@prefix LoadListingRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix ScatterMethod: . @prefix cwl: . @prefix CommandLineTool: . rdfs:comment "By adding this option, reads are centered with respect\nto the fragment length. For paired-end data, the read\nis centered at the fragment length defined by the two\nends of the fragment. For single-end data, the given\nfragment length is used. This option is useful to get\na sharper signal around enriched regions. (default:\nFalse)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--centerReads" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "\tReport depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bg" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bg" ] ; sld:type xsd:boolean , sld:null . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" . rdfs:comment "Print the header from the A file prior to results.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-header" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Possible choices: RPKM, CPM, BPM, RPGC\n\nUse one of the entered methods to normalize the number of reads per bin.\nBy default, no normalization is performed. RPKM = Reads Per Kilobase per\nMillion mapped reads; CPM = Counts Per Million mapped reads, same as\nCPM in RNA-seq; BPM = Bins Per Million mapped reads, same as TPM in\nRNA-seq; RPGC = reads per genomic content (1x normalization);\nMapped reads are considered after blacklist filtering (if applied).\nRPKM (per bin) = number of reads per bin / (number of mapped reads (in millions) * bin length (kb)).\nCPM (per bin) = number of reads per bin / number of mapped reads (in millions).\nBPM (per bin) = number of reads per bin / sum of all reads per bin (in millions).\nRPGC (per bin) = number of reads per bin / scaling factor for 1x average coverage.\nThis scaling factor, in turn, is determined from the sequencing depth:\n(total number of mapped reads * fragment length) / effective genome size.\nThe scaling factor used is the inverse of the sequencing depth\ncomputed for the sample to match the 1x coverage.\nThis option requires –effectiveGenomeSize.\nEach read is considered independently, if you want to only count one\nmate from a pair in paired-end data, then use\nthe –samFlagInclude/–samFlagExclude options.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--normalizeUsing" ] ; sld:type xsd:string , sld:null . rdfs:comment "BUFFER_SIZE\nBuffer size for incrementally increasing internal\narray size to store reads alignment information. In\nmost cases, you don't have to change this parameter.\nHowever, if there are large number of\nchromosomes/contigs/scaffolds in your alignment, it's\nrecommended to specify a smaller buffer size in order\nto decrease memory usage (but it will take longer time\nto read alignment files). Minimum memory requested for\nreading an alignment file is about # of CHROMOSOME *\nBUFFER_SIZE * 2 Bytes. DEFAULT: 100000\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--buffer-size" ] ; sld:type xsd:int , sld:null . rdfs:comment "Bed file to be clipped" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "suffix of the transformed SAM/BAM file (including extension, e.g. .filtered.sam)" ; cwl:default ".sorted.bam" ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:comment "Counts reads in a fastq file" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "count-fastq-reads.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_basename + '.read_count.txt')" . rdfs:comment "BAM file to process " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Whether turn on the auto pair model process. If set, when MACS failed to build paired model, it will use the nomodel settings, the --exsize parameter to extend each tags towards 3' direction. Not to use this automate fixation is a default behavior now. DEFAULT: False " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--fix-bimodal" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "If using BAM input, write output as BED.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bed" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:string . cwl:source . rdfs:comment ", full path and name (or URL) of tagAlign/BAM file (can be gzipped)(FILE EXTENSION MUST BE tagAlign.gz, tagAlign, bam or bam.gz)" ; cwl:inputBinding [ CommandLineBinding:prefix "-c=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.input_file.path.substr(inputs.input_file.path.lastIndexOf('/') + 1, inputs.input_file.path.lastIndexOf('.') - (inputs.input_file.path.lastIndexOf('/') + 1)))" ] ; sld:type xsd:string . rdfs:comment "PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5)" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Adapters file" ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_basename_file + '.masked.bam')" ] ; sld:type cwl:File . rdfs:comment "Minimum FDR (q-value) cutoff for peak detection. DEFAULT: 0.05. -q, and -p are mutually exclusive." ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-q" ] ; sld:type xsd:float , sld:null . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.i.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.bam')" ] ; sld:type cwl:File . rdfs:comment "Read counts of the mapped and filtered BAM files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Bedfile containing ENCODE consensus blacklist regions to be excluded." ; sld:type cwl:File . rdfs:comment "\tReport depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero\ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0\ncoverage by applying: \"grep -w 0$\" to the output.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bga" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bga" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "FILENAME\nOutput file name. (default: input BAM filename with bigwig [*.bw] or bedgraph [*.bdg] extension.)\n" ; sld:type xsd:string , sld:null . a cwl:Workflow ; rdfs:comment "DNase-seq 02 quantification" ; 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . rdfs:comment "Require that the minimum fraction be satisfied for A OR B.\n- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either 90 percent of A is covered OR 10 percent of B is covered.\nWithout -e, both fractions would have to be satisfied.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-e" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "peakshift/phantomPeak results summary plot" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp_cross_corr.pdf\")" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . rdfs:comment "The number of base pairs to subtract from the start coordinate.\n- (Integer) or (Float, e.g. 0.1) if used with -pct.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:float , sld:null . rdfs:comment "show program's version number and exit" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--version" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Genome chromosome sizes file" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-g" ] ; sld:type cwl:File . rdfs:comment "Write the original entry in B for each overlap.\n- Useful for knowing _what_ A overlaps. Restricted by -f and -r.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wb" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" ] ; sld:type cwl:File . rdfs:comment "SEED Set the random seed while down sampling data. Must be\na non-negative integer in order to be effective.\nDEFAULT: not set\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seed" ] ; sld:type xsd:int , sld:null . rdfs:comment "Only report those entries in A that have _no overlaps_ with B.\n- Similar to \"grep -v\" (an homage).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "BED file\nA BED file containing regions that should be excluded\nfrom all analyses. Currently this works by rejecting\ngenomic chunks that happen to overlap an entry.\nConsequently, for BAM files, if a read partially\noverlaps a blacklisted region or a fragment spans over\nit, then the read/fragment might still be considered.\n(default: None)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--blackListFileName" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ; cwl:valueFrom "$(inputs.treatment[0].path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, ''))" ] ) ; cwl:baseCommand ( "macs2" "callpeak" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/macs2" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:string . rdfs:comment "Sorted bed or BAM file" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . rdfs:comment "Extended fragment peaks in narrowPeak file format" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Aligned BAM file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . rdfs:comment "-p= , number of parallel processing nodes, default=0" ; cwl:inputBinding [ CommandLineBinding:prefix "-p=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . rdfs:comment "Bedfile containing ENCODE consensus blacklist regions to be excluded." ; sld:type cwl:File . rdfs:comment "BAM files without PCR artifact reads." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Peak counts within replicate" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:valueFrom "${return 0}" . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-g" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:comment "ChIP-seq - map - PCR Bottleneck Coefficients" ; 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:ScatterFeatureRequirement ] . rdfs:comment "Report end-to-end hits w/ <=v mismatches; ignore qualities" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:int , sld:null . rdfs:comment "FECUTOFF When set, the value will be used to filter out peaks\nwith low fold-enrichment. Note, MACS2 use 1.0 as\npseudocount while calculating fold-enrichment.\nDEFAULT: 1.0\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--fe-cutoff" ] ; sld:type xsd:float , sld:null . rdfs:comment "Treatment sample file(s). If multiple files are given as -t A B C, then they will all be read and pooled together. IMPORTANT: the first sample will be used as the outputs basename." ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--treatment" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\nhttp://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\nuploaded to the Genome Browser as a custom track,\nBUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-trackline" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-trackline" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Number of threads used in sorting" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "File to be converted to BAM with samtools" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . rdfs:comment "\tbed_graph is a four column file in the format: \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:valueFrom ".peak_count.within_replicate.txt" . cwl:source . rdfs:comment "INT\nIf set, only reads that have a mapping quality score\nof at least this are considered. (default: None)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--minMappingQuality" ] ; sld:type xsd:int , sld:null . rdfs:comment "Fragment extended reads bigWig (signal) files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Raw reads bigWig (signal) files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . cwl:in , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "If True, MACS will use fixed background lambda as local lambda for every peak region. Normally, MACS calculates a dynamic local lambda to reflect the local bias due to potential chromatin structure. " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--nolambda" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs." ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-g" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:valueFrom "${return true}" . rdfs:comment "Split alignments based on N and D CIGAR operators.\nForces -split.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-splitD" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "-hist input is a text file containing the observed histogram \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-H" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Increase the BED/GFF/VCF entry -b base pairs in each direction.\n- (Integer) or (Float, e.g. 0.1) if used with -pct.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-b" ] ; sld:type xsd:float , sld:null . rdfs:comment "-filtchr= , Pattern to use to remove tags that map to specific chromosomes e.g. _ will remove all tags that map to chromosomes with _ in their name" ; cwl:inputBinding [ CommandLineBinding:prefix "-filtchr=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:valueFrom "${return 20}" . rdfs:comment "When writing BEDPE (-bedpe) format, \nalways report mate one as the first BEDPE \"block\".\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-mate1" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Define -l and -r based on strand.\nE.g. if used, -l 500 for a negative-stranded feature,\nit will add 500 bp downstream. Default = false.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "When set, random sampling method will scale down the bigger sample. By default, MACS uses linear scaling. Warning: This option will make your result unstable and irreproducible since each time, random reads would be selected. Consider to use 'randsample' script instead. If used together with --SPMR, 1 million unique reads will be randomly picked. Caution: due to the implementation, the final number of selected reads may not be as you expected! DEFAULT: False " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--down-sample" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Read counts of the mapped BAM files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "trim bases from 3' (right) end of reads" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trim3" ] ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "Print the header from the input file prior to results.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-header" ] ; sld:type xsd:boolean , sld:null . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bedtools" "bamtobed" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.bam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.bed')" . cwl:valueFrom ".norm.bw" . rdfs:comment "Preseq c_curve output files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "-speak=, user-defined cross-correlation peak strandshift" ; cwl:inputBinding [ CommandLineBinding:prefix "-speak=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . rdfs:comment "Determine nucleosome positions from MNase-seq data.\nOnly 3 nucleotides at the center of each fragment are\ncounted. The fragment ends are defined by the two mate\nreads. Only fragment lengthsbetween 130 - 200 bp are\nconsidered to avoid dinucleosomes or other\nartifacts.*NOTE*: Requires paired-end data. A bin size\nof 1 is recommended. (default: False)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--MNase" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "TSIZE, --tsize TSIZE\nTag size. This will overide the auto detected tag\nsize. DEFAULT: Not set\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(\"-out=\" + inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp_cross_corr.txt\")" ] [ CommandLineBinding:shellQuote false ; cwl:valueFrom "$(\"-tmpdir=\"+runtime.tmpdir)" ] ) ; cwl:baseCommand ( "run_spp.R" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/spp" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . rdfs:comment "If True, MACS will save signal per million reads for fragment pileup profiles. Require --bdg to be set. Default: False " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--SPMR" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Provide a genome file to enforce consistent chromosome sort order\nacross input files. Only applies when used with -sorted option.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-g" ] ; sld:type xsd:boolean , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "CHR:START:END\nRegion of the genome to limit the operation to - this\nis useful when testing parameters to reduce the\ncomputing time. The format is chr:start:end, for\nexample --region chr10 or --region\nchr10:456700:891000. (default: None)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--region" ] ; sld:type xsd:string , sld:null . cwl:default ".norm.bdg" ; sld:type xsd:string . cwl:source . cwl:valueFrom "${return -100}" . rdfs:comment "Tells MACS to include trackline with bedGraph files. To include this trackline while displaying bedGraph at UCSC genome browser, can show name and description of the file as well. However my suggestion is to convert bedGraph to bigWig, then show the smaller and faster binary bigWig file at UCSC genome browser, as well as downstream analysis. Require --bdg to be set. Default: Not include trackline. " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trackline" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "\t Whether or not to build the shifting model. If True, MACS will not build model. by default it means shifting size = 100, try to set extsize to change it. DEFAULT: False" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--nomodel" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Extract mapped reads from BAM file using Samtools flagstat command" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 10000 ; CommandLineBinding:shellQuote false ; cwl:valueFrom " | head -n1 | cut -f 1 -d ' '" ] ) ; cwl:arguments ( [ CommandLineBinding:position 10000 ; CommandLineBinding:shellQuote false ; cwl:valueFrom " | head -n1 | cut -f 1 -d ' '" ] ) ; cwl:baseCommand ( "samtools" "flagstat" ) ; cwl:baseCommand ( "samtools" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" . rdfs:comment "Input file to be converted to BAM format" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bed_graph.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bed_graph.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bed_graph.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Aligned file in BAM format" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bam')" ] ; sld:type cwl:File . rdfs:comment "Normalized reads bigWig (signal) files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Filtered read count after peak calling" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Treat \"split\" BAM or BED12 entries as distinct BED intervals.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-split" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Peak calling report file" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Read counts of the (unprocessed) input fastq files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bowtie_log.path.replace(/^.*[\\\\\\/]/, '') + '.read_count.mapped')" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "WINDOWSIZE\n Window size threshold for trimming reads that have the same mapping start position.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-w" ] ; sld:type xsd:int , sld:null . rdfs:comment "-verbose print more information \n" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:boolean . rdfs:comment "When using multiple databases, provide an alias for each that\nwill appear instead of a fileId when also printing the DB record.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-names" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-g" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-g" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "BROADCUTOFF\nCutoff for broad region. This option is not available\nunless --broad is set. If -p is set, this is a pvalue\ncutoff, otherwise, it's a qvalue cutoff. DEFAULT: 0.1\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--broad-cutoff" ] ; sld:type xsd:float , sld:null . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-b" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Get number of processed reads from Bowtie log." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "read-count-from-bowtie-log.sh" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.bowtie_log.path.replace(/^.*[\\\\\\/]/, '') + '.read_count.mapped')" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] . cwl:source . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . a cwl:CommandLineTool ; rdfs:comment "Filter BAM file to only include reads overlapping with a BED file" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" "-b" "-h" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '') + '.in_peaks.bam')" . cwl:source . cwl:valueFrom "RPKM" . