCounts", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "Count tables collection from featureCounts", + "name": "featureCounts count table" + } + ], + "label": "featureCounts count table", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 9.641580804428433, + "top": 704.0194730841151 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "12f710b8-757e-4c25-90be-4cfca673f54b", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", + "errors": null, + "id": 6, + "input_connections": { + "infile": { + "id": 0, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Text transformation", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 282.1421365930926, + "top": 0 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput": { + "action_arguments": { + "newtype": "tabular" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/__tc__/\\\\t/g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "3588c02b-15b7-487b-8970-bc76ddf8348a", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, + "id": 7, + "input_connections": { + "infile": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": "Add group: to the tags", + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 842.1424187925072, + "top": 266.17188642026633 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"(\\\\t)(?!group:)\", \"replace_pattern\": \"$1group:\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "b73de223-a60a-46ab-944f-71378f03df16", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 8, + "input_connections": { + "input_param_type|input_param": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": "awk command from strand for STAR counts", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_text", + "type": "expression.json" + } + ], + "position": { + "left": 282.1421709032883, + "top": 401.33828843669767 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_text": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_text" + } + }, + "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\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"NR>4{print $1\\\"\\\\t\\\"$3}\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"NR>4{print $1\\\"\\\\t\\\"$4}\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"NR>4{print $1\\\"\\\\t\\\"$2}\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", + "type": "tool", + "uuid": "2b9a5ca1-e974-450b-99b3-3fcce531154b", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "featureCounts summaries", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "errors": null, + "id": 9, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 1, + "output_name": "output" + }, + "style_cond|type_cond|pick_from_1|value": { + "id": 6, + "output_name": "output" + } + }, + "inputs": [], + "label": "featureCounts summaries", + "name": "Pick parameter value", + "outputs": [ + { + "name": "data_param", + "type": "input" + } + ], + "position": { + "left": 842.1422267022583, + "top": 16 + }, + "post_job_actions": { + "RenameDatasetActiondata_param": { + "action_arguments": { + "newname": "FeatureCounts Summary Table" + }, + "action_type": "RenameDatasetAction", + "output_name": "data_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\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", + "type": "tool", + "uuid": "26eca035-e403-4392-9ba9-08cd471154dd", + "when": null, + "workflow_outputs": [ + { + "label": "FeatureCounts Summary Table", + "output_name": "data_param", + "uuid": "8c15f8aa-f2eb-41bf-bbaa-947263f3bfec" + } + ] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", + "errors": null, + "id": 10, + "input_connections": { + "code": { + "id": 8, + "output_name": "output_param_text" + }, + "infile": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [], + "label": "Extract gene counts", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 562.1422776927999, + "top": 386.17188642026633 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "HTS count like output" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"code\": {\"__class__\": \"ConnectedValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "34922bd3-4676-4f7d-8e05-af0ef0c1efa4", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "Counts Table ", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "errors": null, + "id": 11, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 5, + "output_name": "output" + }, + "style_cond|type_cond|pick_from_1|value": { + "id": 10, + "output_name": "outfile" + } + }, + "inputs": [], + "label": "Counts table", + "name": "Pick parameter value", + "outputs": [ + { + "name": "data_param", + "type": "input" + } + ], + "position": { + "left": 839.142341368268, + "top": 413.1722363660909 + }, + "post_job_actions": { + "RenameDatasetActiondata_param": { + "action_arguments": { + "newname": "Counts Table" + }, + "action_type": "RenameDatasetAction", + "output_name": "data_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\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", + "type": "tool", + "uuid": "d87cdd15-8b7c-4498-a818-7369ee4e006a", + "when": null, + "workflow_outputs": [] + }, + "12": { + "annotation": "Used as input for DESeq2", + "content_id": "__TAG_FROM_FILE__", + "errors": null, + "id": 12, + "input_connections": { + "input": { + "id": 11, + "output_name": "data_param" + }, + "tags": { + "id": 7, + "output_name": "outfile" + } + }, + "inputs": [], + "label": "Tag count bables", + "name": "Tag elements", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 1122.1425598922144, + "top": 278.17188642026633 + }, + "post_job_actions": {}, + "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": "d145af57-9b56-4927-8bee-3cf672caa2f9", + "when": null, + "workflow_outputs": [ + { + "label": "Tagged Count Tables", + "output_name": "output", + "uuid": "ddba8ac1-ab03-4949-8d2e-961c9bd8b398" + } + ] + } + }, + "tags": [], + "uuid": "06461dd0-7388-4676-94d5-c068ea2562a1" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "68669f89-0c91-4a94-bf2c-813a3385275a", + "when": null, + "workflow_outputs": [ + { + "label": "FeatureCounts Summary Table", + "output_name": "FeatureCounts Summary Table", + "uuid": "61a32f3a-5c41-4381-86d5-cd0bd39a0197" + }, + { + "label": "Tagged Count Tables", + "output_name": "Tagged Count Tables", + "uuid": "60594b49-2c52-4da2-8176-25693a483b33" + }, + { + "label": null, + "output_name": "3:output", + "uuid": "c5bfce56-c552-4b85-a4a8-15aaaecf4c57" + } + ] + }, + "23": { + "annotation": "", + "id": 23, + "input_connections": { + "Cutadapt Reports": { + "id": 11, + "input_subworkflow_step_id": 2, + "output_name": "report" + }, + "FASTQ collection": { + "id": 0, + "input_subworkflow_step_id": 0, + "output_name": "output" + }, + "STAR logs": { + "id": 16, + "input_subworkflow_step_id": 3, + "output_name": "output_log" + }, + "STAR paired-end BAM": { + "id": 16, + "input_subworkflow_step_id": 5, + "output_name": "mapped_reads" + }, + "featureCounts summaries": { + "id": 22, + "input_subworkflow_step_id": 1, + "output_name": "FeatureCounts Summary Table" + }, + "reference_annotation_gtf": { + "id": 3, + "input_subworkflow_step_id": 4, + "output_name": "output" + }, + "when": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "", + "name": "Combined MultiQC Quality Report" + } + ], + "label": "Combined MultiQC Quality Report", + "name": "RNA-seq-Paired-QC", + "outputs": [], + "position": { + "left": 2581.8385293658202, + "top": 574.7767421741249 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-5192-126X", + "name": "Pavankumar Videm" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "RNA-seq-Paired-QC", + "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": "RNA-seq paired FASTQ collection", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "RNA-seq paired FASTQ collection", + "name": "FASTQ collection" + } + ], + "label": "FASTQ collection", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 0, + "top": 0 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "1bb12b7e-2ee1-4d8a-80d6-4259bea1efae", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "featureCounts Summaries file", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "featureCounts Summaries file", + "name": "featureCounts summaries" + } + ], + "label": "featureCounts summaries", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 21.653447845324965, + "top": 474.2009198740476 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "5a5cb076-92cb-48bd-80e0-d7bfa19fe969", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "Cutadapt Reports", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Cutadapt Reports", + "name": "Cutadapt Reports" + } + ], + "label": "Cutadapt Reports", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 561.109657767363, + "top": 318.00000311286055 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "43c69a53-b1dc-4089-9801-18e980088a2e", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "STAR log files", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "STAR log files", + "name": "STAR logs" + } + ], + "label": "STAR logs", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 568.1890947745617, + "top": 448.0768645395773 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "5ae91949-4ffe-4aef-81fa-fa3cb4e86f5a", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "Reference annotation", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "Reference annotation", + "name": "reference_annotation_gtf" + } + ], + "label": "reference_annotation_gtf", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 2.1095586103713773, + "top": 757.9999851090132 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "9657bd5f-5510-412b-9128-0bb903e2f572", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "Mapped BAM files from STAR", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "Mapped BAM files from STAR", + "name": "STAR paired-end BAM" + } + ], + "label": "STAR paired-end BAM", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 1.1095706393493272, + "top": 907.0000031128606 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "b3a7345d-49fa-4b34-bd56-565f250f6d97", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", + "errors": null, + "id": 6, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool FastQC", + "name": "adapters" + }, + { + "description": "runtime parameter for tool FastQC", + "name": "contaminants" + }, + { + "description": "runtime parameter for tool FastQC", + "name": "limits" + } + ], + "label": "FastQC check read qualities", + "name": "FastQC", + "outputs": [ + { + "name": "html_file", + "type": "html" + }, + { + "name": "text_file", + "type": "txt" + } + ], + "position": { + "left": 560.0000308495477, + "top": 1.999988137762914 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", + "tool_shed_repository": { + "changeset_revision": "2c64fded1286", + "name": "fastqc", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.74+galaxy1", + "type": "tool", + "uuid": "d4f16966-836e-49cd-8987-18b6e68205b8", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357", + "errors": null, + "id": 7, + "input_connections": { + "gtf_file": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [], + "label": "convert gtf to bed12", + "name": "Convert GTF to BED12", + "outputs": [ + { + "name": "bed_file", + "type": "bed12" + } + ], + "position": { + "left": 281.10957032320283, + "top": 743.0000031128606 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357", + "tool_shed_repository": { + "changeset_revision": "b026dae67fba", + "name": "gtftobed12", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"advanced_options\": {\"advanced_options_selector\": \"default\", \"__current_case__\": 0}, \"gtf_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "357", + "type": "tool", + "uuid": "ed8685b7-7904-4f28-8ea9-2faffb05bacf", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", + "errors": null, + "id": 8, + "input_connections": { + "input": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": "Subsample 200k reads", + "name": "Samtools view", + "outputs": [ + { + "name": "outputsam", + "type": "input" + } + ], + "position": { + "left": 281.10934435907967, + "top": 895.3505751212938 + }, + "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\": null, \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": \"\", \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": \"200000\", \"seed\": \"1\"}}, \"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": "fa918b19-c767-43dd-afb6-fcdb3cd20fa7", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", + "errors": null, + "id": 9, + "input_connections": { + "input": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": "Get reads number per chromosome", + "name": "Samtools idxstats", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 281.1095878752642, + "top": 1102.0000031128604 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", + "tool_shed_repository": { + "changeset_revision": "fa5d3e61e429", + "name": "samtools_idxstats", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.0.5", + "type": "tool", + "uuid": "0c0789f8-21d9-4fdc-80c6-488aded24611", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0", + "errors": null, + "id": 10, + "input_connections": { + "inputFile": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": "Remove duplicates", + "name": "MarkDuplicates", + "outputs": [ + { + "name": "metrics_file", + "type": "txt" + }, + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 279.4598772618595, + "top": 1252.3383843362294 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0", + "tool_shed_repository": { + "changeset_revision": "3f254c5ced1d", + "name": "picard", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"assume_sorted\": true, \"barcode_tag\": \"\", \"comments\": [], \"duplicate_scoring_strategy\": \"SUM_OF_BASE_QUALITIES\", \"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"optical_duplicate_pixel_distance\": \"100\", \"read_name_regex\": \"\", \"remove_duplicates\": false, \"validation_stringency\": \"LENIENT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.1.1.0", + "type": "tool", + "uuid": "c8d04f50-da21-4f5b-9d64-2dc652b71d77", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0", + "errors": null, + "id": 11, + "input_connections": { + "input": { + "id": 5, + "output_name": "output" + }, + "refgene": { + "id": 7, + "output_name": "bed_file" + } + }, + "inputs": [], + "label": "Read distribution over genomic features", + "name": "Read Distribution", + "outputs": [ + { + "name": "output", + "type": "txt" + } + ], + "position": { + "left": 551.1095706393493, + "top": 634.0000031128606 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "27e16a30667a", + "name": "rseqc", + "owner": "nilesh", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"refgene\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.0.3+galaxy0", + "type": "tool", + "uuid": "4ecf1a7a-8648-4224-9c04-ab5d33614d63", + "when": null, + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0", + "errors": null, + "id": 12, + "input_connections": { + "batch_mode|input": { + "id": 8, + "output_name": "outputsam" + }, + "refgene": { + "id": 7, + "output_name": "bed_file" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Gene Body Coverage (BAM)", + "name": "batch_mode" + } + ], + "label": "Get gene body coverage", + "name": "Gene Body Coverage (BAM)", + "outputs": [ + { + "name": "outputcurvespdf", + "type": "pdf" + }, + { + "name": "outputtxt", + "type": "txt" + } + ], + "position": { + "left": 550.109375, + "top": 844 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "27e16a30667a", + "name": "rseqc", + "owner": "nilesh", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"batch_mode\": {\"batch_mode_selector\": \"batch\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"minimum_length\": \"100\", \"refgene\": {\"__class__\": \"ConnectedValue\"}, \"rscript_output\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.0.3+galaxy0", + "type": "tool", + "uuid": "c996512e-789b-422c-833c-de854e30674f", + "when": null, + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", + "errors": null, + "id": 13, + "input_connections": { + "results_0|software_cond|output_0|input": { + "id": 6, + "output_name": "text_file" + }, + "results_1|software_cond|input": { + "id": 2, + "output_name": "output" + }, + "results_2|software_cond|output_0|type|input": { + "id": 3, + "output_name": "output" + }, + "results_3|software_cond|output_0|type|input": { + "id": 11, + "output_name": "output" + }, + "results_4|software_cond|output_0|input": { + "id": 10, + "output_name": "metrics_file" + }, + "results_5|software_cond|output_0|type|input": { + "id": 12, + "output_name": "outputtxt" + }, + "results_6|software_cond|output_0|type|input": { + "id": 9, + "output_name": "output" + }, + "results_7|software_cond|input": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": "Combined Quality Report", + "name": "MultiQC", + "outputs": [ + { + "name": "html_report", + "type": "html" + }, + { + "name": "stats", + "type": "tabular" + } + ], + "position": { + "left": 871.1096398991552, + "top": 404.00000311286055 + }, + "post_job_actions": { + "RenameDatasetActionhtml_report": { + "action_arguments": { + "newname": "MultiQC HTML report" + }, + "action_type": "RenameDatasetAction", + "output_name": "html_report" + }, + "RenameDatasetActionstats": { + "action_arguments": { + "newname": "MultiQC Stats table" + }, + "action_type": "RenameDatasetAction", + "output_name": "stats" + } + }, + "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\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 7, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", + "type": "tool", + "uuid": "b5e9c0d2-62f4-41b2-a1c7-5677d8555fd4", + "when": null, + "workflow_outputs": [ + { + "label": "MultiQC stats", + "output_name": "stats", + "uuid": "cbf99516-9349-4f2a-ad1f-05c732cb5263" + }, + { + "label": "MultiQC HTML report", + "output_name": "html_report", + "uuid": "7306cd4b-1017-4542-bf57-81d2d83d6a97" + } + ] + } + }, + "tags": [], + "uuid": "8518a66b-6e91-4252-a543-0109bf7bb75e" }, - "inputs": [ + "tool_id": null, + "type": "subworkflow", + "uuid": "cf90f07d-b841-425a-89a6-18b2928ca9de", + "when": "$(inputs.when)", + "workflow_outputs": [ { - "description": "runtime parameter for tool StringTie", - "name": "adv" + "label": "MultiQC stats", + "output_name": "MultiQC stats", + "uuid": "b497d2f7-8ff4-4dc0-84c9-b6eabc2b3061" }, { - "description": "runtime parameter for tool StringTie", - "name": "input_options" + "label": "MultiQC HTML report", + "output_name": "MultiQC HTML report", + "uuid": "7c654b48-4142-420d-9c1b-8de88ddfa7d6" + } + ] + }, + "24": { + "annotation": "Count files have a header if featureCounts is used.", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", + "errors": null, + "id": 24, + "input_connections": { + "batch_factors": { + "id": 10, + "output_name": "output" + }, + "header": { + "id": 4, + "output_name": "output" + }, + "select_data|countsFile": { + "id": 22, + "output_name": "Tagged Count Tables" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool DESeq2", + "name": "select_data" } ], - "label": "Compute FPKM with StringTie", - "name": "StringTie", + "label": "Differential expression analysis using DESeq2", + "name": "DESeq2", "outputs": [ { - "name": "output_gtf", - "type": "gtf" + "name": "deseq_out", + "type": "tabular" }, { - "name": "gene_abundance_estimation", - "type": "tabular" + "name": "plots", + "type": "pdf" } ], "position": { - "left": 1224.9188687452759, - "top": 1561.7042971930236 + "left": 2566.26663539139, + "top": 1017.2514257011151 }, "post_job_actions": { - "HideDatasetActionoutput_gtf": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_gtf" + "RenameDatasetActiondeseq_out": { + "action_arguments": { + "newname": "Differential expression analysis using DESeq2" + }, + "action_type": "RenameDatasetAction", + "output_name": "deseq_out" + }, + "RenameDatasetActionplots": { + "action_arguments": { + "newname": "DESeq2 Plots" + }, + "action_type": "RenameDatasetAction", + "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "tool_shed_repository": { - "changeset_revision": "cbf488da3b2c", - "name": "stringtie", + "changeset_revision": "8fe98f7094de", + "name": "deseq2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"abundance_estimation\": true, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": true, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"rna_strandness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.3+galaxy0", + "tool_state": "{\"advanced_options\": {\"esf\": \"\", \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}}, \"batch_factors\": {\"__class__\": \"ConnectedValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.11.40.7+galaxy2", "type": "tool", - "uuid": "d87ca6aa-3738-49a3-8090-41aa896b52fa", - "when": "$(inputs.when)", + "uuid": "d569d7b8-556e-4d79-9e1e-138a8f0ee692", + "when": null, "workflow_outputs": [ { - "label": "genes_expression_stringtie", - "output_name": "gene_abundance_estimation", - "uuid": "07d67129-87be-4281-b82b-64fcb300b0e1" + "label": "Differential Expression Analysis using DESeq2", + "output_name": "deseq_out", + "uuid": "16fe60d6-d1c1-42d7-850a-63d91328e963" + }, + { + "label": "DESeq2 Plots", + "output_name": "plots", + "uuid": "4bdc4546-d7b8-48b2-8fa6-72e887033462" } ] } @@ -1869,6 +3389,6 @@ "tags": [ "RNAseq" ], - "uuid": "6a424c0e-eb24-4f61-8750-adc09f4db1b1", - "version": 1 + "uuid": "047610eb-d2c4-4d6c-aca2-7b70dd351d50", + "version": 3 } \ No newline at end of file From e4bb5bf9250b36437e4b5f40077035e048e41d54 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 22 Oct 2024 18:17:44 +0200 Subject: [PATCH 02/10] update gtf and sample tables links --- workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 86c667abf..e35e5436c 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -2,12 +2,12 @@ job: GTF file of annotation: class: File - path: test-data/GTF file of annotation.gtf + location: https://zenodo.org/records/13951092/files/chr4.gtf filetype: gtf Sample table: class: File - location: https://zenodo.org/records/13951092/files/chr4.gtf - filetype: gtf + location: https://zenodo.org/records/13951092/files/Sample_table.tabular + filetype: tabular Collection single-end FASTQ files: class: Collection collection_type: list From 727ff8d5ceb493e84e1c5cd70ca28ae5ffae50a7 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 22 Oct 2024 18:22:20 +0200 Subject: [PATCH 03/10] fix tests formatting --- workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index e35e5436c..a1ce76e04 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -45,7 +45,8 @@ asserts: has_text_matching: expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" - expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" DESeq2 Plots: + expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" + DESeq2 Plots: has_size: size: 33420 delta: 1500 From 1386a9254b3af64d9be0055d880cbe8c73c263f2 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 28 Oct 2024 19:38:17 +0100 Subject: [PATCH 04/10] add new Yeast test data and remove deseq2 step --- .../rnaseq-sr/rnaseq-sr-tests.yml | 230 +-- .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 1280 +++++++---------- 2 files changed, 579 insertions(+), 931 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index a1ce76e04..4a58034fe 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -1,212 +1,76 @@ -- doc: Test outline for rnaseq-sr +- doc: Test outline for RNAseq_SR job: GTF file of annotation: class: File - location: https://zenodo.org/records/13951092/files/chr4.gtf + location: https://zenodo.org/records/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf filetype: gtf - Sample table: - class: File - location: https://zenodo.org/records/13951092/files/Sample_table.tabular - filetype: tabular - Collection single-end FASTQ files: + Collection paired FASTQ files: class: Collection collection_type: list elements: - class: File - identifier: GSM461177 - location: https://zenodo.org/records/13951092/files/GSM461177_1.fastqsanger - - class: File - identifier: GSM461178 - location: https://zenodo.org/records/13951092/files/GSM461178_1.fastqsanger - - class: File - identifier: GSM461180 - location: https://zenodo.org/records/13951092/files/GSM461180_1.fastqsanger - - class: File - identifier: GSM461181 - location: https://zenodo.org/records/13951092/files/GSM461181_1.fastqsanger - Generate QC reports?: true - Reference genome: dm6 + identifier: SRR5085168 + location: https://zenodo.org/records/13987631/files/SRR5085167_forward.fastqsanger.gz + Forward adapter: AGATCGGAAGAG + Generate QC reports: true + Reference genome: sacCer3 + Strandedness: stranded - forward Use featureCounts for generating count tables: true - strandedness: unstranded - Compute Cufflinks RPKM?: true - GTF with regions to exclude from RPKM normalization with Cufflinks: null - Compute StringTie RPKM?: true - DEseq2 batch factors: null + Compute Cufflinks FPKM: true + GTF with regions to exclude from FPKM normalization with Cufflinks: null + Compute StringTie FPKM: true outputs: MultiQC stats: - has_text_matching: - expression: "GSM461177\t0.04[0-9]*\t80.94[0-9]*\t0.61[0-9]*\t0.05[0-9]*\t0.04[0-9]*\t99.32[0-9]*\t0.04[0-9]*\t95.98\t0.00[0-9]*\t1.86[0-9]*" - expression: "GSM461177_forward\t\t\t\t\t\t\t\t\t\t\t27.95[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" - expression: "GSM461177_reverse\t\t\t\t\t\t\t\t\t\t\t28.22[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" - expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" - expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" - expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" - Differential Expression Analysis using DESeq2: asserts: has_text_matching: - expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" - expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" - DESeq2 Plots: - has_size: - size: 33420 - delta: 1500 - Mapped Reads: - element_tests: - GSM461177: - has_size: - value: 3058282 - delta: 150000 - GSM461178: - has_size: - value: 3032322 - delta: 150000 - GSM461180: - has_size: - value: 3165439 - delta: 150000 - GSM461181: - has_size: - value: 3075214 - delta: 150000 - Transcripts Expression from Cufflinks: + expression: "SRR5085167\t0.11[0-9]*\t18.14[0-9]*\t69.79[0-9]*\t0.37[0-9]*\t0.35[0-9]*\t94.81\t0.12[0-9]*\t34.32\t0.22[0-9]*\t37.78[0-9]*\t36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" + FeatureCounts Summary Table: element_tests: - GSM461177: - asserts: - has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" - GSM461178: - asserts: - has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 370.382 128757 122145 135370 OK" - GSM461180: - asserts: + SRR5085167: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 366.172 122426 116120 128732 OK" - GSM461181: - asserts: - has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 404.198 115973 110059 121886 OK" - Genes Expression from Cufflinks: + line: "Assigned 115717" + Counts Table: element_tests: - GSM461177: - asserts: - has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" - GSM461178: - asserts: - has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 141422 134823 148020 OK" - GSM461180: - asserts: - has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 134779 128494 141063 OK" - GSM461181: - asserts: + SRR5085167: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 127880 121988 133772 OK" - Unstranded Coverage: - element_tests: - GSM461177: - has_size: - value: 445281 - delta: 20000 - GSM461178: - has_size: - value: 406443 - delta: 20000 - GSM461180: - has_size: - value: 423518 - delta: 20000 - GSM461181: - has_size: - value: 455334 - delta: 20000 - Stranded Coverage: + line: "YAL038W 1813" + Mapped Reads: element_tests: - GSM461177_forward: + SRR5085167: has_size: - value: 313382 - delta: 15000 - GSM461178_forward: - has_size: - value: 285608 - delta: 15000 - GSM461180_forward: - has_size: - value: 295650 - delta: 15000 - GSM461181_forward: - has_size: - value: 311698 - delta: 15000 - GSM461177_reverse: - has_size: - value: 313241 - delta: 15000 - GSM461178_reverse: - has_size: - value: 281153 - delta: 15000 - GSM461180_reverse: - has_size: - value: 292239 - delta: 15000 - GSM461181_reverse: - has_size: - value: 322248 - delta: 15000 + value: 56913572 + delta: 2500000 Gene Abundance Estimates from StringTie: element_tests: - GSM461177: - asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" - GSM461178: + SRR5085167: asserts: has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t286.68[0-9]*\t143296.84[0-9]*\t365993.15[0-9]*" - GSM461180: - asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t282.60[0-9]*\t138208.90[0-9]*\t367356.56[0-9]*" - GSM461181: - asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" - FeatureCounts Summary Table: + expression: "YAL038W\tCDC19\tchrI\t\\+\t71786\t73288\t57.46[0-9]*\t3549.28[0-9]*\t3066.13[0-9]*" + Genes Expression from Cufflinks: element_tests: - GSM461177: - asserts: - has_line: - line: "Assigned 45715" - GSM461178: + SRR5085167: asserts: has_line: - line: "Assigned 38738" - GSM461180: - asserts: - has_line: - line: "Assigned 39998" - GSM461181: - asserts: - has_line: - line: "Assigned 44734" - Tagged Count Tables: + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3350.92 3139.33 3562.52 OK" + Transcripts Expression from Cufflinks: element_tests: - GSM461177: + SRR5085167: asserts: has_line: - line: "FBgn0017545 6109" - GSM461178: - asserts: - has_line: - line: "FBgn0017545 5649" - GSM461180: - asserts: - has_line: - line: "FBgn0017545 5600" - GSM461181: - asserts: - has_line: - line: "FBgn0017545 5943" \ No newline at end of file + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 57.4859 3350.92 3139.33 3562.52 OK" + Stranded Coverage: + element_tests: + SRR5085167_forward: + has_size: + value: 635210 + delta: 30000 + SRR5085167_reverse: + has_size: + value: 618578 + delta: 30000 + Unstranded Coverage: + element_tests: + SRR5085167: + has_size: + value: 1140004 + delta: 50000 diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index 952daa985..69c3036a8 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -1,21 +1,21 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of single-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. RPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", + "annotation": "This workflow takes as input a list of single-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. Alternatively, featureCounts can be used to count the reads/fragments per gene. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.\n", "comments": [ { "child_steps": [ - 12, - 18, - 19 + 11, + 19, + 20 ], "color": "yellow", "data": { "title": "Additional quantification" }, - "id": 1, + "id": 2, "position": [ - 1306.2, - 1413.8 + 1391.2086321940171, + 1073.6999999999998 ], "size": [ 860, @@ -25,9 +25,9 @@ }, { "child_steps": [ + 12, 13, - 14, - 15 + 14 ], "color": "lime", "data": { @@ -35,8 +35,8 @@ }, "id": 0, "position": [ - 770.5, - 1592.6 + 855.5086321940169, + 1252.5 ], "size": [ 251, @@ -46,16 +46,16 @@ }, { "child_steps": [ - 20, - 21 + 16, + 17 ], "color": "red", "data": { "title": "Coverage Files" }, - "id": 2, + "id": 1, "position": [ - 2510.1, + 1603.68749985966, 0 ], "size": [ @@ -80,163 +80,163 @@ "format-version": "0.1", "license": "MIT", "release": "0.10", - "name": "rnaseq-sr", + "name": "RNAseq_SR", "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": "A list of single-end RNA-seq fastqs", + "annotation": "Should be a list of paired-end RNA-seq fastqs", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "A list of single-end RNA-seq fastqs", - "name": "Collection single-end FASTQ files" + "description": "Should be a list of paired-end RNA-seq fastqs", + "name": "Collection paired FASTQ files" } ], - "label": "Collection single-end FASTQ files", + "label": "Collection paired FASTQ files", "name": "Input dataset collection", "outputs": [], "position": { "left": 0, - "top": 1007.0008028213834 + "top": 462.87500890145213 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "d237002d-df52-4260-90c9-fffaf8c1816f", + "uuid": "020f7580-f647-471f-b210-dbf9dfcf80bf", "when": null, "workflow_outputs": [] }, "1": { - "annotation": "Whether to report QC", + "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Whether to report QC", - "name": "Generate QC reports?" + "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "name": "Forward adapter" } ], - "label": "Generate QC reports?", + "label": "Forward adapter", "name": "Input parameter", "outputs": [], "position": { - "left": 40.67737161137343, - "top": 1117.6931018245803 + "left": 35.17186494140515, + "top": 567.328103383874 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "6e56335f-7e1d-4268-ba1d-743f149a8f67", + "uuid": "6d1de206-97c4-41ba-8702-a980f748a689", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "f71c8f8f-3a3d-432e-a969-8cfe5c07f73b" + "uuid": "ac090bb1-908d-4de0-88a4-df7154718ed5" } ] }, "2": { - "annotation": "Select the reference genome", + "annotation": "Whether to report QC", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Select the reference genome", - "name": "Reference genome" + "description": "Whether to report QC", + "name": "Generate QC reports" } ], - "label": "Reference genome", + "label": "Generate QC reports", "name": "Input parameter", "outputs": [], "position": { - "left": 70.67734212335759, - "top": 1229.3288050461836 + "left": 114.671875, + "top": 764.5781339014521 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "228cdc54-bca1-4237-a0b8-ec51e2ec29ec", + "uuid": "bea331ce-d6fa-4312-8dce-a8b13bc4e77b", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "6eee62e6-3ed0-410c-8cb6-50be2115625b" + "uuid": "82263d1b-8581-402a-b30c-e7ff3ebc289c" } ] }, "3": { - "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", + "annotation": "Select the reference genome", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", - "name": "GTF file of annotation" + "description": "Select the reference genome", + "name": "Reference genome" } ], - "label": "GTF file of annotation", - "name": "Input dataset", + "label": "Reference genome", + "name": "Input parameter", "outputs": [], "position": { - "left": 120.67736637119827, - "top": 1326.5006367761569 + "left": 157.109375, + "top": 870.218728383874 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, - "type": "data_input", - "uuid": "f9a61edb-782b-4af5-a2c9-163168bee1b9", + "type": "parameter_input", + "uuid": "a72b29ae-65a7-4e4d-a996-2943ab5b02aa", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "be8822c1-1160-4a04-b05d-e5c7ed82eb83" + } + ] }, "4": { - "annotation": "Use featureCounts tool instead of RNA STAR?", + "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "Use featureCounts tool instead of RNA STAR?", - "name": "Use featureCounts for generating count tables" + "description": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", + "name": "GTF file of annotation" } ], - "label": "Use featureCounts for generating count tables", - "name": "Input parameter", + "label": "GTF file of annotation", + "name": "Input dataset", "outputs": [], "position": { - "left": 160.33752190255188, - "top": 1435.2340383001115 + "left": 199.671875, + "top": 977.3906033838739 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, - "type": "parameter_input", - "uuid": "0c6b0c89-1ee2-4de1-8ce5-31dbb24ee1e1", + "type": "data_input", + "uuid": "4987fd01-b72c-4bc0-9d49-a840a0d04b8e", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "50dead7e-db45-40db-8734-6ed48f33dd8b" - } - ] + "workflow_outputs": [] }, "5": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", @@ -247,89 +247,95 @@ "inputs": [ { "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", - "name": "strandedness" + "name": "Strandedness" } ], - "label": "strandedness", + "label": "Strandedness", "name": "Input parameter", "outputs": [], "position": { - "left": 203.8828886044653, - "top": 1570.8860110851008 + "left": 251.890625, + "top": 1073.781228383874 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "1f5b92ff-26f4-4c26-8e1b-f0e0c90f0608", + "uuid": "2ccf2242-dddd-45b6-8cea-746d9b5d49bc", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "de3792de-9587-459d-b8c4-8563f011510d" + "uuid": "ce9da8c4-ef45-4aac-bd43-28018c6567bb" } ] }, "6": { - "annotation": "Whether FPKM values should be computed with Cufflinks", + "annotation": "Use featureCounts tool instead of RNA STAR?", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { - "description": "Whether FPKM values should be computed with Cufflinks", - "name": "Compute Cufflinks RPKM?" + "description": "Use featureCounts tool instead of RNA STAR?", + "name": "Use featureCounts for generating count tables" } ], - "label": "Compute Cufflinks RPKM?", + "label": "Use featureCounts for generating count tables", "name": "Input parameter", "outputs": [], "position": { - "left": 228.7717684962176, - "top": 1666.0254709507822 + "left": 291.34375, + "top": 1173.124978383874 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "d7141054-23ac-40bf-abbb-6834251cf2ef", + "uuid": "f43d45e6-5692-41cb-8cfc-205dbeab1bd0", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "1f3e3c7e-e42e-41b5-ab29-f4cc20170dc4" + "uuid": "ba6886ad-ef06-4787-b939-8aa8816ca720" } ] }, "7": { - "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "annotation": "Whether FPKM values should be computed with Cufflinks", "content_id": null, "errors": null, "id": 7, "input_connections": {}, "inputs": [ { - "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "name": "Sample table" + "description": "Whether FPKM values should be computed with Cufflinks", + "name": "Compute Cufflinks FPKM" } ], - "label": "Sample table", - "name": "Input dataset", + "label": "Compute Cufflinks FPKM", + "name": "Input parameter", "outputs": [], "position": { - "left": 1462.1645523806205, - "top": 909.2581294996864 + "left": 346.83340121591186, + "top": 1309.3879390873915 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, - "type": "data_input", - "uuid": "f7bf6134-db9e-4ae1-9454-689e9a54ddc8", + "type": "parameter_input", + "uuid": "78868cdb-baff-4388-a41a-a700259da1ed", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "e27d8921-adb5-444d-bed3-62f7a82d7dfc" + } + ] }, "8": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", @@ -340,27 +346,27 @@ "inputs": [ { "description": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", - "name": "GTF with regions to exclude from RPKM normalization with Cufflinks" + "name": "GTF with regions to exclude from FPKM normalization with Cufflinks" } ], - "label": "GTF with regions to exclude from RPKM normalization with Cufflinks", + "label": "GTF with regions to exclude from FPKM normalization with Cufflinks", "name": "Input dataset", "outputs": [], "position": { - "left": 260.1137371795465, - "top": 1784.313630812311 + "left": 380.53912206977975, + "top": 1425.307227138327 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "ee50d135-7758-4bd9-a85d-176f3118b103", + "uuid": "0d4e1623-adc9-4ff3-8156-7e1322b1e278", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "4ea1a61a-0c5b-4d51-a23a-187b6a381269" + "uuid": "e8fb1d01-f053-40a0-a164-fac721cbdbf6" } ] }, @@ -373,72 +379,43 @@ "inputs": [ { "description": "Whether FPKM values should be computed with StringTie", - "name": "Compute StringTie RPKM?" + "name": "Compute StringTie FPKM" } ], - "label": "Compute StringTie RPKM?", + "label": "Compute StringTie FPKM", "name": "Input parameter", "outputs": [], "position": { - "left": 268.7808865853354, - "top": 1905.5010561327158 + "left": 406.9259176995931, + "top": 1559.4856968335116 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "dc096947-90a1-4ba3-9e90-22976d894ad2", + "uuid": "056f11f4-bdd9-4361-b037-2c0822320cc2", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "3295d7f4-50f0-4c50-84ea-e0cfbf23671e" + "uuid": "f15cc7f8-5d17-4ad8-ba30-f6e4b430c07f" } ] }, "10": { - "annotation": "Tabular file with additional batch factors to include in the model", - "content_id": null, - "errors": null, - "id": 10, - "input_connections": {}, - "inputs": [ - { - "description": "Tabular file with additional batch factors to include in the model", - "name": "DEseq2 batch factors" - } - ], - "label": "DEseq2 batch factors", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 2203.102316887585, - "top": 1355.0225413410844 - }, - "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "176298e5-b11c-4637-a4b8-034c9c1b418d", - "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "12faad0d-49ae-44d5-bad3-f8032dc01e4b" - } - ] - }, - "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 11, + "id": 10, "input_connections": { "library|input_1": { "id": 0, "output_name": "output" + }, + "library|r1|adapters_0|adapter_source|adapter": { + "id": 1, + "output_name": "output" } }, "inputs": [ @@ -460,8 +437,8 @@ } ], "position": { - "left": 239.35765144976227, - "top": 494.46848655874044 + "left": 378.49997163276, + "top": 300.7500028626845 }, "post_job_actions": { "HideDatasetActionout1": { @@ -487,21 +464,21 @@ "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.9+galaxy1", "type": "tool", - "uuid": "8467e234-b99a-4f4e-9b6d-7bbea18da678", + "uuid": "86b5b52b-cf40-4d34-9b60-7ede0e187b4f", "when": null, "workflow_outputs": [] }, - "12": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, - "id": 12, + "id": 11, "input_connections": { "components_0|param_type|component_value": { - "id": 2, + "id": 3, "output_name": "output" } }, @@ -515,8 +492,8 @@ } ], "position": { - "left": 1412.7865078407585, - "top": 1513.204961480357 + "left": 1497.7951400347756, + "top": 1173.104961480357 }, "post_job_actions": { "HideDatasetActionout1": { @@ -535,15 +512,15 @@ "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.1", "type": "tool", - "uuid": "3512ad84-2d57-44b5-a054-e01c2bf67e20", + "uuid": "bcceb886-0592-4b3f-8b39-26fe79caeb62", "when": null, "workflow_outputs": [] }, - "13": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 13, + "id": 12, "input_connections": { "input_param_type|input_param": { "id": 5, @@ -565,8 +542,8 @@ } ], "position": { - "left": 795.1082525210539, - "top": 1643.2637555172578 + "left": 880.1168847150709, + "top": 1303.1637555172579 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -585,15 +562,15 @@ "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"1\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"2\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"0\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "746d5413-b5a8-4a92-b661-f4654a409b67", + "uuid": "72d7d4d1-d1be-481c-b2a1-1e85192b2661", "when": null, "workflow_outputs": [] }, - "14": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 14, + "id": 13, "input_connections": { "input_param_type|input_param": { "id": 5, @@ -615,8 +592,8 @@ } ], "position": { - "left": 795.3259027398972, - "top": 1823.4515528952898 + "left": 880.334534933914, + "top": 1483.3515528952898 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -635,15 +612,15 @@ "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"fr-secondstrand\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"fr-firststrand\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"fr-unstranded\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "640cfa2b-f2e7-4b4b-8048-387bd0530d6a", + "uuid": "f027f3d5-3b91-4061-b5cd-78553509ce5e", "when": null, "workflow_outputs": [] }, - "15": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 