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QuagmiR.cwl
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{
"stdin": "",
"outputs": [
{
"label": "Collapsed fastq files",
"sbg:fileTypes": "COLLAPSED",
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"description": "Collapsed fastq files.",
"id": "#collapsed_fastqs",
"outputBinding": {
"glob": {
"engine": "#cwl-js-engine",
"class": "Expression",
"script": "{\n function file_name(file){\n return(file.path.split('/').pop())\n }\n function get_file_names(input){\n var input_list = [].concat(input)\n var input_names = []\n for(i=0; i<input_list.length; i++){\n input_names = input_names.concat(file_name(input_list[i]))\n }\n return(input_names)\n }\n function include(fastq_name, collapsed_names){\n len = collapsed_names.length\n var a = 0\n for(i=0; i< len; i++)\n if(collapsed_names[i] == fastq_name + \".collapsed\")\n return(false)\n return(true)\n }\n if($job.inputs.collapsed == null){\n return(\"collapsed/*\")\n }\n else{\n var result = \"{\"\n var fastq_names = get_file_names($job.inputs.fastq_files)\n var collapsed_names = get_file_names($job.inputs.collapsed)\n for(j=0; j< fastq_names.length; j++){\n if(include(fastq_names[j], collapsed_names)){\n result += \"collapsed/\" + fastq_names[j] + \".collapsed,\"\n }\n }\n if(result == \"{\"){\n return(\"\")\n }\n result = result.slice(0, -1) + \"}\"\n if(result.indexOf(\",\") == -1){\n result = result.slice(1, -1)\n }\n return(result)\n }\n}"
},
"sbg:inheritMetadataFrom": "#fastq_files"
}
},
{
"label": "Sequence info",
"sbg:fileTypes": "TSV",
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"description": "TSV file containing information about aligned sequences.",
"id": "#sequence_info",
"outputBinding": {
"glob": "results/*sequence_info.tsv",
"sbg:inheritMetadataFrom": "#fastq_files"
}
},
{
"label": "Nucleotide distribution",
"sbg:fileTypes": "TSV",
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"description": "TSV file containing information regarding the distribution of nucleotides.",
"id": "#nucleotide_dist",
"outputBinding": {
"glob": {
"engine": "#cwl-js-engine",
"class": "Expression",
"script": "{\n if(!($job.inputs.display_nucleotide_dist == false))\n return(\"results/*nucleotide_dist.tsv\")\n}"
},
"sbg:inheritMetadataFrom": "#fastq_files"
}
},
{
"label": "Summary",
"sbg:fileTypes": "TSV",
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"description": "File containing summary information for each reference miRNA sequence (number of reads aligned to it, number of different isomiRs, etc).",
"id": "#summary",
"outputBinding": {
"glob": {
"engine": "#cwl-js-engine",
"class": "Expression",
"script": "{\n if(!($job.inputs.display_summary == false))\n return(\"results/*isomir.tsv\")\n}"
},
"sbg:inheritMetadataFrom": "#fastq_files"
}
},
{
"label": "Group summary",
"sbg:fileTypes": "TSV",
"type": [
"null",
"File"
],
"description": "Summary for all inputs.",
"id": "#group_summary",
"outputBinding": {
"glob": {
"engine": "#cwl-js-engine",
"class": "Expression",
"script": "{\n if(!($job.inputs.display_summary == false) &&\n !($job.inputs.display_group_output == false))\n return(\"group_results/*isomir.tsv\")\n}"
},
"sbg:inheritMetadataFrom": "#fastq_files"
}
},
{
"label": "Group sequence info",
"sbg:fileTypes": "TSV",
"type": [
"null",
"File"
],
"description": "Sequence info for all inputs.",
"id": "#group_sequence_info",
"outputBinding": {
"glob": "group_results/*sequence_info.tsv"
}
},
{
"label": "Group nucleotide distribution",
"sbg:fileTypes": "TSV",
"type": [
"null",
"File"
],
"description": "Nucleotide distribution for all inputs.",
"id": "#group_nucleotide_dist",
"outputBinding": {
"glob": {
"engine": "#cwl-js-engine",
"class": "Expression",
"script": "{\n if(!($job.inputs.display_nucleotide_dist == false) &&\n !($job.inputs.display_group_output == false))\n return(\"group_results/*nucleotide_dist.tsv\")\n}"
}
}
},
{
"label": "GFF",
"sbg:fileTypes": "GFF",
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"description": "GFF.",
"id": "#gff",
"outputBinding": {
"glob": "results/*gff",
"sbg:inheritMetadataFrom": "#fastq_files"
}
}
],
"sbg:toolkitVersion": "1.0",
"inputs": [
{
"label": "Minimum ratio",
"sbg:toolDefaultValue": "-1",
"id": "#min_ratio",
"description": "Minimum percentege a sequence comprises out of total number of reads in order for it not to be discarded. Set to -1 in order to disable.",
