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kallisto_quant.cgc.cwl
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{
"arguments": [
{
"position": 1,
"prefix": "-o",
"separate": true,
"valueFrom": "."
},
{
"position": 99,
"separate": false,
"valueFrom": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "\"&& rename 's/^/\" + ($job.inputs.output_prefix || $job.inputs.fastq1.path.split('/').pop().split('.')[0]) + \"_/' abundance* && rename 's/^/\" + ($job.inputs.output_prefix || $job.inputs.fastq1.path.split('/').pop().split('.')[0]) + \"_/' run_info*\"\n"
}
}
],
"baseCommand": [
"kallisto",
"quant"
],
"class": "CommandLineTool",
"description": "kallisto quant for kallisto v0.43.0",
"hints": [
{
"class": "sbg:CPURequirement",
"value": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "$job.inputs.threads"
}
},
{
"class": "sbg:MemRequirement",
"value": 1000
},
{
"class": "DockerRequirement",
"dockerImageId": "",
"dockerPull": "cgc-images.sbgenomics.com/gauravcgc/kallisto:latest"
}
],
"id": "-",
"inputs": [
{
"description": "Input index file made from a transcripts fasta by kallisto quant",
"id": "#index",
"inputBinding": {
"position": 0,
"prefix": "-i",
"sbg:cmdInclude": true,
"separate": true
},
"label": "Index File",
"sbg:category": "Input",
"sbg:fileTypes": "TXT, INDEX",
"type": [
"File"
]
},
{
"description": "Perform sequence based bias correction",
"id": "#bias",
"inputBinding": {
"position": 2,
"prefix": "--bias",
"sbg:cmdInclude": true,
"separate": false
},
"label": "Bias",
"sbg:category": "Optional",
"sbg:toolDefaultValue": "False",
"type": [
"null",
"boolean"
]
},
{
"description": "Number of bootstrap samples",
"id": "#bootstrap",
"inputBinding": {
"position": 2,
"prefix": "-b",
"sbg:cmdInclude": true,
"separate": true
},
"label": "Bootstrap Samples",
"sbg:category": "Optional",
"sbg:toolDefaultValue": "0",
"type": [
"null",
"int"
]
},
{
"description": "Seed for the bootstrap sampling",
"id": "#seed",
"inputBinding": {
"position": 2,
"prefix": "--seed=",
"sbg:cmdInclude": true,
"separate": false
},
"label": "Seed",
"sbg:category": "Optional",
"sbg:toolDefaultValue": "42",
"type": [
"null",
"int"
]
},
{
"description": "Output plaintext only (no H5)",
"id": "#plaintext",
"inputBinding": {
"position": 2,
"prefix": "--plaintext",
"sbg:cmdInclude": true,
"separate": false
},
"label": "Plaintext Output",
"sbg:category": "Optional",
"sbg:toolDefaultValue": "False",
"type": [
"null",
"boolean"
]
},
{
"description": "Quantify single-end reads",
"id": "#single",
"inputBinding": {
"position": 2,
"prefix": "--single",
"sbg:cmdInclude": true,
"separate": false
},
"label": "Singe-End Reads",
"sbg:category": "Single",
"sbg:toolDefaultValue": "False",
"type": [
"null",
"boolean"
]
},
{
"description": "Strand specific reads, first read forward",
"id": "#fr_stranded",
"inputBinding": {
"position": 2,
"prefix": "--fr-stranded",
"sbg:cmdInclude": true,
"separate": false
},
"label": "First Read Forward",
"sbg:category": "Optional",
"sbg:toolDefaultValue": "False",
"type": [
"null",
"boolean"
]
},
{
"description": "Strand specific reads, first read reverse",
"id": "#rf_stranded",
"inputBinding": {
"position": 2,
"prefix": "--rf-stranded",
"sbg:cmdInclude": true,
"separate": false
},
"label": "First Read Reverse",
"sbg:category": "Optional",
"sbg:toolDefaultValue": "False",
"type": [
"null",
"boolean"
]
},
{
"description": "Estimated average fragment length (required if Single)",
"id": "#fraglength_mean",
"inputBinding": {
"position": 2,
"sbg:cmdInclude": true,
"separate": false,
"valueFrom": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "if ($job.inputs.single) {'-l ' + $job.inputs.fraglength_mean}"
}
},
"label": "Fragment Length",
"sbg:category": "Single",
"sbg:toolDefaultValue": "None",
"type": [
"null",
"float"
]
},
{
"description": "Estimated standard deviation of fragment length (Required if Single)",
"id": "#fraglength_std",
"inputBinding": {
"position": 2,
"sbg:cmdInclude": true,
"separate": false,