15, + "id": 14, "input_connections": { "input_param_type|input_param": { "id": 5, @@ -665,8 +642,8 @@ } ], "position": { - "left": 790.5858684328869, - "top": 1993.6777444451404 + "left": 875.5945006269037, + "top": 1653.5777444451405 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -685,26 +662,26 @@ "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"--fr\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"--rf\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "288968eb-fb08-437e-a60d-3e580c3e5305", + "uuid": "63e6501b-e1de-4184-af42-720cc9a6dfb0", "when": null, "workflow_outputs": [] }, - "16": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, - "id": 16, + "id": 15, "input_connections": { "refGenomeSource|GTFconditional|genomeDir": { - "id": 2, + "id": 3, "output_name": "output" }, "refGenomeSource|GTFconditional|sjdbGTFfile": { - "id": 3, + "id": 4, "output_name": "output" }, "singlePaired|input1": { - "id": 11, + "id": 10, "output_name": "out1" } }, @@ -751,8 +728,8 @@ } ], "position": { - "left": 711.9721344157456, - "top": 703.9857277517348 + "left": 732.1609477893844, + "top": 246.8799136582777 }, "post_job_actions": { "HideDatasetActionsignal_unique_str1": { @@ -802,306 +779,30 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"RuntimeValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"RuntimeValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.11a+galaxy1", - "type": "tool", - "uuid": "34f58f69-4107-4785-96df-f05d2d9f177c", - "when": null, - "workflow_outputs": [ - { - "label": "Mapped Reads", - "output_name": "mapped_reads", - "uuid": "8031b035-383e-4874-8f36-ee671b513a7e" - } - ] - }, - "17": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", - "errors": null, - "id": 17, - "input_connections": { - "alignment": { - "id": 16, - "output_name": "mapped_reads" - }, - "anno|reference_gene_sets": { - "id": 3, - "output_name": "output" - }, - "strand_specificity": { - "id": 13, - "output_name": "output_param_text" - }, - "when": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool featureCounts", - "name": "alignment" - }, - { - "description": "runtime parameter for tool featureCounts", - "name": "anno" - } - ], - "label": null, - "name": "featureCounts", - "outputs": [ - { - "name": "output_short", - "type": "tabular" - }, - { - "name": "output_summary", - "type": "tabular" - } - ], - "position": { - "left": 1451.0321118801053, - "top": 1013.1160326850629 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", - "tool_shed_repository": { - "changeset_revision": "f9d49f5cb597", - "name": "featurecounts", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"alignment\": {\"__class__\": \"RuntimeValue\"}, \"anno\": {\"anno_select\": \"history\", \"__current_case__\": 2, \"reference_gene_sets\": {\"__class__\": \"RuntimeValue\"}, \"gff_feature_type\": \"exon\", \"gff_feature_attribute\": \"gene_id\", \"summarization_level\": false}, \"extended_parameters\": {\"multifeatures\": {\"multifeat\": \"\", \"__current_case__\": 0}, \"exon_exon_junction_read_counting_enabled\": {\"count_exon_exon_junction_reads\": \"\", \"__current_case__\": 1}, \"long_reads\": false, \"by_read_group\": false, \"largest_overlap\": false, \"min_overlap\": \"1\", \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"read_extension_5p\": \"0\", \"read_extension_3p\": \"0\", \"read_reduction\": \"\", \"R\": false}, \"format\": \"tabdel_short\", \"include_feature_length_file\": false, \"pe_parameters\": {\"paired_end_status\": \"single_end\", \"__current_case__\": 0}, \"read_filtering_parameters\": {\"mapping_quality\": \"0\", \"splitonly\": \"\", \"primary\": false, \"ignore_dup\": false}, \"strand_specificity\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0.3+galaxy2", - "type": "tool", - "uuid": "f2fd89e8-c03e-441a-a94c-6f8af0802299", - "when": "$(inputs.when)", - "workflow_outputs": [] - }, - "18": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", - "errors": null, - "id": 18, - "input_connections": { - "guide|guide_source|ref_hist": { - "id": 3, - "output_name": "output" - }, - "input_options|input_bam": { - "id": 16, - "output_name": "mapped_reads" - }, - "rna_strandness": { - "id": 15, - "output_name": "output_param_text" - }, - "when": { - "id": 9, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool StringTie", - "name": "adv" - }, - { - "description": "runtime parameter for tool StringTie", - "name": "input_options" - } - ], - "label": "Compute RPKM with StringTie", - "name": "StringTie", - "outputs": [ - { - "name": "output_gtf", - "type": "gtf" - }, - { - "name": "gene_abundance_estimation", - "type": "tabular" - } - ], - "position": { - "left": 1646.7273564460595, - "top": 1764.3142641508387 - }, - "post_job_actions": { - "HideDatasetActionoutput_gtf": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_gtf" - }, - "RenameDatasetActiongene_abundance_estimation": { - "action_arguments": { - "newname": "Gene abundance estimates from StringTie" - }, - "action_type": "RenameDatasetAction", - "output_name": "gene_abundance_estimation" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", - "tool_shed_repository": { - "changeset_revision": "cbf488da3b2c", - "name": "stringtie", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"adv\": {\"abundance_estimation\": true, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": true, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"rna_strandness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.3+galaxy0", - "type": "tool", - "uuid": "b5bf2f84-4b28-48ae-90f6-beb477781643", - "when": "$(inputs.when)", - "workflow_outputs": [ - { - "label": "Gene Abundance Estimates from StringTie", - "output_name": "gene_abundance_estimation", - "uuid": "f74d4707-f37b-4bb4-97a7-1ebf95cf5009" - } - ] - }, - "19": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", - "errors": null, - "id": 19, - "input_connections": { - "advanced_settings|library_type": { - "id": 14, - "output_name": "output_param_text" - }, - "advanced_settings|mask_file": { - "id": 8, - "output_name": "output" - }, - "bias_correction|seq_source|index": { - "id": 12, - "output_name": "out1" - }, - "input": { - "id": 16, - "output_name": "mapped_reads" - }, - "reference_annotation|reference_annotation_file": { - "id": 3, - "output_name": "output" - }, - "when": { - "id": 6, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Cufflinks", - "name": "advanced_settings" - }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "advanced_settings" - }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "reference_annotation" - } - ], - "label": "Compute RPKM with cufflinks", - "name": "Cufflinks", - "outputs": [ - { - "name": "genes_expression", - "type": "tabular" - }, - { - "name": "transcripts_expression", - "type": "tabular" - }, - { - "name": "assembled_isoforms", - "type": "gtf" - }, - { - "name": "total_map_mass", - "type": "txt" - }, - { - "name": "skipped", - "type": "gtf" - } - ], - "position": { - "left": 1912.2865371888552, - "top": 1491.4458958341904 - }, - "post_job_actions": { - "HideDatasetActionassembled_isoforms": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "assembled_isoforms" - }, - "HideDatasetActionskipped": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "skipped" - }, - "HideDatasetActiontotal_map_mass": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "total_map_mass" - }, - "RenameDatasetActiongenes_expression": { - "action_arguments": { - "newname": "Genes Expression from Cufflinks" - }, - "action_type": "RenameDatasetAction", - "output_name": "genes_expression" - }, - "RenameDatasetActiontranscripts_expression": { - "action_arguments": { - "newname": "Transcripts Expression from Cufflinks" - }, - "action_type": "RenameDatasetAction", - "output_name": "transcripts_expression" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", - "tool_shed_repository": { - "changeset_revision": "d080005cffe1", - "name": "cufflinks", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.1.3", + "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.11a+galaxy1", "type": "tool", - "uuid": "5f38ce95-689a-4c5e-904c-0aaa219c4252", - "when": "$(inputs.when)", + "uuid": "be1a277d-6d0d-4aaf-acea-9735426932b0", + "when": null, "workflow_outputs": [ { - "label": "Transcripts Expression from Cufflinks", - "output_name": "transcripts_expression", - "uuid": "30246471-43f3-49ec-b0f3-ee9555c35a79" - }, - { - "label": "Genes Expression from Cufflinks", - "output_name": "genes_expression", - "uuid": "afa8e60c-8ce1-48e7-b404-9a96df9c9715" + "label": "Mapped Reads", + "output_name": "mapped_reads", + "uuid": "f5722954-fd5c-4e66-aed0-4cd099dd9b1c" } ] }, - "20": { + "16": { "annotation": "", - "id": 20, + "id": 16, "input_connections": { "STAR BAM": { - "id": 16, + "id": 15, "input_subworkflow_step_id": 1, "output_name": "mapped_reads" }, "STAR log": { - "id": 16, + "id": 15, "input_subworkflow_step_id": 0, "output_name": "output_log" } @@ -1116,8 +817,8 @@ "name": "Get Uniquely mapped unstranded coverage", "outputs": [], "position": { - "left": 2589.7316316136303, - "top": 86.74550095753672 + "left": 1683.2031849964808, + "top": 86.70584740647254 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1440,27 +1141,27 @@ }, "tool_id": null, "type": "subworkflow", - "uuid": "c472b674-81d0-4430-af81-3c15dfd5304d", + "uuid": "6ce6314b-d339-40bf-9f0e-53ca525204be", "when": null, "workflow_outputs": [ { "label": "Unstranded Coverage", "output_name": "Both Strands Coverage", - "uuid": "db62edb2-0797-4b07-9325-37f8a0ad5d8f" + "uuid": "f90cc885-438b-49ee-b1d1-8ed45f7dea5c" } ] }, - "21": { + "17": { "annotation": "", - "id": 21, + "id": 17, "input_connections": { "Bedgraph strand 1": { - "id": 16, + "id": 15, "input_subworkflow_step_id": 1, "output_name": "signal_unique_str1" }, "Bedgraph strand 2": { - "id": 16, + "id": 15, "input_subworkflow_step_id": 2, "output_name": "signal_unique_str2" }, @@ -1480,8 +1181,8 @@ "name": "Re-arrange Stranded RNA-seq coverage", "outputs": [], "position": { - "left": 2598.7389363604525, - "top": 282.08680861650623 + "left": 1692.210489743303, + "top": 282.0471550654421 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2022,52 +1723,319 @@ ] } }, - "tags": [], - "uuid": "f5bde9df-1387-4d76-a90c-1043c93e8de5" + "tags": [], + "uuid": "f5bde9df-1387-4d76-a90c-1043c93e8de5" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "bf990b24-1ec8-4e67-acec-fecf26a3d49f", + "when": null, + "workflow_outputs": [ + { + "label": "Stranded Coverage", + "output_name": "Uniquely Mapped Stranded Coverage", + "uuid": "9161f772-6904-4479-aff4-566295f5b3b2" + }, + { + "label": null, + "output_name": "0:output", + "uuid": "7f19f39e-9570-4bbd-add0-21f6997f9940" + } + ] + }, + "18": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", + "errors": null, + "id": 18, + "input_connections": { + "alignment": { + "id": 15, + "output_name": "mapped_reads" + }, + "anno|reference_gene_sets": { + "id": 4, + "output_name": "output" + }, + "strand_specificity": { + "id": 12, + "output_name": "output_param_text" + }, + "when": { + "id": 6, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool featureCounts", + "name": "anno" + } + ], + "label": null, + "name": "featureCounts", + "outputs": [ + { + "name": "output_short", + "type": "tabular" + }, + { + "name": "output_summary", + "type": "tabular" + } + ], + "position": { + "left": 1713.913195680125, + "top": 672.9994811085061 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", + "tool_shed_repository": { + "changeset_revision": "f9d49f5cb597", + "name": "featurecounts", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"alignment\": {\"__class__\": \"ConnectedValue\"}, \"anno\": {\"anno_select\": \"history\", \"__current_case__\": 2, \"reference_gene_sets\": {\"__class__\": \"ConnectedValue\"}, \"gff_feature_type\": \"exon\", \"gff_feature_attribute\": \"gene_id\", \"summarization_level\": false}, \"extended_parameters\": {\"multifeatures\": {\"multifeat\": \"\", \"__current_case__\": 0}, \"exon_exon_junction_read_counting_enabled\": {\"count_exon_exon_junction_reads\": \"\", \"__current_case__\": 1}, \"long_reads\": false, \"by_read_group\": false, \"largest_overlap\": false, \"min_overlap\": \"1\", \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"read_extension_5p\": \"0\", \"read_extension_3p\": \"0\", \"read_reduction\": \"\", \"R\": false}, \"format\": \"tabdel_short\", \"include_feature_length_file\": false, \"pe_parameters\": {\"paired_end_status\": \"single_end\", \"__current_case__\": 0}, \"read_filtering_parameters\": {\"mapping_quality\": \"0\", \"splitonly\": \"\", \"primary\": false, \"ignore_dup\": false}, \"strand_specificity\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.0.3+galaxy2", + "type": "tool", + "uuid": "5a03b546-eb3f-4e99-b845-24c8f54ed183", + "when": "$(inputs.when)", + "workflow_outputs": [] + }, + "19": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", + "errors": null, + "id": 19, + "input_connections": { + "guide|guide_source|ref_hist": { + "id": 4, + "output_name": "output" + }, + "input_options|input_bam": { + "id": 15, + "output_name": "mapped_reads" + }, + "rna_strandness": { + "id": 14, + "output_name": "output_param_text" + }, + "when": { + "id": 9, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool StringTie", + "name": "adv" + }, + { + "description": "runtime parameter for tool StringTie", + "name": "input_options" + } + ], + "label": "Compute FPKM with StringTie", + "name": "StringTie", + "outputs": [ + { + "name": "output_gtf", + "type": "gtf" + }, + { + "name": "gene_abundance_estimation", + "type": "tabular" + } + ], + "position": { + "left": 1731.7359886400766, + "top": 1424.2142641508385 + }, + "post_job_actions": { + "HideDatasetActionoutput_gtf": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_gtf" + }, + "RenameDatasetActiongene_abundance_estimation": { + "action_arguments": { + "newname": "Gene abundance estimates from StringTie" + }, + "action_type": "RenameDatasetAction", + "output_name": "gene_abundance_estimation" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "cbf488da3b2c", + "name": "stringtie", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"adv\": {\"abundance_estimation\": true, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": true, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"rna_strandness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2.3+galaxy0", + "type": "tool", + "uuid": "5a796064-9c52-4b5c-b5da-02c43f6c742f", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "Gene