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\" operations\nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-split" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-split" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Require same strandedness. That is, only report hits in B\nthat overlap A on the _same_ strand.\n- By default, overlaps are reported without respect to strand.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Sort by read name" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '') + inputs.output_suffix)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:default 1 ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_basename + '.read_count.txt')" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5') towards 5'->3' direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3'->5' direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * half of EXTSIZE together with EXTSIZE option for detecting enriched cutting loci such as certain DNAseI-Seq datasets. Note, you can't set values other than 0 if format is BAMPE for paired-end data. DEFAULT: 0." ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--shift" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Control sample file." ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--control" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "INT bp\nThis parameter allows the extension of reads to\nfragment size. If set, each read is extended, without\nexception. *NOTE*: This feature is generally NOT\nrecommended for spliced-read data, such as RNA-seq, as\nit would extend reads over skipped regions. *Single-\nend*: Requires a user specified value for the final\nfragment length. Reads that already exceed this\nfragment length will not be extended. *Paired-end*:\nReads with mates are always extended to match the\nfragment size defined by the two read mates. Unmated\nreads, mate reads that map too far apart (>4x fragment\nlength) or even map to different chromosomes are\ntreated like single-end reads. The input of a fragment\nlength value is optional. If no value is specified, it\nis estimated from the data (mean of the fragment size\nof all mate reads). (default: False)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--extendReads" ] ; sld:type xsd:int , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Scale BedGraph file by scaling factor computed using the number of uniq. mapped reads (library size)" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "scale-bedgraph-by-lib-uniq-reads.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:inputs , , ; cwl:outputs ; cwl:stdout "$(inputs.bedgraph_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.bdg$/, '') + inputs.output_suffix)" . sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:comment "Usage: c_curve [OPTIONS] \n\nOptions:\n -o, -output yield output file (default: stdout) \n -s, -step step size in extrapolations (default: 1e+06) \n -v, -verbose print more information \n -P, -pe input is paired end read file \n -H, -hist input is a text file containing the observed histogram \n -V, -vals input is a text file containing only the observed counts \n -B, -bam input is in BAM format \n -l, -seg_len maximum segment length when merging paired end bam reads \n (default: 5000) \n\nHelp options:\n -?, -help print this help message \n -about print about message" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "preseq" "c_curve" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/preseq:2.0" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_file_basename + '.preseq_c_curve.txt')" . a cwl:CommandLineTool ; rdfs:comment "Extracts the base name of a file" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "echo" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment " number of alignment threads to launch (default: 1)" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--threads" ] ; sld:type xsd:int . rdfs:comment "Use BAM edit distance (NM tag) for BED score.\n- Default for BED is to use mapping quality.\n- Default for BEDPE is to use the minimum of\nthe two mapping qualities for the pair.\n- When -ed is used with -bedpe, the total edit\ndistance from the two mates is reported.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-ed" ] ; sld:type xsd:boolean , sld:null . cwl:valueFrom "${return true}" . sld:type xsd:string . rdfs:comment "Bowtie log file with mapping stats" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Basename for the output file" ; sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Suffix used for output file (input BAM filename + suffix)" ; sld:type xsd:string , sld:null . rdfs:comment "Percentage of uniq reads from preseq c_curve output" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default 1 ; sld:type xsd:int . rdfs:comment "peakshift/phantomPeak extended fragment results file" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Filtered aligned BAM file by BED coordinates file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '') + '.in_peaks.bam')" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_basename + '.preseq_c_curve.txt')" ] ; sld:type cwl:File . rdfs:comment "CUTOFF\n threshold for concentration at a single base\n within a window to cutoff\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-c" ] ; sld:type xsd:float , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" "-b" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bam')" . rdfs:comment "trim bases from 5' (left) end of reads" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trim5" ] ; sld:type xsd:int , sld:null . rdfs:comment "Bowtie log file." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "-seg_len maximum segment length when merging paired end bam reads \n(default: 5000)\nHelp options:\n-?, -help print this help message\n-about print about message\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:int , sld:null . rdfs:comment "First file (extension .1.ebwt) of the Bowtie index files generated for the reference genome (see http://bowtie-bio.sourceforge.net/tutorial.shtml#newi)" ; cwl:inputBinding [ CommandLineBinding:position 9 ; cwl:valueFrom "$(self.path.split('.').splice(0,self.path.split('.').length-2).join(\".\"))" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Number of threads required for the 04-peakcall step" ; sld:type xsd:int . rdfs:comment "Input BAM file to be converted to BED format" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . rdfs:comment "Write uncompressed BAM output. Default writes compressed BAM.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-ubam" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "The smooth length defines a window, larger than the\nbinSize, to average the number of reads. For example,\nif the –binSize is set to 20 and the –smoothLength is\nset to 60, then, for each bin, the average of the bin\nand its left and right neighbors is considered.\nAny value smaller than –binSize will be ignored and\nno smoothing will be applied. (default: 1.0)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scaleFactor" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "best_frag_length" ; CommandOutputBinding:outputEval "$(Number(self[0].contents.replace('\\n', '')))" ; cwl:loadContents true ] ; sld:type xsd:float . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . rdfs:comment "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-sorted" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Tool: bedtools slop (aka slopBed)\nVersion: v2.25.0\nSummary: Add requested base pairs of \"slop\" to each feature.\n\nUsage: bedtools slop [OPTIONS] -i -g [-b or (-l and -r)]\n\nOptions: \n\t-b\tIncrease the BED/GFF/VCF entry -b base pairs in each direction.\n\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct.\n\n\t-l\tThe number of base pairs to subtract from the start coordinate.\n\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct.\n\n\t-r\tThe number of base pairs to add to the end coordinate.\n\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct.\n\n\t-s\tDefine -l and -r based on strand.\n\t\tE.g. if used, -l 500 for a negative-stranded feature, \n\t\tit will add 500 bp downstream. Default = false.\n\n\t-pct\tDefine -l and -r as a fraction of the feature's length.\n\t\tE.g. if used on a 1000bp feature, -l 0.50, \n\t\twill add 500 bp \"upstream\". Default = false.\n\n\t-header\tPrint the header from the input file prior to results.\n\nNotes: \n\t(1) Starts will be set to 0 if options would force it below 0.\n\t(2) Ends will be set to the chromosome length if requested slop would\n\tforce it above the max chrom length.\n\t(3) The genome file should tab delimited and structured as follows:\n\n\t\n\n\tFor example, Human (hg19):\n\tchr1\t249250621\n\tchr2\t243199373\n\t...\n\tchr18_gl000207_random\t4262\n\nTips: \n\tOne can use the UCSC Genome Browser's MySQL database to extract\n\tchromosome sizes. For example, H. sapiens:\n\n\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\\n\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bedtools" "slop" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.i.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" . rdfs:comment "-vals input is a text file containing only the observed counts \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-V" ] ; sld:type cwl:File , sld:null . rdfs:comment "Input format autodetected" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-S" ] ; sld:type xsd:boolean . rdfs:comment "{forward,reverse}\nSelects RNA-seq reads (single-end or paired-end) in\nthe given strand. (default: None)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--filterRNAstrand" ] ; sld:type xsd:string , sld:null . rdfs:comment "Peak counts within replicate" ; 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 "--skipNonCoveredRegions, --skipNAs\nThis parameter determines if non-covered regions\n(regions without overlapping reads) in a BAM file\nshould be skipped. The default is to treat those\nregions as having a value of zero. The decision to\nskip non-covered regions depends on the interpretation\nof the data. Non-covered regions may represent, for\nexample, repetitive regions that should be skipped.\n(default: False)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--skipNonCoveredRegions" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "bedSort - Sort a .bed file by chrom,chromStart\nusage:\n bedSort in.bed out.bed\nin.bed and out.bed may be the same.