"type": [
"null",
"float"
],
"sbg:category": "Filtering parameters"
},
{
"label": "Min reads",
"sbg:toolDefaultValue": "-1",
"id": "#min_read",
"description": "Minimum coverage a sequence can have in order for it not to be discarded. Set to -1 in order to disable.",
"type": [
"null",
"int"
],
"sbg:category": "Filtering parameters"
},
{
"label": "Motif-consensus file",
"sbg:fileTypes": "FA",
"id": "#motif_consensus_file",
"description": "Reference file containing name, motif sequence, and mature miRNA sequence for each miRNA.",
"type": [
"File"
],
"sbg:category": "Input files"
},
{
"label": "Destructive motif pull",
"sbg:toolDefaultValue": "False",
"id": "#destructive_motif_pull",
"description": "When turned on, only the best fitting alignment position is kept, while all other possibilities are discarded.",
"type": [
"null",
"boolean"
],
"sbg:category": "Input parameters"
},
{
"label": "Input reads",
"sbg:stageInput": "link",
"sbg:fileTypes": "FASTQ",
"id": "#fastq_files",
"description": "Input miRNA-Seq reads. It can be one sample, or multiple, in which case QuagmiR will use all of available threads so the task's run time would be as short as possible.",
"type": [
{
"items": "File",
"type": "array"
}
],
"sbg:category": "Input files"
},
{
"label": "Number of threads",
"description": "Number of threads for QuagmiR to use. If there is 36 files or less, it is recommended to use one thread per file. If there are more files it is best to use divider of the number of files, or in case number of files exceeds 100, set it to 36. Default number of threads is set to number of files in case there is no more than 36 files, and to 36 otherwise.",
"type": [
"null",
"int"
],
"id": "#number_of_threads",
"sbg:category": "Input parameters"
},
{
"label": "Collapsed files",
"sbg:stageInput": "link",
"sbg:fileTypes": "COLLAPSED",
"id": "#collapsed",
"description": "Collapsed files made by previous tun of the tool. They must be named same like the fastqs with \".collapsed\" at the end of the file name.",
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"sbg:category": "Input files"
},
{
"label": "Display group output",
"sbg:toolDefaultValue": "True",
"id": "#display_group_output",
"description": "Option to output group result files for all files.",
"type": [
"null",
"boolean"
],
"sbg:category": "Output options"
},
{
"label": "Group output name",
"description": "Prefix for group output files.",
"type": [
"null",
"string"
],
"id": "#group_output_name",
"sbg:category": "Output options"
},
{
"label": "Edit distance filtering treshold on 3' end",
"sbg:toolDefaultValue": "-1",
"id": "#edit_distance_treshold_3p",
"description": "Filter out every read that has edit distance on 3' between miRNA sequence and reference greater than set number. To be set to -1 in case filtering on 3' end needs to be swiched off.",
"type": [
"null",
"int"
],
"sbg:category": "Filtering parameters"
},
{
"label": "Edit distance filtering threshold on 5' end",
"sbg:toolDefaultValue": "-1",
"id": "#edit_distance_treshold_5p",
"description": "Filter out every read that has edit distance on 5' between miRNA sequence and reference greater than set number. To be set to -1 in case filtering on 5' end needs to be swiched off.",
"type": [
"null",
"int"
],
"sbg:category": "Filtering parameters"
},
{
"label": "Ambiguous letters support",
"sbg:toolDefaultValue": "False",
"id": "#ambiguous_letters",
"description": "In case ambiguous letters support is on, the program will be able to work with letters such as N, R, Y, etc, but it will work slower. If it is switched off, all ambiguous letters (even Ns in fastq files) will be treted as missmatches against all bases.",
"type": [
"null",
"boolean"
],
"sbg:category": "Input parameters"
},
{
"label": "Deletion score",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"id": "#deletion_score",
"description": "Deletion score for calculating edit distance.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "Insertion score",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"id": "#insertion_score",
"description": "Insertion score for edit distance calculation.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "Substitution score",
"description": "Substitution score for edit distance calculation.",