Abundance Estimates from StringTie", + "output_name": "gene_abundance_estimation", + "uuid": "9bcb277a-bb4d-4629-8c71-4cac7cee4c63" + } + ] + }, + "20": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", + "errors": null, + "id": 20, + "input_connections": { + "advanced_settings|library_type": { + "id": 13, + "output_name": "output_param_text" + }, + "advanced_settings|mask_file": { + "id": 8, + "output_name": "output" + }, + "bias_correction|seq_source|index": { + "id": 11, + "output_name": "out1" + }, + "input": { + "id": 15, + "output_name": "mapped_reads" + }, + "reference_annotation|reference_annotation_file": { + "id": 4, + "output_name": "output" + }, + "when": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Cufflinks", + "name": "advanced_settings" + }, + { + "description": "runtime parameter for tool Cufflinks", + "name": "advanced_settings" + }, + { + "description": "runtime parameter for tool Cufflinks", + "name": "reference_annotation" + } + ], + "label": "Compute FPKM with cufflinks", + "name": "Cufflinks", + "outputs": [ + { + "name": "genes_expression", + "type": "tabular" + }, + { + "name": "transcripts_expression", + "type": "tabular" + }, + { + "name": "assembled_isoforms", + "type": "gtf" + }, + { + "name": "total_map_mass", + "type": "txt" + }, + { + "name": "skipped", + "type": "gtf" + } + ], + "position": { + "left": 1998.2812719123385, + "top": 1150.343757982693 + }, + "post_job_actions": { + "HideDatasetActionassembled_isoforms": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "assembled_isoforms" + }, + "HideDatasetActionskipped": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "skipped" + }, + "HideDatasetActiontotal_map_mass": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "total_map_mass" + }, + "RenameDatasetActiongenes_expression": { + "action_arguments": { + "newname": "Genes Expression from Cufflinks" + }, + "action_type": "RenameDatasetAction", + "output_name": "genes_expression" + }, + "RenameDatasetActiontranscripts_expression": { + "action_arguments": { + "newname": "Transcripts Expression from Cufflinks" + }, + "action_type": "RenameDatasetAction", + "output_name": "transcripts_expression" + } }, - "tool_id": null, - "type": "subworkflow", - "uuid": "be76fba3-55f5-4907-8f56-1de05fe3cf8d", - "when": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", + "tool_shed_repository": { + "changeset_revision": "d080005cffe1", + "name": "cufflinks", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2.1.3", + "type": "tool", + "uuid": "af5419b7-ae6b-498c-8123-f609b8fcd8b4", + "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "Stranded Coverage", - "output_name": "Uniquely Mapped Stranded Coverage", - "uuid": "bb9eec4c-9d26-4f9b-8ee3-58d6bd3a71fa" + "label": "Genes Expression from Cufflinks", + "output_name": "genes_expression", + "uuid": "3bd4fbda-f241-4ebd-b7a5-dea7271c521e" }, { - "label": null, - "output_name": "0:output", - "uuid": "dc44e70a-0705-48bf-a99d-33f354e00957" + "label": "Transcripts Expression from Cufflinks", + "output_name": "transcripts_expression", + "uuid": "2c13ef79-948c-4f5f-8516-a769550128fd" } ] }, - "22": { + "21": { "annotation": "", - "id": 22, + "id": 21, "input_connections": { "RNA STAR count tables": { - "id": 16, - "input_subworkflow_step_id": 4, + "id": 15, + "input_subworkflow_step_id": 3, "output_name": "reads_per_gene" }, - "Sample table to add tags": { - "id": 7, - "input_subworkflow_step_id": 2, - "output_name": "output" - }, "Strandness param": { "id": 5, - "input_subworkflow_step_id": 3, + "input_subworkflow_step_id": 2, "output_name": "output" }, "featureCounts count table": { - "id": 17, - "input_subworkflow_step_id": 5, + "id": 18, + "input_subworkflow_step_id": 4, "output_name": "output_short" }, "featureCounts summaries collection": { - "id": 17, + "id": 18, "input_subworkflow_step_id": 1, "output_name": "output_summary" } @@ -2077,8 +2045,8 @@ "name": "Process Count files", "outputs": [], "position": { - "left": 1875.6228149071408, - "top": 962.4763887841759 + "left": 2161.105895746449, + "top": 665.1799212422835 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2119,7 +2087,7 @@ } ], "position": { - "left": 2.142187583634133, + "left": 0, "top": 16 }, "post_job_actions": {}, @@ -2153,7 +2121,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 4.490321414251932, + "left": 2.3481338306177992, "top": 215.26828327443155 }, "tool_id": null, @@ -2165,37 +2133,10 @@ "workflow_outputs": [] }, "2": { - "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "content_id": null, - "errors": null, - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "name": "Sample table to add tags" - } - ], - "label": "Sample table to add tags", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 0, - "top": 320.17684220773725 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "9b903f17-a37b-48d9-a214-bcdf393a7574", - "when": null, - "workflow_outputs": [] - }, - "3": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", "content_id": null, "errors": null, - "id": 3, + "id": 2, "input_connections": {}, "inputs": [ { @@ -2207,7 +2148,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 2.142204774107931, + "left": 1.7190473798223138e-05, "top": 433.85391433745605 }, "tool_id": null, @@ -2220,15 +2161,15 @@ { "label": null, "output_name": "output", - "uuid": "f2007283-e5e7-47e6-b922-ef6b95e50354" + "uuid": "d0e53d5e-1b5f-40d7-80e6-f15c5e2ffbc8" } ] }, - "4": { + "3": { "annotation": "Count tables collection from RNA STAR", "content_id": null, "errors": null, - "id": 4, + "id": 3, "input_connections": {}, "inputs": [ { @@ -2240,7 +2181,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 7.511091326709437, + "left": 5.368903743075304, "top": 589.5341644488473 }, "tool_id": null, @@ -2251,11 +2192,11 @@ "when": null, "workflow_outputs": [] }, - "5": { + "4": { "annotation": "Count tables collection from featureCounts", "content_id": null, "errors": null, - "id": 5, + "id": 4, "input_connections": {}, "inputs": [ { @@ -2267,7 +2208,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 9.641580804428433, + "left": 7.4993932207943, "top": 704.0194730841151 }, "tool_id": null, @@ -2278,11 +2219,11 @@ "when": null, "workflow_outputs": [] }, - "6": { + "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", "errors": null, - "id": 6, + "id": 5, "input_connections": { "infile": { "id": 0, @@ -2299,7 +2240,7 @@ } ], "position": { - "left": 282.1421365930926, + "left": 279.9999490094584, "top": 0 }, "post_job_actions": { @@ -2325,53 +2266,14 @@ "when": null, "workflow_outputs": [] }, - "7": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", - "errors": null, - "id": 7, - "input_connections": { - "infile": { - "id": 2, - "output_name": "output" - } - }, - "inputs": [], - "label": "Add group: to the tags", - "name": "Replace", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 842.1424187925072, - "top": 266.17188642026633 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", - "tool_shed_repository": { - "changeset_revision": "86755160afbf", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"(\\\\t)(?!group:)\", \"replace_pattern\": \"$1group:\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", - "type": "tool", - "uuid": "b73de223-a60a-46ab-944f-71378f03df16", - "when": null, - "workflow_outputs": [] - }, - "8": { + "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 8, + "id": 6, "input_connections": { "input_param_type|input_param": { - "id": 3, + "id": 2, "output_name": "output" } }, @@ -2390,7 +2292,7 @@ } ], "position": { - "left": 282.1421709032883, + "left": 279.9999833196541, "top": 401.33828843669767 }, "post_job_actions": { @@ -2414,18 +2316,18 @@ "when": null, "workflow_outputs": [] }, - "9": { + "7": { "annotation": "featureCounts summaries", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 9, + "id": 7, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 1, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 6, + "id": 5, "output_name": "output" } }, @@ -2439,7 +2341,7 @@ } ], "position": { - "left": 842.1422267022583, + "left": 840.0000391186242, "top": 16 }, "post_job_actions": { @@ -2471,18 +2373,18 @@ } ] }, - "10": { + "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 10, + "id": 8, "input_connections": { "code": { - "id": 8, + "id": 6, "output_name": "output_param_text" }, "infile": { - "id": 4, + "id": 3, "output_name": "output" } }, @@ -2496,7 +2398,7 @@ } ], "position": { - "left": 562.1422776927999, + "left": 560.0000901091657, "top": 386.17188642026633 }, "post_job_actions": { @@ -2522,18 +2424,18 @@ "when": null, "workflow_outputs": [] }, - "11": { + "9": { "annotation": "Counts Table ", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 11, + "id": 9, "input_connections": { "style_cond|type_cond|pick_from_0|value": { - "id": 5, + "id": 4, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 10, + "id": 8, "output_name": "outfile" } }, @@ -2547,7 +2449,7 @@ } ], "position": { - "left": 839.142341368268, + "left": 837.0001537846339, "top": 413.1722363660909 }, "post_job_actions": { @@ -2571,83 +2473,46 @@ "type": "tool", "uuid": "d87cdd15-8b7c-4498-a818-7369ee4e006a", "when": null, - "workflow_outputs": [] - }, - "12": { - "annotation": "Used as input for DESeq2", - "content_id": "__TAG_FROM_FILE__", - "errors": null, - "id": 12, - "input_connections": { - "input": { - "id": 11, - "output_name": "data_param" - }, - "tags": { - "id": 7, - "output_name": "outfile" - } - }, - "inputs": [], - "label": "Tag count bables", - "name": "Tag elements", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 1122.1425598922144, - "top": 278.17188642026633 - }, - "post_job_actions": {}, - "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": "d145af57-9b56-4927-8bee-3cf672caa2f9", - "when": null, "workflow_outputs": [ { - "label": "Tagged Count Tables", - "output_name": "output", - "uuid": "ddba8ac1-ab03-4949-8d2e-961c9bd8b398" + "label": "Counts Table", + "output_name": "data_param", + "uuid": "bb7b60bf-81b1-4d58-9724-9814e9284ab3" } ] } }, "tags": [], - "uuid": "06461dd0-7388-4676-94d5-c068ea2562a1" + "uuid": "1d5779a5-fb3a-453a-9fec-8acd491ce5ab" }, "tool_id": null, "type": "subworkflow", - "uuid": "68669f89-0c91-4a94-bf2c-813a3385275a", + "uuid": "6957fcb0-4312-4764-9d80-c5306759f914", "when": null, "workflow_outputs": [ { - "label": "FeatureCounts Summary Table", - "output_name": "FeatureCounts Summary Table", - "uuid": "61a32f3a-5c41-4381-86d5-cd0bd39a0197" + "label": null, + "output_name": "2:output", + "uuid": "3f546719-c4a9-4c37-8239-b8e74d9e31b7" }, { - "label": "Tagged Count Tables", - "output_name": "Tagged Count Tables", - "uuid": "60594b49-2c52-4da2-8176-25693a483b33" + "label": "Counts Table", + "output_name": "Counts Table", + "uuid": "dfe40af6-1361-4953-aac7-fbca6cfdb47a" }, { - "label": null, - "output_name": "3:output", - "uuid": "c5bfce56-c552-4b85-a4a8-15aaaecf4c57" + "label": "FeatureCounts Summary Table", + "output_name": "FeatureCounts Summary Table", + "uuid": "6bebc1fb-139b-4aba-82c2-4f53476f59af" } ] }, - "23": { + "22": { "annotation": "", - "id": 23, + "id": 22, "input_connections": { "Cutadapt Reports": { - "id": 11, + "id": 10, "input_subworkflow_step_id": 2, "output_name": "report" }, @@ -2656,28 +2521,28 @@ "input_subworkflow_step_id": 0, "output_name": "output" }, + "STAR BAM": { + "id": 15, + "input_subworkflow_step_id": 5, + "output_name": "mapped_reads" + }, "STAR logs": { - "id": 16, + "id": 15, "input_subworkflow_step_id": 3, "output_name": "output_log" }, - "STAR paired-end BAM": { - "id": 16, - "input_subworkflow_step_id": 5, - "output_name": "mapped_reads" - }, "featureCounts summaries": { - "id": 22, + "id": 21, "input_subworkflow_step_id": 1, "output_name": "FeatureCounts Summary Table" }, "reference_annotation_gtf": { - "id": 3, + "id": 4, "input_subworkflow_step_id": 4, "output_name": "output" }, "when": { - "id": 1, + "id": 2, "output_name": "output" } }, @@ -2691,8 +2556,8 @@ "name": "RNA-seq-Paired-QC", "outputs": [], "position": { - "left": 2581.8385293658202, - "top": 574.7767421741249 + "left": 2465.503860179348, + "top": 451.63585583919314 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2856,10 +2721,10 @@ "inputs": [ { "description": "Mapped BAM files from STAR", - "name": "STAR paired-end BAM" + "name": "STAR BAM" } ], - "label": "STAR paired-end BAM", + "label": "STAR BAM", "name": "Input dataset collection", "outputs": [], "position": { @@ -3284,111 +3149,30 @@ } }, "tags": [], - "uuid": "8518a66b-6e91-4252-a543-0109bf7bb75e" + "uuid": "7ceb54f7-213d-4e2e-8e1a-757336d64623" }, "tool_id": null, "type": "subworkflow", - "uuid": "cf90f07d-b841-425a-89a6-18b2928ca9de", + "uuid": "c0aaa16c-8a9b-4fe1-8c3d-9e77f64da413", "when": "$(inputs.when)", "workflow_outputs": [ { "label": "MultiQC stats", "output_name": "MultiQC stats", - "uuid": "b497d2f7-8ff4-4dc0-84c9-b6eabc2b3061" + "uuid": "43ed1ffc-7df8-42a6-95f7-dc2b2060a910" }, { "label": "MultiQC HTML report", "output_name": "MultiQC HTML report", - "uuid": "7c654b48-4142-420d-9c1b-8de88ddfa7d6" - } - ] - }, - "24": { - "annotation": "Count files have a header if featureCounts is used.", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", - "errors": null, - "id": 24, - "input_connections": { - "batch_factors": { - "id": 10, - "output_name": "output" - }, - "header": { - "id": 4, - "output_name": "output" - }, - "select_data|countsFile": { - "id": 22, - "output_name": "Tagged Count Tables" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool DESeq2", - "name": "select_data" - } - ], - "label": "Differential expression analysis using DESeq2", - "name": "DESeq2", - "outputs": [ - { - "name": "deseq_out", - "type": "tabular" - }, - { - "name": "plots", - "type": "pdf" - } - ], - "position": { - "left": 2566.26663539139, - "top": 1017.2514257011151 - }, - "post_job_actions": { - "RenameDatasetActiondeseq_out": { - "action_arguments": { - "newname": "Differential expression analysis using DESeq2" - }, - "action_type": "RenameDatasetAction", - "output_name": "deseq_out" - }, - "RenameDatasetActionplots": { - "action_arguments": { - "newname": "DESeq2 