@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ResourceRequirement: .
rdfs:comment "Input file: BED, SAM, bowtie, etc.\n" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
rdfs:comment "<#> and -maxlen <#> (Filter reads with lengths outside this range)\n" ;
cwl:inputBinding [ CommandLineBinding:position 14 ;
CommandLineBinding:prefix "-minlen"
] ;
sld:type xsd:int , sld:null .
a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/homer:4.11--pl5262h4ac6f70_9" .
rdfs:comment "check Sequence bias, requires \"-genome\"\n" ;
cwl:inputBinding [ CommandLineBinding:position 16 ;
CommandLineBinding:prefix "-checkGC"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Output directory name with tags files\n" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type xsd:string .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.o)" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-annStats"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "File to write output to.\n" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--output-file"
] ;
sld:type xsd:string .
rdfs:comment "Input file format: BED, SAM, bowtie, etc.\n" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-format"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "GTF definition file\n" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-gtf"
] ;
sld:type cwl:File , sld:null .
rdfs:comment "(Use current tag directory for QC/processing, do not parse new alignment files)\n" ;
cwl:inputBinding [ CommandLineBinding:position 11 ;
CommandLineBinding:prefix "-update"
] ;
sld:type xsd:boolean , sld:null .
sld:type [ sld:items [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type sld:array
] .
sld:type xsd:string .
rdfs:comment "Files containing peaks and scores.\n" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--samples"
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:valueFrom " ${ return inputs.input.nameroot + \"_tags\";}" .
cwl:outputSource ;
sld:type [ sld:items [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type sld:array
] .
rdfs:comment "flip strand of each read, i.e. might want to use with some RNA-seq\n" ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-flip"
] ;
sld:type xsd:boolean , sld:null .
cwl:valueFrom "${ return inputs.input.basename + \"_annStats.txt\";}" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.annStats)" ] ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "homer" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/homer" ;
SoftwarePackage:version "4.11"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "homer" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/homer" ;
SoftwarePackage:version "4.11"
] .
rdfs:comment "Peak/BED file\n" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
sld:type xsd:float , sld:null .
rdfs:comment "Output file type. Defaults to input file type when available, otherwise bed.\n" ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--output-file-type"
] ;
sld:type xsd:string , sld:null .
cwl:default true .
sld:type cwl:File , sld:null .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Irreproducible Discovery Rate (IDR)" ;
rdfs:label "idr" ;
ns1:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "idr" ) ;
cwl:cwlVersion ;
cwl:hints , ;
cwl:inputs , , , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 1024
] .
cwl:source .
cwl:source .
a cwl:Workflow ;
rdfs:comment "Irreproducible Discovery Rate (IDR) workflow with Homer annotation" ;
rdfs:label "IDR workflow" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
rdfs:comment "Genome version: hg19, hg38\n" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
sld:type cwl:File .
rdfs:comment "<#> (Maximum tags per bp, default: no maximum)\n" ;
cwl:inputBinding [ CommandLineBinding:position 12 ;
CommandLineBinding:prefix "-tbp"
] ;
sld:type xsd:int , sld:null .
a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/idr:2.0.4.2--py39hec16e2b_10" .
cwl:default "bed" .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_file)" ] ;
sld:type cwl:File .
cwl:source .
rdfs:comment "<1|2|3> (number of decimal places to use for tag totals, default: 1)\n" ;
cwl:inputBinding [ CommandLineBinding:position 13 ;
CommandLineBinding:prefix "-precision"
] ;
sld:type xsd:int , sld:null .
rdfs:label "HOMER-makeTagDirectory" ;
cwl:in , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
sld:type xsd:string .
cwl:source .
rdfs:comment "Report statistics for peaks with a global idr below this value but return all peaks with an idr below --idr.\nDefault: 0.05\n" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--soft-idr-threshold"
] ;
sld:type xsd:float , sld:null .
cwl:source .
cwl:default true .
rdfs:comment "Options: signal.value p.value q.value columnIndex\nDefaults:\n narrowPeak/broadPeak: signal.value\n bed: score\n" ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "--rank"
] ;
sld:type xsd:string , sld:null .
rdfs:label "idr" ;
cwl:in , , , , , , , ;
cwl:out , ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
a cwl:CommandLineTool ;
rdfs:comment "Software for motif discovery and next generation sequencing analysis" ;
rdfs:label "HOMER-makeTagDirectory" ;
ns1:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "makeTagDirectory" ) ;
cwl:cwlVersion ;
cwl:hints , ;
cwl:inputs , , , , , , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 1024
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_file)*.png" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:source .
cwl:default true .
rdfs:comment "Only return peaks with a global idr threshold below this value.\nDefault: report all peaks\n" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--idr-threshold"
] ;
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-fpkm"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "(Create a single tags.tsv file for all \"chromosomes\" - i.e. if >100 chromosomes)\n" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "-single"
] ;
sld:type xsd:boolean , sld:null .
a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "idr" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/idr" ;
SoftwarePackage:version "2.0.4.2"
] .
rdfs:comment "Plot the results to [OFNAME].png\n" ;
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "--plot"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
rdfs:comment "Set estimated fragment length or use PE length - given: use read lengths\n" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-fragLength"
] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tags_directory_name)" ] ;
sld:type cwl:Directory .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Software for motif discovery and next generation sequencing analysis" ;
rdfs:label "HOMER-annotatePeaks" ;
ns1:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "annotatePeaks.pl" ) ;
cwl:cwlVersion ;
cwl:hints , ;
cwl:inputs , , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 1024
] ;
cwl:stdout "$(inputs.o)" .
cwl:outputSource ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "(5th column of BED file contains # of reads mapping to position)\n" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "-force5th"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "GFF definition file\n" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-gff"
] ;
sld:type cwl:File , sld:null .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Set the IDR value for a group of multi summit peaks (a group of peaks with the same chr/start/stop but\ndifferent summits) to the best value across all of these peaks. This is a work around for peak callers\nthat don't do a good job splitting scores across multi summit peaks (e.g. MACS).\nIf set in conjunction with --plot two plots will be created - one with alternate summits and\none without. Use this option with care.\n" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--use-best-multisummit-IDR"
] ;
sld:type xsd:boolean , sld:null .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:in , , , , , , ;
cwl:out , ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
rdfs:comment " [tag directory 2] ... (add Tag directory to new tag directory)\n" ;
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "-d"
] ;
sld:type sld:null ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
rdfs:comment "\n" ;
cwl:inputBinding [ CommandLineBinding:position 15 ;
CommandLineBinding:prefix "-genome"
] ;
sld:type cwl:File .
rdfs:comment "File type of --samples and --peak-list: narrowPeak, broadPeak, bed, gff\n" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--input-file-type"
] ;
sld:type xsd:string .
cwl:source .
rdfs:comment "If provided, all peaks will be taken from this file.\n" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--peak-list"
] ;
sld:type cwl:File , sld:null .
rdfs:comment "<#|all|default> (set the effective total number of reads - all includes multimappers)\n" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-totalReads"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-d"
] ;
sld:type cwl:Directory , sld:null .
cwl:valueFrom "${ return inputs.input.basename + \"_annotation.txt\";}" .
rdfs:comment " [tag file 2] ... (add tag file i.e. *.tags.tsv to new tag directory)\n" ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "-t"
] ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "GFF3 definition file\n" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-gff3"
] ;
sld:type cwl:File , sld:null .
cwl:default true .