\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.bed_file.path.replace(/^.*[\\\\\\/]/, '') + \"_sorted\")" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.bed_file.path.replace(/^.*[\\\\\\/]/, '') + \"_sorted\")" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.bed_file.path.replace(/^.*[\\\\\\/]/, '') + \"_sorted\")" ] ) ; cwl:baseCommand ( "bedSort" ) ; cwl:baseCommand ( "bedSort" ) ; cwl:baseCommand ( "bedSort" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dleehr/docker-hubutils" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dleehr/docker-hubutils" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dleehr/docker-hubutils" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:comment "peakshift/phantomPeak results file" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "maximum insert size for paired-end alignment (default: 250)" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-X" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "narrowPeak output file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp.narrowPeak\")" ] ; sld:type cwl:File , sld:null . rdfs:comment "Require different strandedness. That is, only report hits in B\nthat overlap A on the _opposite_ strand.\n- By default, overlaps are reported without respect to strand.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-S" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "A list of space-delimited chromosome names containing those chromosomes\nthat should be excluded for computing the normalization. This is useful\nwhen considering samples with unequal coverage across chromosomes, like\nmale samples. An usage examples is –ignoreForNormalization chrX chrM.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--ignoreForNormalization" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:comment "Filter out reads from a BED file that are too concentrated within a base-pair window." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "windowTrimmer.py" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/windowtrimmer" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.filtered.bed')" . rdfs:comment "Pvalue cutoff for peak detection. DEFAULT: not set. -q, and -p are mutually exclusive. If pvalue cutoff is set, qvalue will not be calculated and reported as -1 in the final .xls file.." ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-p" ] ; sld:type xsd:float , sld:null . cwl:valueFrom "${return 50}" . rdfs:comment "Bedfile used to only include reads overlapping this BED FILE" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.PBC.txt')" ] ; sld:type cwl:File . cwl:valueFrom "${return 200}" . a cwl:CommandLineTool ; rdfs:comment "Get number of processed reads from Bowtie log." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "percent-uniq-reads-from-preseq.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.preseq_c_curve_outfile.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.percentage_unique_reads.txt')" . rdfs:comment "Raw reads bigWig (signal) files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "RATIO When set, use a custom scaling ratio of ChIP/control\n(e.g. calculated using NCIS) for linear scaling.\nDEFAULT: ingore\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--ratio" ] ; sld:type xsd:float , sld:null . rdfs:comment "Peaks in narrowPeak file format" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "-savn= OR -savn NarrowPeak file name (fixed width peaks)" ; cwl:inputBinding [ cwl:valueFrom "${ if (self) return \"-savn=\" + inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp.narrowPeak\"; return null}" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Write the original entry in A for each overlap.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wa" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "regionPeak output file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp.regionPeak\")" ] ; sld:type cwl:File , sld:null . rdfs:comment "The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3' end, then pile them up. It's exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5'->3' direction to middle of fragment by 1/2 d, then extended to both direction with 1/2 d. This is equivalent to say each read is extended towards 5'->3' into a d size fragment. DEFAULT: 200. EXTSIZE and SHIFT can be combined when necessary. Check SHIFT option." ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--extsize" ] ; sld:type xsd:float , sld:null . rdfs:comment "Disable buffered output. Using this option will cause each line\nof output to be printed as it is generated, rather than saved\nin a buffer. This will make printing large output files\nnoticeably slower, but can be useful in conjunction with\nother software tools and scripts that need to process one\nline of bedtools output at a time.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-nobuf" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Query input FASTQ file." ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File . rdfs:comment "Write the original A entry _once_ if _any_ overlaps found in B.\n- In other words, just report the fact >=1 hit was found.\n- Overlaps restricted by -f and -r.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-u" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Hits guaranteed best stratum; ties broken by quality" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--best" ] ; sld:type xsd:boolean . rdfs:comment "Number of threads required for the 03-map step" ; sld:type xsd:int . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:default ".count" ; sld:type xsd:string . cwl:source . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:source . cwl:source . rdfs:comment "-step step size in extrapolations (default: 1e+06) \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:float , sld:null . rdfs:comment "Write \"blocked\" BED format (aka \"BED12\"). Forces -split.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bed12" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "max mismatches in seed (between [0, 3], default: 2)" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedmms" ] ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:source . rdfs:comment "\tReport the depth at each genome position (with one-based coordinates).\nDefault behavior is to report a histogram.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-d" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-d" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Bowtie first index files for reference genome (e.g. *1.ebwt). The rest of the files should be in the same folder." ; sld:type cwl:File . rdfs:comment "\tgenome_sizes is two column: .\n" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . rdfs:comment "Filtered read count reported by MACS2" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "peakshift/phantomPeak results summary file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp_cross_corr.txt\")" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Counts lines in a file and returns a suffixed file with that number" ; ns1:original_cwlVersion "v1.0" ; CommandLineTool:stdin "$(inputs.input_file.path)" ; cwl:baseCommand ( "wc" "-l" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '') + inputs.output_suffix)" . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out , , , , , , , ; cwl:run . rdfs:comment "-fdr= , false discovery rate threshold for peak calling" ; cwl:inputBinding [ CommandLineBinding:prefix "-fdr=" ; CommandLineBinding:separate false ] ; sld:type xsd:float , sld:null . cwl:source . rdfs:comment "Number of threads required for the 05-quantification step" ; sld:type xsd:int . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "Writes additional track line definition parameters in the first line.\n- Example:\n-trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\nNote the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-trackopts" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-trackopts" ] ; sld:type xsd:string , sld:null . rdfs:comment "Rdata file from the run_spp.R run" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp.Rdata\")" ] ; sld:type cwl:File , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . a cwl:Workflow ; rdfs:comment "DNase-seq 01 mapping - reads: SE" ; 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . rdfs:comment "When using multiple databases, sort the output DB hits\nfor each record.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-sortout" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Tool: bedtools genomecov (aka genomeCoverageBed)\nVersion: v2.25.0\nSummary: Compute the coverage of a feature file among a genome.\n\nUsage: bedtools genomecov [OPTIONS] -i -g \n\nOptions: \n\t-ibam\t\tThe input file is in BAM format.\n\t\t\tNote: BAM _must_ be sorted by position\n\n\t-d\t\tReport the depth at each genome position (with one-based coordinates).\n\t\t\tDefault behavior is to report a histogram.\n\n\t-dz\t\tReport the depth at each genome position (with zero-based coordinates).\n\t\t\tReports only non-zero positions.\n\t\t\tDefault behavior is to report a histogram.\n\n\t-bg\t\tReport depth in BedGraph format. For details, see:\n\t\t\tgenome.ucsc.edu/goldenPath/help/bedgraph.html\n\n\t-bga\t\tReport depth in BedGraph format, as above (-bg).\n\t\t\tHowever with this option, regions with zero \n\t\t\tcoverage are also reported. This allows one to\n\t\t\tquickly extract all regions of a genome with 0 \n\t\t\tcoverage by applying: \"grep -w 0$\" to the output.\n\n\t-split\t\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\n\t\t\twhen computing coverage.\n\t\t\tFor BAM files, this uses the CIGAR \"N\" and \"D\" operations \n\t\t\tto infer the blocks for computing coverage.\n\t\t\tFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\n\t\t\tfields (i.e., columns 10,11,12).\n\n\t-strand\t\tCalculate coverage of intervals from a specific strand.\n\t\t\tWith BED files, requires at least 6 columns (strand is column 6). \n\t\t\t- (STRING): can be + or -\n\n\t-5\t\tCalculate coverage of 5\" positions (instead of entire interval).\n\n\t-3\t\tCalculate coverage of 3\" positions (instead of entire interval).