Plots" - }, - "action_type": "RenameDatasetAction", - "output_name": "plots" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", - "tool_shed_repository": { - "changeset_revision": "8fe98f7094de", - "name": "deseq2", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"advanced_options\": {\"esf\": \"\", \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}}, \"batch_factors\": {\"__class__\": \"ConnectedValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.11.40.7+galaxy2", - "type": "tool", - "uuid": "d569d7b8-556e-4d79-9e1e-138a8f0ee692", - "when": null, - "workflow_outputs": [ - { - "label": "Differential Expression Analysis using DESeq2", - "output_name": "deseq_out", - "uuid": "16fe60d6-d1c1-42d7-850a-63d91328e963" - }, - { - "label": "DESeq2 Plots", - "output_name": "plots", - "uuid": "4bdc4546-d7b8-48b2-8fa6-72e887033462" + "uuid": "717627ed-188d-4cb5-9a03-b1eec15f7922" } ] } }, "tags": [ - "RNAseq" + "RNAseq", + "transcriptomics" ], - "uuid": "047610eb-d2c4-4d6c-aca2-7b70dd351d50", + "uuid": "72595f60-4d6e-49bd-ab53-6d0f170f466d", "version": 3 } \ No newline at end of file From 4bf47c85b72e73afc584df3bdf49d6e7551914f7 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 28 Oct 2024 19:50:09 +0100 Subject: [PATCH 05/10] update changelog and dockstore.yml --- workflows/transcriptomics/rnaseq-sr/.dockstore.yml | 2 ++ workflows/transcriptomics/rnaseq-sr/CHANGELOG.md | 6 +++--- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/.dockstore.yml b/workflows/transcriptomics/rnaseq-sr/.dockstore.yml index 61f298b5c..a41c35c2d 100644 --- a/workflows/transcriptomics/rnaseq-sr/.dockstore.yml +++ b/workflows/transcriptomics/rnaseq-sr/.dockstore.yml @@ -9,3 +9,5 @@ workflows: authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 + - name: Pavankumar Videm + orcid: 0000-0002-5192-126X \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index 92d1c363a..a2da05dcc 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -3,9 +3,9 @@ ## [0.10] 2024-10-22 ### Manual update -- Using a new subsampled test data from Zenodo record https://zenodo.org/records/13951092 -- Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, Picard reports -- Added DESeq2 step that uses tags to choose factors +- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/4541751 +- Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, featureCounts and Picard reports +- Added featureCounts as an alternative way to generate count files ## [0.9] 2024-09-23 From 0549752d54137916de6dde55b79863c50dfab0f7 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 29 Oct 2024 10:59:05 +0100 Subject: [PATCH 06/10] correct the collection element id --- workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 4a58034fe..ba5a42be3 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -9,7 +9,7 @@ collection_type: list elements: - class: File - identifier: SRR5085168 + identifier: SRR5085167 location: https://zenodo.org/records/13987631/files/SRR5085167_forward.fastqsanger.gz Forward adapter: AGATCGGAAGAG Generate QC reports: true From c4c76efc9bf8661c59b169c5ca1ff97a05c5fc8b Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 30 Oct 2024 07:49:12 +0100 Subject: [PATCH 07/10] correct the Zenodo record in the CHANGELOG --- workflows/transcriptomics/rnaseq-sr/CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index a2da05dcc..07d3c8227 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -3,7 +3,7 @@ ## [0.10] 2024-10-22 ### Manual update -- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/4541751 +- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631 - Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, featureCounts and Picard reports - Added featureCounts as an alternative way to generate count files From a46b479dcc3cd41bbb2051894cffcfd37ba1a965 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 16:02:49 +0100 Subject: [PATCH 08/10] - use verion 1.0 - improve changelog - use fastp instead of cutadapt - update cufflinks - add multiQC even if no additional QC are performed. - hide intermediate steps - change some parameter names - update README to better description of parameters - add missing asserts in tests --- .../transcriptomics/rnaseq-sr/CHANGELOG.md | 14 +- workflows/transcriptomics/rnaseq-sr/README.md | 24 +- .../rnaseq-sr/rnaseq-sr-tests.yml | 48 +- .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 763 +++++++++++------- 4 files changed, 520 insertions(+), 329 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index 07d3c8227..a389faa24 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -1,11 +1,17 @@ # Changelog -## [0.10] 2024-10-22 +## [1.0] 2024-10-22 -### Manual update +### Changes in workflows +- Add an optional subworkflow with more QC: FastQC, Picard, Read distribution on genomic features, gene body coverage, reads per chromosomes. +- Add featureCounts as an alternative way to generate count files +- Use fastp instead of cutadapt which uses pair overlap and allows to have optional adapter sequences + +### Tool update +- `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4` + +### Test dataset - Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631 -- Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, featureCounts and Picard reports -- Added featureCounts as an alternative way to generate count files ## [0.9] 2024-09-23 diff --git a/workflows/transcriptomics/rnaseq-sr/README.md b/workflows/transcriptomics/rnaseq-sr/README.md index 09236c628..7e3de2c65 100644 --- a/workflows/transcriptomics/rnaseq-sr/README.md +++ b/workflows/transcriptomics/rnaseq-sr/README.md @@ -2,9 +2,9 @@ ## Inputs dataset -- The workflow needs a list of datasets of fastqsanger. -- As well as a gtf file with genes -- Optional, but recommended: a gtf file with regions to exclude from normalization in Cufflinks. +- Collection of FASTQ files: The workflow needs a list of datasets of fastqsanger. +- GTF file of annotation: A gtf file with genes annotation. +- GTF with regions to exclude from FPKM normalization with Cufflinks: Optional, but recommended. A gtf file with regions to exclude from normalization in Cufflinks. - For instance a gtf that masks chrM for the mm10 genome: @@ -15,11 +15,13 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM ## Inputs values -- forward adapter sequence: this depends on the library preparation. Usually classical Illumina RNA libraries are Truseq and ISML (relatively new Illumina library) is Nextera. If you don't know, use FastQC to determine if it is Truseq or Nextera. If the read length is relatively short (50bp), there is probably no adapter so it will not impact your results. -- reference_genome: this field will be adapted to the genomes available for STAR -- strandedness: For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence. This will only count alignments that are compatible with your library preparation strategy. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie. -- cufflinks_FPKM: Whether you want to get FPKM with Cufflinks (pretty long) -- stringtie_FPKM: Whether you want to get FPKM/TPM etc... with Stringtie. +- Forward adapter (optional): If not provided, fastp will try to guess the adapter sequence from the data. Its sequences depends on the library preparation. Usually classical Illumina RNA libraries are Truseq and ISML (relatively new Illumina library) is Nextera. If you don't know, use FastQC to determine if it is Truseq or Nextera. If the read length is relatively short (50bp), there is probably no adapter so it will not impact your results. +- Generate additional QC reports: whether to compute additional QC: FastQC, Picard, Read distribution on genomic features, gene body coverage, reads per chromosomes. +- Reference genome: this field will be adapted to the genomes available for STAR. +- Strandedness: For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence. This will only count alignments that are compatible with your library preparation strategy. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie. +- Use featureCounts for generating count tables: Whether to use count tables from featureCounts instead of from STAR. +- Compute Cufflinks FPKM: Whether you want to get FPKM with Cufflinks (pretty long). +- Compute StringTie FPKM: Whether you want to get FPKM/TPM etc... with StringTie. ## Processing @@ -41,6 +43,12 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM ## Contribution +### Version 0.1 + @lldelisle wrote the workflow and the tests. @nagoue updated the tools, made it work in usegalaxy.org, fixed some best practices. + +### Version 1.0 + +@pavanvidem added the new features (featurecount + additional QC) and found a smaller test dataset. diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index ba5a42be3..e202d36c7 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -4,7 +4,7 @@ class: File location: https://zenodo.org/records/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf filetype: gtf - Collection paired FASTQ files: + Collection of FASTQ files: class: Collection collection_type: list elements: @@ -12,7 +12,7 @@ identifier: SRR5085167 location: https://zenodo.org/records/13987631/files/SRR5085167_forward.fastqsanger.gz Forward adapter: AGATCGGAAGAG - Generate QC reports: true + Generate additional QC reports: true Reference genome: sacCer3 Strandedness: stranded - forward Use featureCounts for generating count tables: true @@ -23,54 +23,54 @@ MultiQC stats: asserts: has_text_matching: - expression: "SRR5085167\t0.11[0-9]*\t18.14[0-9]*\t69.79[0-9]*\t0.37[0-9]*\t0.35[0-9]*\t94.81\t0.12[0-9]*\t34.32\t0.22[0-9]*\t37.78[0-9]*\t36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" - FeatureCounts Summary Table: - element_tests: - SRR5085167: - has_line: - line: "Assigned 115717" + expression: "SRR5085167\t0.11[0-9]*\t18.3[0-9]*\t69.6[0-9]*\t0.3[0-9]*\t0.3[0-9]*\t94.62\t0.12[0-9]*\t34.43\t0.2[0-9]*\t28.[0-9]*\t90.[0-9]*\t16.[0-9]*\t0.36[0-9]*\t43.[0-9]*\t91.[0-9]*\t70.[0-9]*\t36.[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" Counts Table: element_tests: SRR5085167: + asserts: has_line: - line: "YAL038W 1813" + line: "YAL038W 1775" Mapped Reads: element_tests: SRR5085167: - has_size: - value: 56913572 - delta: 2500000 + asserts: + has_size: + value: 31570787 + delta: 3000000 Gene Abundance Estimates from StringTie: element_tests: SRR5085167: asserts: has_text_matching: - expression: "YAL038W\tCDC19\tchrI\t\\+\t71786\t73288\t57.46[0-9]*\t3549.28[0-9]*\t3066.13[0-9]*" + expression: "YAL038W\tCDC19\tchrI\t\\+\t71786\t73288\t57.[0-9]*\t3575.[0-9]*\t3084.[0-9]*" Genes Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3350.92 3139.33 3562.52 OK" + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3375.85 3161.36 3590.33 OK" Transcripts Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 57.4859 3350.92 3139.33 3562.52 OK" + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 57.5601 3375.85 3161.36 3590.33 OK" Stranded Coverage: element_tests: SRR5085167_forward: - has_size: - value: 635210 - delta: 30000 + asserts: + has_size: + value: 555489 + delta: 50000 SRR5085167_reverse: - has_size: - value: 618578 - delta: 30000 + asserts: + has_size: + value: 526952 + delta: 50000 Unstranded Coverage: element_tests: SRR5085167: - has_size: - value: 1140004 - delta: 50000 + asserts: + has_size: + value: 978542 + delta: 90000 diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index 69c3036a8..5cc544c3e 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -1,12 +1,12 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of single-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. Alternatively, featureCounts can be used to count the reads/fragments per gene. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.\n", + "annotation": "This workflow takes as input a list of single-end fastqs. Adapters and bad quality bases are removed with fastp. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. Alternatively, featureCounts can be used to count the reads/fragments per gene. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.\n", "comments": [ { "child_steps": [ - 11, - 19, - 20 + 12, + 20, + 21 ], "color": "yellow", "data": { @@ -25,42 +25,42 @@ }, { "child_steps": [ - 12, - 13, - 14 + 17, + 18 ], - "color": "lime", + "color": "red", "data": { - "title": "Map Strandedness parameter" + "title": "Coverage Files" }, - "id": 0, + "id": 1, "position": [ - 855.5086321940169, - 1252.5 + 1603.68749985966, + 0 ], "size": [ - 251, - 558 + 375, + 538 ], "type": "frame" }, { "child_steps": [ - 16, - 17 + 13, + 14, + 15 ], - "color": "red", + "color": "lime", "data": { - "title": "Coverage Files" + "title": "Map Strandedness parameter" }, - "id": 1, + "id": 0, "position": [ - 1603.68749985966, - 0 + 855.5086321940169, + 1252.5 ], "size": [ - 375, - 538 + 251, + 558 ], "type": "frame" } @@ -79,25 +79,25 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.10", - "name": "RNAseq_SR", + "release": "1.0", + "name": "RNA-seq for Single-read fastqs", "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": "Should be a list of paired-end RNA-seq fastqs", + "annotation": "Should be a list of single-read RNA-seq fastqs", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "Should be a list of paired-end RNA-seq fastqs", - "name": "Collection paired FASTQ files" + "description": "Should be a list of single-read RNA-seq fastqs", + "name": "Collection of FASTQ files" } ], - "label": "Collection paired FASTQ files", + "label": "Collection of FASTQ files", "name": "Input dataset collection", "outputs": [], "position": { @@ -113,14 +113,14 @@ "workflow_outputs": [] }, "1": { - "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "annotation": "This is optional. If not provided, fastp will try to guess the sequence. If you want to specify, for Nextera use: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, for TruSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "description": "This is optional. If not provided, fastp will try to guess the sequence. If you want to specify, for Nextera use: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, for TruSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "name": "Forward adapter" } ], @@ -132,32 +132,26 @@ "top": 567.328103383874 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "6d1de206-97c4-41ba-8702-a980f748a689", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "ac090bb1-908d-4de0-88a4-df7154718ed5" - } - ] + "workflow_outputs": [] }, "2": { - "annotation": "Whether to report QC", + "annotation": "Whether to compute additional QC like fastQC, gene body coverage etc...", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Whether to report QC", - "name": "Generate QC reports" + "description": "Whether