"type": [
"null",
{
"name": "substitution_score",
"type": "record",
"fields": [
{
"label": "A->C",
"name": "ac",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for A to C substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "A->G",
"name": "ag",
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for A to G substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "A->T",
"name": "at",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for A to T substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "C->A",
"name": "ca",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for C to A substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "C->G",
"name": "cg",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for C to G substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "C->T",
"name": "ct",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for C to T substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "G->A",
"name": "ga",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for G to A substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "G->C",
"name": "gc",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for G to C substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "G->T",
"name": "gt",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for G to T substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "T->A",
"name": "ta",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for T to A substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "T->C",
"name": "tc",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for T to C substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
},
{
"label": "T->G",
"name": "tg",
"sbg:stageInput": null,
"sbg:toolDefaultValue": "1",
"description": "Edit distance score for T to G substitution.",
"type": [
"null",
"float"
],
"sbg:category": "Edit distance parameters"
}
]
}
],
"id": "#substitution_score",
"sbg:category": "Edit distance parameters"
},
{
"label": "Reference file",
"sbg:stageInput": "link",
"sbg:fileTypes": "TSV",
"id": "#reference_file",
"description": "Reference file.",
"type": [
"File"
]
},
{
"label": "miRBase version",
"description": "miRBase version.",
"type": [
"null",
"string"
],
"id": "#mirbase_version",
"sbg:toolDefaultValue": "21"
},
{
"label": "Source ontology",
"description": "Source ontology.",
"type": [
"null",
"string"
],
"id": "#source_ontology",
"sbg:toolDefaultValue": "miRBase v21 doi:10.25504/fairsharing.hmgte8"
}
],
"sbg:job": {
"allocatedResources": {
"cpu": 4,
"mem": 1000
},
"inputs": {
"source_ontology": "source_ontology-string-value",
"reference_file": {
"path": "/path/to/reference_file.ext",
"size": 0,
"secondaryFiles": [],
"class": "File"
},
"number_of_threads": null,
"display_group_output": true,
"insertion_score": 9.969961420283253,
"fastq_files": [
{
"path": "/path/to/fastq_file-1.ext",
"size": 0,
"metadata": {
"sample_group": "test1"
},
"secondaryFiles": [],
"class": "File"
},
{
"path": "/path/to/fastq_file-2.ext",
"size": 0,
"metadata": {
"sample_group": "test2"
},
"secondaryFiles": [],
"class": "File"
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"path": "/path/to/motif_consensus_file.ext",
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}
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{
"label": "QuagmiR Homepage",
"id": "https://github.com/duxan/quagmir"
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"label": "QuagmiR Source Code",
"id": "https://github.com/duxan/quagmir"
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"label": "QuagmiR Download",
"id": "https://github.com/duxan/quagmir"
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"engine": "#cwl-js-engine",
"class": "Expression",
"script": "{\n var nthreads = $job.inputs.number_of_threads || [].concat($job.inputs.fastq_files).length\n if(nthreads > 36) nthreads = 36\n return(nthreads)\n}"
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"filename": "config.yaml",
"fileContent": {
"engine": "#cwl-js-engine",
"class": "Expression",