\n\n\t-max\t\tCombine all positions with a depth >= max into\n\t\t\ta single bin in the histogram. Irrelevant\n\t\t\tfor -d and -bedGraph\n\t\t\t- (INTEGER)\n\n\t-scale\t\tScale the coverage by a constant factor.\n\t\t\tEach coverage value is multiplied by this factor before being reported.\n\t\t\tUseful for normalizing coverage by, e.g., reads per million (RPM).\n\t\t\t- Default is 1.0; i.e., unscaled.\n\t\t\t- (FLOAT)\n\n\t-trackline\tAdds a UCSC/Genome-Browser track line definition in the first line of the output.\n\t\t\t- See here for more details about track line definition:\n\t\t\t http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n\t\t\t- NOTE: When adding a trackline definition, the output BedGraph can be easily\n\t\t\t uploaded to the Genome Browser as a custom track,\n\t\t\t BUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n\n\t-trackopts\tWrites additional track line definition parameters in the first line.\n\t\t\t- Example:\n\t\t\t -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\n\t\t\t Note the use of single-quotes if you have spaces in your parameters.\n\t\t\t- (TEXT)\n\nNotes: \n\t(1) The genome file should tab delimited and structured as follows:\n\t \n\n\tFor example, Human (hg19):\n\tchr1\t249250621\n\tchr2\t243199373\n\t...\n\tchr18_gl000207_random\t4262\n\n\t(2) The input BED (-i) file must be grouped by chromosome.\n\t A simple \"sort -k 1,1 > .sorted\" will suffice.\n\n\t(3) The input BAM (-ibam) file must be sorted by position.\n\t A \"samtools sort \" should suffice.\n\nTips: \n\tOne can use the UCSC Genome Browser's MySQL database to extract\n\tchromosome sizes. For example, H. sapiens:\n\n\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\\n\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "bedtools" "genomecov" ) ; cwl:baseCommand ( "bedtools" "genomecov" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" . rdfs:comment "Filter unmapped reads in aligned file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.accepted_hits.bam')" ] ; sld:type cwl:File . rdfs:comment "Filtered BAM files (post-processing end point)" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Normalized reads bigWig (signal) files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "PCR Bottleneck Coeficient files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:Workflow ; rdfs:comment "DNase-seq - map - Filter PCR Artifacts" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . a cwl:CommandLineTool ; rdfs:comment "Count number of dedup-ed reads used in peak calling" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "count-filtered-reads-macs2.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.peak_xls_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\_peaks\\.xls$/, '_read_count.txt'))" . rdfs:comment "Write the original A and B entries plus the number of base\npairs of overlap between the two features.\n- Overlapping features restricted by -f and -r.\nHowever, A features w/o overlap are also reported\nwith a NULL B feature and overlap = 0.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wao" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Number of threads used in sorting" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:in , , , , ; cwl:out , , , , , , , ; cwl:run . cwl:source . a cwl:Workflow ; rdfs:comment "DNase-seq pipeline - reads: SE" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:comment "An R,G,B string for the color used with BED12 format.\nDefault is (255,0,0).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-color" ] ; sld:type xsd:string , sld:null . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "${ if (inputs.outFileName) return inputs.outFileName; if (inputs.output_suffix) return inputs.bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix; if (inputs.outFileFormat == \"bedgraph\") return inputs.bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".bdg\"; return inputs.bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".bw\"; }" ] ; sld:type cwl:File . rdfs:comment "-x=:, strand shifts to exclude (This is mainly to avoid region around phantom peak) default=10:(readlen+10)" ; cwl:inputBinding [ CommandLineBinding:prefix "-x=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . rdfs:comment "-savd= OR -savd, save Rdata file" ; cwl:inputBinding [ cwl:valueFrom "${ if (self) return \"-savd=\" + inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp.Rdata\"; return null}" ] ; sld:type xsd:boolean , sld:null . cwl:valueFrom "${return true}" . cwl:source . cwl:valueFrom ".mapped_and_filtered.read_count.txt" . cwl:source . rdfs:comment "Write hits in SAM format (default: BAM)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--sam" ] ; sld:type xsd:boolean . cwl:in , , , , , , ; cwl:out , , ; cwl:run ; cwl:scatter ( ) . rdfs:comment "The number of base pairs to add to the end coordinate.\n- (Integer) or (Float, e.g. 0.1) if used with -pct.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-r" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:default true . rdfs:comment "INT \nInclude reads based on the SAM flag. For example, to\nget only reads that are the first mate, use a flag of\n64. This is useful to count properly paired reads only\nonce, as otherwise the second mate will be also\nconsidered for the coverage. (default: None)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--samFlagInclude" ] ; sld:type xsd:int , sld:null . rdfs:comment "Indexed BAM file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default 1 ; sld:type xsd:int . rdfs:comment "If set, reads that have the same orientation and start\nposition will be considered only once. If reads are\npaired, the mate's position also has to coincide to\nignore a read. (default: False)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--ignoreDuplicates" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "VERBOSE_LEVEL Set verbose level of runtime message. 0: only show\ncritical message, 1: show additional warning message,\n2: show process information, 3: show debug messages.\nDEFAULT:2\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--verbose" ] ; sld:type xsd:int , sld:null . cwl:valueFrom ".fragment_extended.bw" . rdfs:comment "Peak calling output file in narrowPeak|broadPeak format." ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.treatment[0].path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '_peaks.*Peak')" ; CommandOutputBinding:outputEval "$(self[0])" ] ; sld:type cwl:File . rdfs:comment "Filtered BED file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.filtered.bed')" ] ; sld:type cwl:File . rdfs:comment "\tCalculate coverage of intervals from a specific strand.\nWith BED files, requires at least 6 columns (strand is column 6).\n- (STRING): can be + or -\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-strand" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-strand" ] ; sld:type xsd:string , sld:null . rdfs:comment "-bam input is in BAM format \n" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-B" ] ; sld:type xsd:boolean . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Tool: bedtools intersect (aka intersectBed)\nVersion: v2.25.0\nSummary: Report overlaps between two feature files.\n\nUsage: bedtools intersect [OPTIONS] -a -b \n\n\tNote: -b may be followed with multiple databases and/or \n\twildcard (*) character(s). \nOptions: \n\t-wa\tWrite the original entry in A for each overlap.\n\n\t-wb\tWrite the original entry in B for each overlap.\n\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r.\n\n\t-loj\tPerform a \"left outer join\". That is, for each feature in A\n\t\treport each overlap with B. If no overlaps are found, \n\t\treport a NULL feature for B.\n\n\t-wo\tWrite the original A and B entries plus the number of base\n\t\tpairs of overlap between the two features.\n\t\t- Overlaps restricted by -f and -r.\n\t\t Only A features with overlap are reported.\n\n\t-wao\tWrite the original A and B entries plus the number of base\n\t\tpairs of overlap between the two features.\n\t\t- Overlapping features restricted by -f and -r.\n\t\t However, A features w/o overlap are also reported\n\t\t with a NULL B feature and overlap = 0.\n\n\t-u\tWrite the original A entry _once_ if _any_ overlaps found in B.\n\t\t- In other words, just report the fact >=1 hit was found.\n\t\t- Overlaps restricted by -f and -r.\n\n\t-c\tFor each entry in A, report the number of overlaps with B.\n\t\t- Reports 0 for A entries that have no overlap with B.\n\t\t- Overlaps restricted by -f and -r.\n\n\t-v\tOnly report those entries in A that have _no overlaps_ with B.\n\t\t- Similar to \"grep -v\" (an homage).\n\n\t-ubam\tWrite uncompressed BAM output. Default writes compressed BAM.\n\n\t-s\tRequire same strandedness. That is, only report hits in B\n\t\tthat overlap A on the _same_ strand.\n\t\t- By default, overlaps are reported without respect to strand.\n\n\t-S\tRequire different strandedness. That is, only report hits in B\n\t\tthat overlap A on the _opposite_ strand.\n\t\t- By default, overlaps are reported without respect to strand.\n\n\t-f\tMinimum overlap required as a fraction of A.\n\t\t- Default is 1E-9 (i.e., 1bp).\n\t\t- FLOAT (e.g. 0.50)\n\n\t-F\tMinimum overlap required as a fraction of B.\n\t\t- Default is 1E-9 (i.e., 1bp).\n\t\t- FLOAT (e.g. 0.50)\n\n\t-r\tRequire that the fraction overlap be reciprocal for A AND B.\n\t\t- In other words, if -f is 0.90 and -r is used, this requires\n\t\t that B overlap 90 percent of A and A _also_ overlaps 90 percent of B.\n\n\t-e\tRequire that the minimum fraction be satisfied for A OR B.\n\t\t- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\n\t\t that either 90 percent of A is covered OR 10 percent of B is covered.\n\t\t Without -e, both fractions would have to be satisfied.\n\n\t-split\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\n\n\t-g\tProvide a genome file to enforce consistent chromosome sort order\n\t\tacross input files. Only applies when used with -sorted option.\n\n\t-nonamecheck\tFor sorted data, don't throw an error if the file has different naming conventions\n\t\t\tfor the same chromosome. ex. \"chr1\" vs \"chr01\".\n\n\t-sorted\tUse the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n\n\t-names\tWhen using multiple databases, provide an alias for each that\n\t\twill appear instead of a fileId when also printing the DB record.