to compute additional QC like fastQC, gene body coverage etc...", + "name": "Generate additional QC reports" } ], - "label": "Generate QC reports", + "label": "Generate additional QC reports", "name": "Input parameter", "outputs": [], "position": { @@ -170,13 +164,7 @@ "type": "parameter_input", "uuid": "bea331ce-d6fa-4312-8dce-a8b13bc4e77b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "82263d1b-8581-402a-b30c-e7ff3ebc289c" - } - ] + "workflow_outputs": [] }, "3": { "annotation": "Select the reference genome", @@ -203,13 +191,7 @@ "type": "parameter_input", "uuid": "a72b29ae-65a7-4e4d-a996-2943ab5b02aa", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "be8822c1-1160-4a04-b05d-e5c7ed82eb83" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", @@ -263,13 +245,7 @@ "type": "parameter_input", "uuid": "2ccf2242-dddd-45b6-8cea-746d9b5d49bc", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "ce9da8c4-ef45-4aac-bd43-28018c6567bb" - } - ] + "workflow_outputs": [] }, "6": { "annotation": "Use featureCounts tool instead of RNA STAR?", @@ -296,13 +272,7 @@ "type": "parameter_input", "uuid": "f43d45e6-5692-41cb-8cfc-205dbeab1bd0", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "ba6886ad-ef06-4787-b939-8aa8816ca720" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "Whether FPKM values should be computed with Cufflinks", @@ -329,13 +299,7 @@ "type": "parameter_input", "uuid": "78868cdb-baff-4388-a41a-a700259da1ed", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e27d8921-adb5-444d-bed3-62f7a82d7dfc" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", @@ -362,13 +326,7 @@ "type": "data_input", "uuid": "0d4e1623-adc9-4ff3-8156-7e1322b1e278", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e8fb1d01-f053-40a0-a164-fac721cbdbf6" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "Whether FPKM values should be computed with StringTie", @@ -395,87 +353,133 @@ "type": "parameter_input", "uuid": "056f11f4-bdd9-4361-b037-2c0822320cc2", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "f15cc7f8-5d17-4ad8-ba30-f6e4b430c07f" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2", "errors": null, "id": 10, "input_connections": { - "library|input_1": { - "id": 0, + "single_paired|adapter_trimming_options|adapter_sequence1": { + "id": 1, "output_name": "output" }, - "library|r1|adapters_0|adapter_source|adapter": { - "id": 1, + "single_paired|in1": { + "id": 0, "output_name": "output" } }, "inputs": [ { - "description": "runtime parameter for tool Cutadapt", - "name": "library" + "description": "runtime parameter for tool fastp", + "name": "single_paired" } ], - "label": "Cutadapt (remove adapter + bad quality bases)", - "name": "Cutadapt", + "label": "remove adapters + bad quality bases", + "name": "fastp", "outputs": [ { "name": "out1", - "type": "fastqsanger" + "type": "auto" }, { - "name": "report", - "type": "txt" + "name": "report_json", + "type": "json" } ], "position": { - "left": 378.49997163276, - "top": 300.7500028626845 + "left": 377, + "top": 106.21400000000001 }, "post_job_actions": { + "ChangeDatatypeActionout1": { + "action_arguments": { + "newtype": "fastqsanger" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "out1" + }, "HideDatasetActionout1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out1" }, - "HideDatasetActionout_pairs": { + "HideDatasetActionreport_json": { "action_arguments": {}, "action_type": "HideDatasetAction", - "output_name": "out_pairs" - }, - "HideDatasetActionreport": { + "output_name": "report_json" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2", + "tool_shed_repository": { + "changeset_revision": "dbfc505896e9", + "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\": \"15\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": false, \"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\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": {\"__class__\": \"ConnectedValue\"}}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.23.4+galaxy2", + "type": "tool", + "uuid": "e31141cc-c8a5-4dde-882f-72c1b8aabe97", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 11, + "input_connections": { + "input_param_type|input_param": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": "no additional QC", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 2139.879611894974, + "top": 184.34956182248365 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { "action_arguments": {}, "action_type": "HideDatasetAction", - "output_name": "report" + "output_name": "output_param_boolean" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "tool_shed_repository": { - "changeset_revision": "5eb7e84243f2", - "name": "cutadapt", - "owner": "lparsons", + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy1", + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"true\"}, {\"__index__\": 1, \"from\": true, \"to\": \"false\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", "type": "tool", - "uuid": "86b5b52b-cf40-4d34-9b60-7ede0e187b4f", + "uuid": "68188ffa-f288-4da4-8d29-1f3d3b689937", "when": null, "workflow_outputs": [] }, - "11": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, - "id": 11, + "id": 12, "input_connections": { "components_0|param_type|component_value": { "id": 3, @@ -516,11 +520,11 @@ "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 12, + "id": 13, "input_connections": { "input_param_type|input_param": { "id": 5, @@ -566,11 +570,11 @@ "when": null, "workflow_outputs": [] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 13, + "id": 14, "input_connections": { "input_param_type|input_param": { "id": 5, @@ -616,11 +620,11 @@ "when": null, "workflow_outputs": [] }, - "14": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 14, + "id": 15, "input_connections": { "input_param_type|input_param": { "id": 5, @@ -666,11 +670,11 @@ "when": null, "workflow_outputs": [] }, - "15": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, - "id": 15, + "id": 16, "input_connections": { "refGenomeSource|GTFconditional|genomeDir": { "id": 3, @@ -732,6 +736,16 @@ "top": 246.8799136582777 }, "post_job_actions": { + "HideDatasetActionoutput_log": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_log" + }, + "HideDatasetActionreads_per_gene": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "reads_per_gene" + }, "HideDatasetActionsignal_unique_str1": { "action_arguments": {}, "action_type": "HideDatasetAction", @@ -792,17 +806,17 @@ } ] }, - "16": { + "17": { "annotation": "", - "id": 16, + "id": 17, "input_connections": { "STAR BAM": { - "id": 15, + "id": 16, "input_subworkflow_step_id": 1, "output_name": "mapped_reads" }, "STAR log": { - "id": 15, + "id": 16, "input_subworkflow_step_id": 0, "output_name": "output_log" } @@ -1151,17 +1165,17 @@ } ] }, - "17": { + "18": { "annotation": "", - "id": 17, + "id": 18, "input_connections": { "Bedgraph strand 1": { - "id": 15, + "id": 16, "input_subworkflow_step_id": 1, "output_name": "signal_unique_str1" }, "Bedgraph strand 2": { - "id": 15, + "id": 16, "input_subworkflow_step_id": 2, "output_name": "signal_unique_str2" }, @@ -1735,22 +1749,17 @@ "label": "Stranded Coverage", "output_name": "Uniquely Mapped Stranded Coverage", "uuid": "9161f772-6904-4479-aff4-566295f5b3b2" - }, - { - "label": null, - "output_name": "0:output", - "uuid": "7f19f39e-9570-4bbd-add0-21f6997f9940" } ] }, - "18": { + "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "errors": null, - "id": 18, + "id": 19, "input_connections": { "alignment": { - "id": 15, + "id": 16, "output_name": "mapped_reads" }, "anno|reference_gene_sets": { @@ -1758,7 +1767,7 @@ "output_name": "output" }, "strand_specificity": { - "id": 12, + "id": 13, "output_name": "output_param_text" }, "when": { @@ -1788,7 +1797,18 @@ "left": 1713.913195680125, "top": 672.9994811085061 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionoutput_short": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_short" + }, + "HideDatasetActionoutput_summary": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_summary" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "tool_shed_repository": { "changeset_revision": "f9d49f5cb597", @@ -1803,22 +1823,22 @@ "when": "$(inputs.when)", "workflow_outputs": [] }, - "19": { + "20": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", "errors": null, - "id": 19, + "id": 20, "input_connections": { "guide|guide_source|ref_hist": { "id": 4, "output_name": "output" }, "input_options|input_bam": { - "id": 15, + "id": 16, "output_name": "mapped_reads" }, "rna_strandness": { - "id": 14, + "id": 15, "output_name": "output_param_text" }, "when": { @@ -1886,14 +1906,14 @@ } ] }, - "20": { + "21": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4", "errors": null, - "id": 20, + "id": 21, "input_connections": { "advanced_settings|library_type": { - "id": 13, + "id": 14, "output_name": "output_param_text" }, "advanced_settings|mask_file": { @@ -1901,11 +1921,11 @@ "output_name": "output" }, "bias_correction|seq_source|index": { - "id": 11, + "id": 12, "output_name": "out1" }, "input": { - "id": 15, + "id": 16, "output_name": "mapped_reads" }, "reference_annotation|reference_annotation_file": { @@ -1926,6 +1946,10 @@ "description": "runtime parameter for tool Cufflinks", "name": "advanced_settings" }, + { + "description": "runtime parameter for tool Cufflinks", + "name": "input" + }, { "description": "runtime parameter for tool Cufflinks", "name": "reference_annotation" @@ -1990,37 +2014,37 @@ "output_name": "transcripts_expression" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4", "tool_shed_repository": { - "changeset_revision": "d080005cffe1", + "changeset_revision": "6926716bbfb5", "name": "cufflinks", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.1.3", + "tool_state": "{\"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"RuntimeValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"RuntimeValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"RuntimeValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2.1.4", "type": "tool", "uuid": "af5419b7-ae6b-498c-8123-f609b8fcd8b4", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "Genes Expression from Cufflinks", - "output_name": "genes_expression", - "uuid": "3bd4fbda-f241-4ebd-b7a5-dea7271c521e" - }, { "label": "Transcripts Expression from Cufflinks", "output_name": "transcripts_expression", "uuid": "2c13ef79-948c-4f5f-8516-a769550128fd" + }, + { + "label": "Genes Expression from Cufflinks", + "output_name": "genes_expression", + "uuid": "3bd4fbda-f241-4ebd-b7a5-dea7271c521e" } ] }, - "21": { + "22": { "annotation": "", - "id": 21, + "id": 22, "input_connections": { "RNA STAR count tables": { - "id": 15, + "id": 16, "input_subworkflow_step_id": 3, "output_name": "reads_per_gene" }, @@ -2030,12 +2054,12 @@ "output_name": "output" }, "featureCounts count table": { - "id": 18, + "id": 19, "input_subworkflow_step_id": 4, "output_name": "output_short" }, "featureCounts summaries collection": { - "id": 18, + "id": 19, "input_subworkflow_step_id": 1, "output_name": "output_summary" } @@ -2490,55 +2514,120 @@ "uuid": "6957fcb0-4312-4764-9d80-c5306759f914", "when": null, "workflow_outputs": [ - { - "label": null, - "output_name": "2:output", - "uuid": "3f546719-c4a9-4c37-8239-b8e74d9e31b7" - }, { "label": "Counts Table", "output_name": "Counts Table", "uuid": "dfe40af6-1361-4953-aac7-fbca6cfdb47a" - }, - { - "label": "FeatureCounts Summary Table", - "output_name": "FeatureCounts Summary Table", - "uuid": "6bebc1fb-139b-4aba-82c2-4f53476f59af" } ] }, - "22": { + "23": { "annotation": "", - "id": 22, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", + "errors": null, + "id": 23, "input_connections": { - "Cutadapt Reports": { + "results_0|software_cond|input": { "id": 10, - "input_subworkflow_step_id": 2, - "output_name": "report" + "output_name": "report_json" + }, + "results_1|software_cond|output_0|type|input": { + "id": 16, + "output_name": "output_log" + }, + "results_1|software_cond|output_1|type|input": { + "id": 16, + "output_name": "reads_per_gene" + }, + "results_2|software_cond|input": { + "id": 22, + "output_name": "FeatureCounts Summary Table" + }, + "when": { + "id": 11, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "Combined MultiQC without additional QC", + "name": "MultiQC", + "outputs": [ + { + "name": "html_report", + "type": "html" }, + { + "name": "stats", + "type": "tabular" + } + ], + "position": { + "left": 2423.9455325643053, + "top": 32.99591513431855 + }, + "post_job_actions": {}, + "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\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"RuntimeValue\"}}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", + "type": "tool", + "uuid": "e5335a24-fec9-422c-b93c-c172ad7e1b8c", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "Small MultiQC stats", + "output_name": "stats", + "uuid": "f9eecf9b-d360-4d97-962f-24efc44d5b99" + }, + { + "label": "Small MultiQC HTML report", + "output_name": "html_report", + "uuid": "24cf626f-6539-4123-85d6-214b88e2c4b7" + } + ] + }, + "24": { + "annotation": "", + "id": 24, + "input_connections": { "FASTQ collection": { "id": 0, "input_subworkflow_step_id": 0, "output_name": "output" }, "STAR BAM": { - "id": 15, - "input_subworkflow_step_id": 5, + "id": 16, + "input_subworkflow_step_id": 6, "output_name": "mapped_reads" }, - "STAR logs": { - "id": 15, + "STAR counts": { + "id": 16, "input_subworkflow_step_id": 3, + "output_name": "reads_per_gene" + }, + "STAR logs": { + "id": 16, + "input_subworkflow_step_id": 2, "output_name": "output_log" }, - "featureCounts summaries": { - "id": 21, + "fastp Reports": { + "id": 10, "input_subworkflow_step_id": 1, + "output_name": "report_json" + }, + "featureCounts summaries": { + "id": 22, + "input_subworkflow_step_id": 4, "output_name": "FeatureCounts Summary Table" }, "reference_annotation_gtf": { "id": 4, - "input_subworkflow_step_id": 4, + "input_subworkflow_step_id": 5, "output_name": "output" }, "when": { @@ -2553,7 +2642,7 @@ } ], "label": "Combined MultiQC Quality Report", - "name": "RNA-seq-Paired-QC", + "name": "RNA-seq-QC", "outputs": [], "position": { "left": 2465.503860179348, @@ -2572,7 +2661,7 @@ ], "format-version": "0.1", "license": "MIT", - "name": "RNA-seq-Paired-QC", + "name": "RNA-seq-QC", "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" }, @@ -2594,7 +2683,7 @@ "outputs": [], "position": { "left": 0, - "top": 0 + "top": 13.596214101155162 