"valueFrom": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "if ($job.inputs.single) {'-s ' + $job.inputs.fraglength_std}"
}
},
"label": "Fragment Length Stdev",
"sbg:category": "Single",
"sbg:toolDefaultValue": "None",
"type": [
"null",
"float"
]
},
{
"description": "Numbers of threads (Note: if using pseudobam, this will be overriden to equal 1)",
"id": "#threads",
"inputBinding": {
"position": 2,
"prefix": "-t",
"sbg:cmdInclude": true,
"separate": true,
"valueFrom": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "if ($job.inputs.pseudobam) {\n 1\n} else {\n $job.inputs.threads\n}"
}
},
"label": "Threads",
"sbg:category": "Optional",
"sbg:toolDefaultValue": "1",
"type": [
"null",
"int"
]
},
{
"description": "Output pseudoalignments in SAM format to stdout",
"id": "#pseudobam",
"inputBinding": {
"position": 2,
"prefix": "--pseudobam",
"sbg:cmdInclude": true,
"separate": false
},
"label": "SAM Output",
"sbg:category": "Pseudobam",
"sbg:toolDefaultValue": "False",
"type": [
"null",
"boolean"
]
},
{
"description": "Filename for output pseudobam file (ext: SAM)",
"id": "#pseudobam_filename",
"label": "Pseudobam SAM Filename",
"sbg:category": "Pseudobam",
"sbg:toolDefaultValue": "pseudobam.sam",
"type": [
"null",
"string"
]
},
{
"description": "Input FASTQ file 1",
"id": "#TUMOR_FASTQ_1",
"inputBinding": {
"position": 3,
"sbg:cmdInclude": true,
"separate": false
},
"label": "TUMOR_FASTQ_1",
"sbg:category": "FASTQ",
"sbg:fileTypes": "FASTQ, FQ, FASTQ.GZ, FQ.GZ",
"type": [
"File"
]
},
{
"description": "Input FASTQ 2",
"id": "#TUMOR_FASTQ_2",
"inputBinding": {
"position": 3,
"sbg:cmdInclude": true,
"separate": false
},
"label": "TUMOR_FASTQ_2",
"sbg:category": "FASTQ",
"sbg:fileTypes": "FASTQ, FQ, FASTQ.GZ, FQ.GZ",
"type": [
"null",
"File"
]
},
{
"description": "Specify prefix for output filenames",
"id": "#output_prefix",
"label": "Output Filename Prefix",
"sbg:category": "Output",
"sbg:toolDefaultValue": "Uses FASTQ1 basename if none specified",
"type": [
"null",
"string"
]
},
{
"description": "Determine whether to save the Run JSON",
"id": "#save_json",
"label": "Save Run JSON",
"sbg:category": "Output",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "False",
"type": [
"null",
"boolean"
]
}
],
"label": "kallisto-quant",
"outputs": [
{
"description": "Run Info JSON",
"id": "#json",
"label": "JSON",
"outputBinding": {
"glob": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "if ($job.inputs.save_json) { '*run_info.json' } "
},
"sbg:inheritMetadataFrom": "#fastq1"
},
"sbg:fileTypes": "JSON",
"type": [
"null",
"File"
]
},
{
"description": "Abundances in h5 format",
"id": "#abundance_h5",
"label": "Abundance H5",
"outputBinding": {
"glob": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "if ($job.inputs.plaintext==false) { '*abundance.h5' } "
},
"sbg:inheritMetadataFrom": "#fastq1"
},
"sbg:fileTypes": "H5",
"type": [
"null",
"File"
]
},
{
"description": "Abundance by gene in TSV format",
"id": "#abundance_tsv",
"label": "Abundance TSV",
"outputBinding": {
"glob": "*abundance.tsv",
"sbg:inheritMetadataFrom": "#fastq1"
},
"sbg:fileTypes": "TSV",
"type": [
"File"
]
},
{
"description": "Pseudobam file output if true",
"id": "#sam",
"label": "SAM",
"outputBinding": {
"glob": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "if ($job.inputs.pseudobam) { '*.sam' }"
},
"sbg:inheritMetadataFrom": "#fastq1"
},
"sbg:fileTypes": "SAM",
"type": [
"null",
"File"
]
}
],
"requirements": [
{
"class": "ExpressionEngineRequirement",
"id": "#cwl-js-engine",
"requirements": [
{
"class": "DockerRequirement",
"dockerPull": "rabix/js-engine"
}
]
}
],
"sbg:categories": [
"RNA"
],
"sbg:id": "gauravCGC/kallisto-dream/kallisto-quant/1",
"sbg:toolAuthor": "Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L.",
"sbg:toolkit": "kallisto",
"stdin": "",
"stdout": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "if ($job.inputs.pseudobam) { \n ($job.inputs.pseudobam_filename.split('.')[0] || 'pseudobam') + '.sam' \n}"
},
"successCodes": [],
"temporaryFailCodes": []
}