\n\n\t-filenames\tWhen using multiple databases, show each complete filename\n\t\t\tinstead of a fileId when also printing the DB record.\n\n\t-sortout\tWhen using multiple databases, sort the output DB hits\n\t\t\tfor each record.\n\n\t-bed\tIf using BAM input, write output as BED.\n\n\t-header\tPrint the header from the A file prior to results.\n\n\t-nobuf\tDisable buffered output. Using this option will cause each line\n\t\tof output to be printed as it is generated, rather than saved\n\t\tin a buffer. This will make printing large output files \n\t\tnoticeably slower, but can be useful in conjunction with\n\t\tother software tools and scripts that need to process one\n\t\tline of bedtools output at a time.\n\n\t-iobuf\tSpecify amount of memory to use for input buffer.\n\t\tTakes an integer argument. Optional suffixes K/M/G supported.\n\t\tNote: currently has no effect with compressed files.\n\nNotes: \n\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,\n\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not\n\treported, as we are only testing for one or more overlaps." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bedtools" "intersect" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_basename_file + '.masked.bam')" . rdfs:comment "Perform a \"left outer join\". That is, for each feature in A\nreport each overlap with B. If no overlaps are found,\nreport a NULL feature for B.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-loj" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "\tCalculate coverage of 3\" positions (instead of entire interval).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-3" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-3" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "-s=:: , strand shifts at which cross-correlation is evaluated, default=-500:5:1500" ; cwl:inputBinding [ CommandLineBinding:prefix "-s=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Add the CIGAR string to the BED entry as a 7th column.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-cigar" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:comment "Compute PCR Bottleneck Coeficient from BedGraph file." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "awk" "$4==1 {N1 += $3 - $2}; $4>=1 {Nd += $3 - $2} END {print N1/Nd}" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:stdout "$(inputs.output_filename + '.PBC.txt')" . rdfs:comment "Minimum overlap required as a fraction of A.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; sld:type xsd:float , sld:null . cwl:source . rdfs:comment "INT \nExclude reads based on the SAM flag. For example, to\nget only reads that map to the forward strand, use\n--samFlagExclude 16, where 16 is the SAM flag for\nreads that map to the reverse strand. (default: None)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--samFlagExclude" ] ; sld:type xsd:int , sld:null . rdfs:comment "save cross-correlation plot" ; cwl:inputBinding [ cwl:valueFrom "${ if (self) return \"-savp=\" + inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp_cross_corr.pdf\"; return null}" ] ; sld:type xsd:boolean , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "\tgenome_sizes is two column: .\n" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . rdfs:comment "Normalized fragment extended reads bigWig (signal) files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in , , , , , ; cwl:out , , , ; cwl:run . rdfs:comment "Report \"split\" BAM alignments as separate BED entries.\nSplits only on N CIGAR operations.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-split" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "For sorted data, don't throw an error if the file has different naming conventions\nfor the same chromosome. ex. \"chr1\" vs \"chr01\".\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-nonamecheck" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Fragment extended reads bigWig (signal) files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "peakshift/phantomPeak results file" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "MFOLD MFOLD, --mfold MFOLD MFOLD\nSelect the regions within MFOLD range of high-\nconfidence enrichment ratio against background to\nbuild model. Fold-enrichment in regions must be lower\nthan upper limit, and higher than the lower limit. Use\nas \"-m 10 30\". DEFAULT:5 50\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-m" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.bed')" ] ; sld:type cwl:File . rdfs:comment "Bed or bedGraph file to be sorted" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" "-F" "4" "-b" "-h" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_filename + '.accepted_hits.bam')" . rdfs:comment "\tScale the coverage by a constant factor.\nEach coverage value is multiplied by this factor before being reported.\nUseful for normalizing coverage by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-scale" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-scale" ] ; sld:type xsd:float , sld:null . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Sorted aligned file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; sld:type cwl:File . rdfs:comment "--verbose \nSet to see processing messages. (default: False)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--verbose" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "While set, MACS2 will analyze number or total length of peaks that can be called by different p-value cutoff then output a summary table to help user decide a better cutoff. The table will be saved in NAME_cutoff_analysis.txt file. Note, minlen and maxgap may affect the results. WARNING: May take ~30 folds longer time to finish. DEFAULT: False Post-processing options: " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--cutoff-analysis" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Use other NUMERIC BAM alignment tag for BED score.\n- Default for BED is to use mapping quality.\nDisallowed with BEDPE output.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-tag" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Hits in sub-optimal strata aren't reported (requires --best)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--strata" ] ; sld:type xsd:boolean . cwl:source . rdfs:comment "When set, scale the small sample up to the bigger sample. By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. DEFAULT: False " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--to-large" ] ; sld:type xsd:boolean , sld:null . cwl:valueFrom "${return 30}" . rdfs:comment "Input file" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-a" ] ; sld:type cwl:File . rdfs:comment "-npeak=, threshold on number of peaks to call" ; cwl:inputBinding [ CommandLineBinding:prefix "-npeak=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . cwl:source . cwl:valueFrom ".raw.bw" . cwl:source . rdfs:comment "Read counts of the mapped BAM files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Write BEDPE format.\n- Requires BAM to be grouped or sorted by query.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bedpe" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Require that the fraction overlap be reciprocal for A AND B.\n- In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap 90 percent of A and A _also_ overlaps 90 percent of B.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-r" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Whether or not to save extended fragment pileup, and local lambda tracks (two files) at every bp into a bedGraph file. DEFAULT: True" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bdg" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bedgraph_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.bdg$/, '') + inputs.output_suffix)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 11 ; cwl:valueFrom "$(inputs.output_filename + '.sam')" ] ) ; cwl:baseCommand ( "bowtie" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bowtie" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stderr "$(inputs.output_filename + '.bowtie.log')" . rdfs:comment "\tThe input file is in BAM format.\nNote: BAM _must_ be sorted by position\n" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-ibam" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-ibam" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "\tReport the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-dz" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-dz" ] ; sld:type xsd:boolean , sld:null . cwl:valueFrom "${return 1}" . rdfs:comment "Write the original A and B entries plus the number of base\npairs of overlap between the two features.\n- Overlaps restricted by -f and -r.\nOnly A features with overlap are reported.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wo" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; sld:type cwl:File . rdfs:comment "BW Band width for picking regions to compute fragment\nsize. This value is only used while building the\nshifting model. DEFAULT: 300\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bw" ] ; sld:type xsd:int , sld:null . rdfs:comment "Bedgraph with extended fragment pileup." ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.treatment[0].path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '_treat_pileup.bdg')" ] ; sld:type cwl:File , sld:null . rdfs:comment "BED file containing the reads to be filter." ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . rdfs:comment "{bigwig,bedgraph}, -of {bigwig,bedgraph}\nOutput file type. Either \"bigwig\" or \"bedgraph\".\n(default: bigwig)\n" ; cwl:default "bigwig" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFileFormat" ] ; sld:type xsd:string . cwl:valueFrom "${return 0.10}" . cwl:default ".slop" ; sld:type xsd:string . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE}, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE} Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\" or \"BAMPE\". The default AUTO option will let MACS decide which format the file is. Note that MACS can't detect \"BAMPE\" or \"BEDPE\" format with \"AUTO\", and you have to implicitly specify the format for \"BAMPE\" and \"BEDPE\". DEFAULT: \"AUTO\"." ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; sld:type xsd:string , sld:null . rdfs:comment "INT bp\nThe smooth length defines a window, larger than the\nbinSize, to average the number of reads. For example,\nif the --binSize is set to 20 and the --smoothLength\nis set to 60, then, for each bin, the average of the\nbin and its left and right neighbors is considered.\nAny value smaller than --binSize will be ignored and\nno smoothing will be applied. (default: None)\nRead processing options:\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--smoothLength" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.peak_xls_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\_peaks\\.xls$/, '_read_count.txt'))" ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "\tCombine all positions with a depth >= max into\na single bin in the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-max" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-max" ] ; sld:type xsd:int , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:valueFrom ".fragment_extended.bw" . cwl:source . rdfs:comment "Peak counts within replicate" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "overwrite (force remove) output files in case they exist. Default: true" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:prefix "-rf" ] ; sld:type xsd:boolean . cwl:default ".clip" ; sld:type xsd:string . rdfs:comment "Read counts of the (unprocessed) input fastq files" ; 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 "Minimum overlap required as a fraction of B.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-F" ] ; sld:type xsd:float , sld:null . rdfs:comment "Peak calling report file (*_peaks.xls file produced by MACS2)" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:valueFrom "BAM" . rdfs:comment "SMALLLOCAL The small nearby region in basepairs to calculate\ndynamic lambda. This is used to capture the bias near\nthe peak summit region. Invalid if there is no control\ndata. If you set this to 0, MACS will skip slocal\nlambda calculation. *Note* that MACS will always\nperform a d-size local lambda calculation. The final\nlocal bias should be the maximum of the lambda value\nfrom d, slocal, and llocal size windows. DEFAULT: 1000\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--slocal" ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:comment "DNase-seq 03 quantification" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:CommandLineTool ; rdfs:comment "\"Tool: bedClip - Remove lines from bed file that refer to off-chromosome places.\nusage:\n bedClip input.bed chrom.sizes output.bed\nchrom.sizes is a two-column file/URL: \nIf the assembly is hosted by UCSC, chrom.sizes can be a URL like\n http://hgdownload.cse.ucsc.edu/goldenPath//bigZips/.chrom.sizes\nor you may use the script fetchChromSizes to download the chrom.sizes file.\nIf not hosted by UCSC, a chrom.sizes file can be generated by running\ntwoBitInfo on the assembly .2bit file.\noptions:\n -verbose=2 - set to get list of lines clipped and why\"\n" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 3 ; cwl:valueFrom "$(inputs.bed_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ) ; cwl:baseCommand ( "bedClip" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dleehr/docker-hubutils" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source ; cwl:valueFrom "$([self])" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bed_file.path.replace(/^.*[\\\\\\/]/, '') + \"_sorted\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bed_file.path.replace(/^.*[\\\\\\/]/, '') + \"_sorted\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bed_file.path.replace(/^.*[\\\\\\/]/, '') + \"_sorted\")" ] ; sld:type cwl:File . rdfs:comment "SPP strand cross correlation plot" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "Peak counts within replicate" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Read counts of the mapped and filtered BAM files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Peaks information/report file." ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.treatment[0].path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '_peaks.xls')" ] ; sld:type cwl:File . rdfs:comment "Suppress all alignments if > exist (def: 1)" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-m" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.i.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; sld:type cwl:File . rdfs:comment "\tCalculate coverage of 5\" positions (instead of entire interval).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-5" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-5" ] ; sld:type xsd:boolean , sld:null . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:valueFrom "${return 200}" . rdfs:comment "When using multiple databases, show each complete filename\ninstead of a fileId when also printing the DB record.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-filenames" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Tool: bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format." ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 3 ; cwl:valueFrom "$(inputs.bed_graph.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ) ; cwl:arguments ( [ CommandLineBinding:position 3 ; cwl:valueFrom "$(inputs.bed_graph.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ) ; cwl:arguments ( [ CommandLineBinding:position 3 ; cwl:valueFrom "$(inputs.bed_graph.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ) ; cwl:baseCommand ( "bedGraphToBigWig" ) ; cwl:baseCommand ( "bedGraphToBigWig" ) ; cwl:baseCommand ( "bedGraphToBigWig" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedgraphtobigwig" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedgraphtobigwig" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedgraphtobigwig" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:comment "INT\nNumber of processors to use. Type \"max/2\" to use half\nthe maximum number of processors or \"max\" to use all\navailable processors. (default: max/2)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--numberOfProcessors" ] ; sld:type xsd:int , sld:null . rdfs:comment "Normalized fragment extended reads bigWig (signal) files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "-savr= OR -savr RegionPeak file name (variable width peaks with regions of enrichment)" ; cwl:inputBinding [ cwl:valueFrom "${ if (self) return \"-savr=\" + inputs.input_bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".spp.regionPeak\"; return null}" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; sld:type cwl:File . rdfs:comment "The number of megabytes of memory a given thread is given to store path descriptors in --best mode. (Default: 256)" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--chunkmbs" ] ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:default true . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment ", full path and name (or URL) of tagAlign/BAM file (can be gzipped) (FILE EXTENSION MUST BE tagAlign.gz, tagAlign, bam or bam.gz)" ; cwl:inputBinding [ CommandLineBinding:prefix "-i=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:inputBinding [] ; sld:type cwl:File . cwl:valueFrom "${return true}" . cwl:source . rdfs:comment "If set, MACS will use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region. DEFAULT: False " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--call-summits" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "The BED file is in BED12 format. The BAM CIGAR\nstring will reflect BED \"blocks\".\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bed12" ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "SPP strand cross correlation summary" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bed_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; sld:type cwl:File . rdfs:comment "For each entry in A, report the number of overlaps with B.\n- Reports 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f and -r.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-c" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "LARGELOCAL The large nearby region in basepairs to calculate\ndynamic lambda. This is used to capture the surround\nbias. If you set this to 0, MACS will skip llocal\nlambda calculation. *Note* that MACS will always\nperform a d-size local lambda calculation. The final\nlocal bias should be the maximum of the lambda value\nfrom d, slocal, and llocal size windows. DEFAULT:\n10000.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--llocal" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type xsd:string . rdfs:comment "Percentage of uniq reads from preseq c_curve output" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Samtools Flagstat report file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; sld:type cwl:File . cwl:source . rdfs:comment "Write uncompressed BAM output. Default writes compressed BAM.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-ubam" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Tool: bedtools bedtobam (aka bedToBam)\nVersion: v2.25.0\nSummary: Converts feature records to BAM format.\n\nUsage: bedtools bedtobam [OPTIONS] -i -g \n\nOptions: \n\t-mapq\tSet the mappinq quality for the BAM records.\n\t\t(INT) Default: 255\n\n\t-bed12\tThe BED file is in BED12 format. The BAM CIGAR\n\t\tstring will reflect BED \"blocks\".\n\n\t-ubam\tWrite uncompressed BAM output. Default writes compressed BAM.\n\nNotes: \n\t(1) BED files must be at least BED4 to create BAM (needs name field)." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bedtools" "bedtobam" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.i.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.bam')" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Aligned BAM file to filter" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type cwl:File . rdfs:comment "Peaks summits bedfile." ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.treatment[0].path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '_summits.bed')" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:comment "usage: An example usage is:$ bamCoverage -b reads.bam -o coverage.bw\n\nThis tool takes an alignment of reads or fragments as input (BAM file) and\ngenerates a coverage track (bigWig or bedGraph) as output. The coverage is\ncalculated as the number of reads per bin, where bins are short consecutive\ncounting windows of a defined size. It is possible to extended the length of\nthe reads to better reflect the actual fragment length. *bamCoverage* offers\nnormalization by scaling factor, Reads Per Kilobase per Million mapped reads\n(RPKM), and 1x depth (reads per genome coverage, RPGC).