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", @@ -2605,92 +2694,119 @@ "workflow_outputs": [] }, "1": { - "annotation": "featureCounts Summaries file", + "annotation": "fastp Reports", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "featureCounts Summaries file", - "name": "featureCounts summaries" + "description": "fastp Reports", + "name": "fastp Reports" } ], - "label": "featureCounts summaries", + "label": "fastp Reports", "name": "Input dataset collection", "outputs": [], "position": { - "left": 21.653447845324965, - "top": 474.2009198740476 + "left": 61.11669921875, + "top": 134.59621410115517 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "5a5cb076-92cb-48bd-80e0-d7bfa19fe969", + "uuid": "43c69a53-b1dc-4089-9801-18e980088a2e", "when": null, "workflow_outputs": [] }, "2": { - "annotation": "Cutadapt Reports", + "annotation": "STAR log files", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Cutadapt Reports", - "name": "Cutadapt Reports" + "description": "STAR log files", + "name": "STAR logs" } ], - "label": "Cutadapt Reports", + "label": "STAR logs", "name": "Input dataset collection", "outputs": [], "position": { - "left": 561.109657767363, - "top": 318.00000311286055 + "left": 103.183349609375, + "top": 232.67952708943642 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "43c69a53-b1dc-4089-9801-18e980088a2e", + "uuid": "5ae91949-4ffe-4aef-81fa-fa3cb4e86f5a", "when": null, "workflow_outputs": [] }, "3": { - "annotation": "STAR log files", + "annotation": "", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "STAR log files", - "name": "STAR logs" + "description": "", + "name": "STAR counts" } ], - "label": "STAR logs", + "label": "STAR counts", "name": "Input dataset collection", "outputs": [], "position": { - "left": 568.1890947745617, - "top": 448.0768645395773 + "left": 135, + "top": 311.09621410115517 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "5ae91949-4ffe-4aef-81fa-fa3cb4e86f5a", + "uuid": "57b8e456-2987-42aa-8ee3-3d25a0d5fecf", "when": null, "workflow_outputs": [] }, "4": { - "annotation": "Reference annotation", + "annotation": "featureCounts Summaries file", "content_id": null, "errors": null, "id": 4, "input_connections": {}, + "inputs": [ + { + "description": "featureCounts Summaries file", + "name": "featureCounts summaries" + } + ], + "label": "featureCounts summaries", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 168.6500244140625, + "top": 397.7962263081864 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "5a5cb076-92cb-48bd-80e0-d7bfa19fe969", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "Reference annotation", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, "inputs": [ { "description": "Reference annotation", @@ -2701,8 +2817,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 2.1095586103713773, - "top": 757.9999851090132 + "left": 236.05178147043327, + "top": 521.1329885056177 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -2712,11 +2828,11 @@ "when": null, "workflow_outputs": [] }, - "5": { + "6": { "annotation": "Mapped BAM files from STAR", "content_id": null, "errors": null, - "id": 5, + "id": 6, "input_connections": {}, "inputs": [ { @@ -2728,8 +2844,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 1.1095706393493272, - "top": 907.0000031128606 + "left": 287.0148354755526, + "top": 645.9144573009889 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", @@ -2739,11 +2855,11 @@ "when": null, "workflow_outputs": [] }, - "6": { + "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "errors": null, - "id": 6, + "id": 7, "input_connections": { "input_file": { "id": 0, @@ -2777,10 +2893,21 @@ } ], "position": { - "left": 560.0000308495477, - "top": 1.999988137762914 + "left": 709.0902620065212, + "top": 0.0 + }, + "post_job_actions": { + "HideDatasetActionhtml_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "html_file" + }, + "HideDatasetActiontext_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "text_file" + } }, - "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "tool_shed_repository": { "changeset_revision": "2c64fded1286", @@ -2795,14 +2922,14 @@ "when": null, "workflow_outputs": [] }, - "7": { + "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357", "errors": null, - "id": 7, + "id": 8, "input_connections": { "gtf_file": { - "id": 4, + "id": 5, "output_name": "output" } }, @@ -2816,10 +2943,16 @@ } ], "position": { - "left": 281.10957032320283, - "top": 743.0000031128606 + "left": 650.1095703232029, + "top": 767.5962172140157 + }, + "post_job_actions": { + "HideDatasetActionbed_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "bed_file" + } }, - "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357", "tool_shed_repository": { "changeset_revision": "b026dae67fba", @@ -2834,14 +2967,14 @@ "when": null, "workflow_outputs": [] }, - "8": { + "9": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, - "id": 8, + "id": 9, "input_connections": { "input": { - "id": 5, + "id": 6, "output_name": "output" } }, @@ -2855,10 +2988,16 @@ } ], "position": { - "left": 281.10934435907967, - "top": 895.3505751212938 + "left": 650.1093443590796, + "top": 919.946789222449 + }, + "post_job_actions": { + "HideDatasetActionoutputsam": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outputsam" + } }, - "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", @@ -2873,14 +3012,14 @@ "when": null, "workflow_outputs": [] }, - "9": { + "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", "errors": null, - "id": 9, + "id": 10, "input_connections": { "input": { - "id": 5, + "id": 6, "output_name": "output" } }, @@ -2894,10 +3033,16 @@ } ], "position": { - "left": 281.1095878752642, - "top": 1102.0000031128604 + "left": 650.1095878752642, + "top": 1126.5962172140155 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } }, - "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", "tool_shed_repository": { "changeset_revision": "fa5d3e61e429", @@ -2912,14 +3057,14 @@ "when": null, "workflow_outputs": [] }, - "10": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0", "errors": null, - "id": 10, + "id": 11, "input_connections": { "inputFile": { - "id": 5, + "id": 6, "output_name": "output" } }, @@ -2937,10 +3082,21 @@ } ], "position": { - "left": 279.4598772618595, - "top": 1252.3383843362294 + "left": 648.4598772618594, + "top": 1276.9345984373845 + }, + "post_job_actions": { + "HideDatasetActionmetrics_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "metrics_file" + }, + "HideDatasetActionoutFile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outFile" + } }, - "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0", "tool_shed_repository": { "changeset_revision": "3f254c5ced1d", @@ -2955,18 +3111,18 @@ "when": null, "workflow_outputs": [] }, - "11": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0", "errors": null, - "id": 11, + "id": 12, "input_connections": { "input": { - "id": 5, + "id": 6, "output_name": "output" }, "refgene": { - "id": 7, + "id": 8, "output_name": "bed_file" } }, @@ -2980,10 +3136,16 @@ } ], "position": { - "left": 551.1095706393493, - "top": 634.0000031128606 + "left": 920.1095706393493, + "top": 658.5962172140157 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } }, - "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0", "tool_shed_repository": { "changeset_revision": "27e16a30667a", @@ -2998,18 +3160,18 @@ "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0", "errors": null, - "id": 12, + "id": 13, "input_connections": { "batch_mode|input": { - "id": 8, + "id": 9, "output_name": "outputsam" }, "refgene": { - "id": 7, + "id": 8, "output_name": "bed_file" } }, @@ -3032,10 +3194,21 @@ } ], "position": { - "left": 550.109375, - "top": 844 + "left": 919.109375, + "top": 868.5962141011552 + }, + "post_job_actions": { + "HideDatasetActionoutputcurvespdf": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outputcurvespdf" + }, + "HideDatasetActionoutputtxt": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outputtxt" + } }, - "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0", "tool_shed_repository": { "changeset_revision": "27e16a30667a", @@ -3050,43 +3223,47 @@ "when": null, "workflow_outputs": [] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, - "id": 13, + "id": 14, "input_connections": { "results_0|software_cond|output_0|input": { - "id": 6, + "id": 7, "output_name": "text_file" }, "results_1|software_cond|input": { - "id": 2, + "id": 1, "output_name": "output" }, "results_2|software_cond|output_0|type|input": { - "id": 3, + "id": 2, "output_name": "output" }, - "results_3|software_cond|output_0|type|input": { - "id": 11, + "results_2|software_cond|output_1|type|input": { + "id": 3, "output_name": "output" }, - "results_4|software_cond|output_0|input": { - "id": 10, - "output_name": "metrics_file" + "results_3|software_cond|input": { + "id": 4, + "output_name": "output" }, - "results_5|software_cond|output_0|type|input": { + "results_4|software_cond|output_0|type|input": { "id": 12, + "output_name": "output" + }, + "results_4|software_cond|output_1|type|input": { + "id": 13, "output_name": "outputtxt" }, - "results_6|software_cond|output_0|type|input": { - "id": 9, + "results_5|software_cond|output_0|type|input": { + "id": 10, "output_name": "output" }, - "results_7|software_cond|input": { - "id": 1, - "output_name": "output" + "results_6|software_cond|output_0|input": { + "id": 11, + "output_name": "metrics_file" } }, "inputs": [], @@ -3103,8 +3280,8 @@ } ], "position": { - "left": 871.1096398991552, - "top": 404.00000311286055 + "left": 1240.1096398991554, + "top": 428.5962172140157 }, "post_job_actions": { "RenameDatasetActionhtml_report": { @@ -3129,7 +3306,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 7, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "b5e9c0d2-62f4-41b2-a1c7-5677d8555fd4", @@ -3149,22 +3326,22 @@ } }, "tags": [], - "uuid": "7ceb54f7-213d-4e2e-8e1a-757336d64623" + "uuid": "3db32329-f64a-4233-a795-dde75648b802" }, "tool_id": null, "type": "subworkflow", "uuid": "c0aaa16c-8a9b-4fe1-8c3d-9e77f64da413", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "MultiQC stats", - "output_name": "MultiQC stats", - "uuid": "43ed1ffc-7df8-42a6-95f7-dc2b2060a910" - }, { "label": "MultiQC HTML report", "output_name": "MultiQC HTML report", "uuid": "717627ed-188d-4cb5-9a03-b1eec15f7922" + }, + { + "label": "MultiQC stats", + "output_name": "MultiQC stats", + "uuid": "43ed1ffc-7df8-42a6-95f7-dc2b2060a910" } ] } @@ -3173,6 +3350,6 @@ "RNAseq", "transcriptomics" ], - "uuid": "72595f60-4d6e-49bd-ab53-6d0f170f466d", - "version": 3 + "uuid": "f572ef14-31f2-4b9f-bd8f-4b74a7a5e2a5", + "version": 7 } \ No newline at end of file From 74ffa976c314889c77777b054732cf922aebde51 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 21:49:49 +0100 Subject: [PATCH 09/10] Hide more intermediate results --- .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index 5cc544c3e..dfc9330a7 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -2114,7 +2114,13 @@ "left": 0, "top": 16 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { "changeset_revision": "86755160afbf", @@ -2274,6 +2280,11 @@ }, "action_type": "ChangeDatatypeAction", "output_name": "output" + }, + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", @@ -2426,6 +2437,11 @@ "top": 386.17188642026633 }, "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + }, "RenameDatasetActionoutfile": { "action_arguments": { "newname": "HTS count like output" From be09ee1a58d59277a18a06ab48890fee37b5d45b Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 18 Nov 2024 09:04:29 +0100 Subject: [PATCH 10/10] upgrade fastp --- .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 31 ++++++------------- 1 file changed, 10 insertions(+), 21 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index 5cc544c3e..5e29293d7 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -357,7 +357,7 @@ }, "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3", "errors": null, "id": 10, "input_connections": { @@ -381,7 +381,7 @@ "outputs": [ { "name": "out1", - "type": "auto" + "type": "input" }, { "name": "report_json", @@ -393,13 +393,6 @@ "top": 106.21400000000001 }, "post_job_actions": { - "ChangeDatatypeActionout1": { - "action_arguments": { - "newtype": "fastqsanger" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "out1" - }, "HideDatasetActionout1": { "action_arguments": {}, "action_type": "HideDatasetAction", @@ -411,15 +404,15 @@ "output_name": "report_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3", "tool_shed_repository": { - "changeset_revision": "dbfc505896e9", + "changeset_revision": "a626e8c0e1ba", "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\": \"15\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": false, \"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\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": {\"__class__\": \"ConnectedValue\"}}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.23.4+galaxy2", + "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\": \"15\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": false, \"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\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"RuntimeValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": {\"__class__\": \"ConnectedValue\"}}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.24.0+galaxy3", "type": "tool", "uuid": "e31141cc-c8a5-4dde-882f-72c1b8aabe97", "when": null, @@ -1946,10 +1939,6 @@ "description": "runtime parameter for tool Cufflinks", "name": "advanced_settings" }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "input" - }, { "description": "runtime parameter for tool Cufflinks", "name": "reference_annotation" @@ -2021,7 +2010,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"RuntimeValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"RuntimeValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"RuntimeValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1.4", "type": "tool", "uuid": "af5419b7-ae6b-498c-8123-f609b8fcd8b4", @@ -2573,7 +2562,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"RuntimeValue\"}}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "e5335a24-fec9-422c-b93c-c172ad7e1b8c", @@ -3350,6 +3339,6 @@ "RNAseq", "transcriptomics" ], - "uuid": "f572ef14-31f2-4b9f-bd8f-4b74a7a5e2a5", - "version": 7 + "uuid": "885ec907-9f61-4a11-9d23-2243389e7335", + "version": 1 } \ No newline at end of file