"script": "{\n var motif_consensus_file = $job.inputs.motif_consensus_file.path\n var reference_file = $job.inputs.reference_file.path\n var min_ratio = $job.inputs.min_ratio || -1\n var min_read = $job.inputs.min_read || -1\n var destructive_motif_pull = $job.inputs.destructive_motif_pull || \"False\"\n if(destructive_motif_pull == true)destructive_motif_pull = \"True\"\n var ambiguous_letters = $job.inputs.ambiguous_letters || \"False\"\n if(ambiguous_letters == true)ambiguous_letters = \"True\"\n var display_summary = $job.inputs.display_summary || \"False\"\n if($job.inputs.display_summary == false) var display_summary = \"False\"\n else var display_summary = \"True\"\n if($job.inputs.display_sequence_info == false) var display_sequence_info = \"False\"\n else var display_sequence_info = \"True\" \n if($job.inputs.display_nucleotide_dist == false) var display_nucleotide_dist = \"False\"\n else var display_nucleotide_dist = \"True\"\n if($job.inputs.display_group_output == false) var display_group_output = \"False\"\n else var display_group_output = \"True\"\n if($job.inputs.group_output_name == null ||\n $job.inputs.group_output_name == \"\") var group_output_name = \"group_output\"\n else var group_output_name = $job.inputs.group_output_name\n var mirbase_version = $job.inputs.mirbase_version || \"21\"\n var source_ontology = $job.inputs.source_ontology || \"miRBase v21 doi:10.25504/fairsharing.hmgte8\"\n \n var edit_distance_3p = $job.inputs.edit_distance_treshold_3p || -1\n var edit_distance_5p = $job.inputs.edit_distance_treshold_5p || -1\n \n //edit distance parameters\n var deletion_score = $job.inputs.deletion_score || 1\n var insertion_score = $job.inputs.insertion_score || 1\n if($job.inputs.substitution_score){\n var ac = $job.inputs.substitution_score.ac || 1\n var ag = $job.inputs.substitution_score.ag || 1\n var at = $job.inputs.substitution_score.at || 1\n var ca = $job.inputs.substitution_score.ca || 1\n var cg = $job.inputs.substitution_score.cg || 1\n var ct = $job.inputs.substitution_score.ct || 1\n var ga = $job.inputs.substitution_score.ga || 1\n var gc = $job.inputs.substitution_score.gc || 1\n var gt = $job.inputs.substitution_score.gt || 1\n var ta = $job.inputs.substitution_score.ta || 1\n var tc = $job.inputs.substitution_score.tc || 1\n var tg = $job.inputs.substitution_score.tg || 1\n }\n else{\n var ac = 1\n var ag = 1\n var at = 1\n var ca = 1\n var cg = 1\n var ct = 1\n var ga = 1\n var gc = 1\n var gt = 1\n var ta = 1\n var tc = 1\n var tg = 1\n }\n \n return(\"# FILTERING\\n\" + \n \"min_ratio: \" + min_ratio + \"\\n\" + //.1 \n \"min_read: \" + min_read + \"\\n\" + //9\n \"edit_distance_3p: \" + edit_distance_3p + \"\\n\" + //-1\n \"edit_distance_5p: \" + edit_distance_5p + \"\\n\\n\" + //-1\n\n \"# DISPLAY\\n\" +\n \"display_summary: \" + display_summary + \"\\n\" +//True\n \"display_sequence_info: \" + display_sequence_info + \"\\n\" + //True\n \"display_nucleotide_dist: \" + display_nucleotide_dist + \"\\n\" + //True\n \"display_group_output: \" + display_group_output + \"\\n\\n\" + //True\n \n \"# AMBIGUOUS LETTERS\\n\" +\n \"ambiguous_letters: \" + ambiguous_letters + \"\\n\\n\" + //True\n \n \"# DESTRUCTIVE MOTIF PULL\\n\" +\n \"destructive_motif_pull: \" + destructive_motif_pull + \"\\n\\n\" + //False\n\n \"# INPUT\\n\" +\n \"data: data\\n\" + // input folder\n \"motif_consensus_file: \" + motif_consensus_file + \"\\n\" +\n \"reference_file: \" + reference_file + '\\n' +\n \"mirbase_version: \" + mirbase_version + \"\\n\" + // version of miRBase being used for reference files\n \"source_ontology: \" + source_ontology + \"\\n\\n\" +\n \n \"# OUTPUT\\n\" +\n \"group_output_name: \" + group_output_name + \"\\n\\n\" +\n \n \"# DISTANCE METRIC\\n\" +\n \"deletion_score: \" + deletion_score + \"\\n\" +\n \"insertion_score: \" + insertion_score + \"\\n\" +\n \"substitution_AG: \" + ag + \" # transition\\n\" +\n \"substitution_GA: \" + ga + \" # transition\\n\" +\n \"substitution_CT: \" + ct + \" # transition\\n\" +\n \"substitution_TC: \" + tc + \" # transition\\n\" +\n \"substitution_AT: \" + at + \" # transversion\\n\" +\n \"substitution_TA: \" + ta + \" # transversion\\n\" +\n \"substitution_AC: \" + ac + \" # transversion\\n\" +\n \"substitution_CA: \" + ca + \" # transversion\\n\" +\n \"substitution_GC: \" + gc + \" # transversion\\n\" +\n \"substitution_CG: \" + cg + \" # transversion\\n\" +\n \"substitution_GT: \" + gt + \" # transversion\\n\" +\n \"substitution_TG: \" + tg + \" # transversion\\n\")\n}"
}
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}
}
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