\nRequired arguments:\n --bam BAM file, -b BAM file\n BAM file to process (default: None)\nOutput:\n --outFileName FILENAME, -o FILENAME\n Output file name. (default: None)\n --outFileFormat {bigwig,bedgraph}, -of {bigwig,bedgraph}\n Output file type. Either \"bigwig\" or \"bedgraph\".\n (default: bigwig)\nOptional arguments:\n --help, -h show this help message and exit\n --scaleFactor SCALEFACTOR\n The smooth length defines a window, larger than the\n binSize, to average the number of reads. For example,\n if the –binSize is set to 20 and the –smoothLength is\n set to 60, then, for each bin, the average of the bin\n and its left and right neighbors is considered.\n Any value smaller than –binSize will be ignored and\n no smoothing will be applied. (default: 1.0)\n --MNase Determine nucleosome positions from MNase-seq data.\n Only 3 nucleotides at the center of each fragment are\n counted. The fragment ends are defined by the two mate\n reads. Only fragment lengthsbetween 130 - 200 bp are\n considered to avoid dinucleosomes or other\n artifacts.*NOTE*: Requires paired-end data. A bin size\n of 1 is recommended. (default: False)\n --filterRNAstrand {forward,reverse}\n Selects RNA-seq reads (single-end or paired-end) in\n the given strand. (default: None)\n --version show program's version number and exit\n --binSize INT bp, -bs INT bp\n Size of the bins, in bases, for the output of the\n bigwig/bedgraph file. (default: 50)\n --region CHR:START:END, -r CHR:START:END\n Region of the genome to limit the operation to - this\n is useful when testing parameters to reduce the\n computing time. The format is chr:start:end, for\n example --region chr10 or --region\n chr10:456700:891000. (default: None)\n --blackListFileName BED file, -bl BED file\n A BED file containing regions that should be excluded\n from all analyses. Currently this works by rejecting\n genomic chunks that happen to overlap an entry.\n Consequently, for BAM files, if a read partially\n overlaps a blacklisted region or a fragment spans over\n it, then the read/fragment might still be considered.\n (default: None)\n --numberOfProcessors INT, -p INT\n Number of processors to use. Type \"max/2\" to use half\n the maximum number of processors or \"max\" to use all\n available processors. (default: max/2)\n --verbose, -v Set to see processing messages. (default: False)\nRead coverage normalization options:\n --normalizeTo1x EFFECTIVE GENOME SIZE LENGTH\n Report read coverage normalized to 1x sequencing depth\n (also known as Reads Per Genomic Content (RPGC)).\n Sequencing depth is defined as: (total number of\n mapped reads * fragment length) / effective genome\n size. The scaling factor used is the inverse of the\n sequencing depth computed for the sample to match the\n 1x coverage. To use this option, the effective genome\n size has to be indicated after the option. The\n effective genome size is the portion of the genome\n that is mappable. Large fractions of the genome are\n stretches of NNNN that should be discarded. Also, if\n repetitive regions were not included in the mapping of\n reads, the effective genome size needs to be adjusted\n accordingly. Common values are: mm9: 2,150,570,000;\n hg19:2,451,960,000; dm3:121,400,000 and\n ce10:93,260,000. See Table 2 of http://www.plosone.org\n /article/info:doi/10.1371/journal.pone.0030377 or http\n ://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_\n T1.html for several effective genome sizes. (default:\n None)\n--ignoreForNormalization IGNOREFORNORMALIZATION [IGNOREFORNORMALIZATION ...]\n A list of space-delimited chromosome names containing\n those chromosomes that should be excluded for\n computing the normalization. This is useful when\n considering samples with unequal coverage across\n chromosomes, like male samples. An usage examples is\n --ignoreForNormalization chrX chrM. (default: None)\n --skipNonCoveredRegions, --skipNAs\n This parameter determines if non-covered regions\n (regions without overlapping reads) in a BAM file\n should be skipped. The default is to treat those\n regions as having a value of zero. The decision to\n skip non-covered regions depends on the interpretation\n of the data. Non-covered regions may represent, for\n example, repetitive regions that should be skipped.\n (default: False)\n --smoothLength INT bp\n The smooth length defines a window, larger than the\n binSize, to average the number of reads. For example,\n if the --binSize is set to 20 and the --smoothLength\n is set to 60, then, for each bin, the average of the\n bin and its left and right neighbors is considered.\n Any value smaller than --binSize will be ignored and\n no smoothing will be applied. (default: None)\nRead processing options:\n --extendReads [INT bp], -e [INT bp]\n This parameter allows the extension of reads to\n fragment size. If set, each read is extended, without\n exception. *NOTE*: This feature is generally NOT\n recommended for spliced-read data, such as RNA-seq, as\n it would extend reads over skipped regions. *Single-\n end*: Requires a user specified value for the final\n fragment length. Reads that already exceed this\n fragment length will not be extended. *Paired-end*:\n Reads with mates are always extended to match the\n fragment size defined by the two read mates. Unmated\n reads, mate reads that map too far apart (>4x fragment\n length) or even map to different chromosomes are\n treated like single-end reads. The input of a fragment\n length value is optional. If no value is specified, it\n is estimated from the data (mean of the fragment size\n of all mate reads). (default: False)\n --ignoreDuplicates If set, reads that have the same orientation and start\n position will be considered only once. If reads are\n paired, the mate's position also has to coincide to\n ignore a read. (default: False)\n --minMappingQuality INT\n If set, only reads that have a mapping quality score\n of at least this are considered. (default: None)\n --centerReads By adding this option, reads are centered with respect\n to the fragment length. For paired-end data, the read\n is centered at the fragment length defined by the two\n ends of the fragment. For single-end data, the given\n fragment length is used. This option is useful to get\n a sharper signal around enriched regions. (default:\n False)\n --samFlagInclude INT Include reads based on the SAM flag. For example, to\n get only reads that are the first mate, use a flag of\n 64. This is useful to count properly paired reads only\n once, as otherwise the second mate will be also\n considered for the coverage. (default: None)\n --samFlagExclude INT Exclude reads based on the SAM flag. For example, to\n get only reads that map to the forward strand, use\n --samFlagExclude 16, where 16 is the SAM flag for\n reads that map to the reverse strand. (default: None)\n" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--outFileName" ; cwl:valueFrom "${ if (inputs.outFileName) return inputs.outFileName; if (inputs.output_suffix) return inputs.bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix; if (inputs.outFileFormat == \"bedgraph\") return inputs.bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".bdg\"; return inputs.bam.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, \"\") + \".bw\"; }" ] ) ; cwl:baseCommand ( "bamCoverage" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/deeptools:3.0.1" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:comment "INT bp\nSize of the bins, in bases, for the output of the\nbigwig/bedgraph file. (default: 50)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--binSize" ] ; sld:type xsd:int , sld:null . cwl:valueFrom ".read_count.in_peaks.within_reps.txt" . rdfs:comment "Preseq c_curve output files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "Genome sizes tab-delimited file (used in samtools)" ; sld:type cwl:File . cwl:source . cwl:default ".bw" ; sld:type xsd:string . rdfs:comment "-pe input is paired end read file \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-P" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . rdfs:comment "Genome sizes tab-delimited file (used in samtools)" ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Extracts best fragment length from SPP output text file" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "extract-best-frag-length.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:inputs ; cwl:outputs ; cwl:stdout "best_frag_length" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "If set, MACS will try to call broad peaks by linking nearby highly enriched regions. The linking region is controlled by another cutoff through --linking-cutoff. The maximum linking region length is 4 times of d from MACS. DEFAULT: False " ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--broad" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Number of threads used" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:source . rdfs:comment "Print wall-clock time taken by search phases" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:boolean . rdfs:comment "BAM or BAMPE for single-end and paired-end reads respectively (default: BAM)" ; cwl:default "BAM" ; sld:type xsd:string . rdfs:comment "\"First index file of Bowtie reference genome with extension 1.ebwt. \\ (Note: the rest of the index files MUST be in the same folder)\" " ; sld:type cwl:File . cwl:source . rdfs:comment "seed length for -n (default: 28)" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedlen" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Input fastq files" ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.bowtie.log')" ] ; sld:type cwl:File . rdfs:comment "Define -l and -r as a fraction of the feature's length.\nE.g. if used on a 1000bp feature, -l 0.50,\nwill add 500 bp \"upstream\". Default = false.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-pct" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Specify amount of memory to use for input buffer.\nTakes an integer argument. Optional suffixes K/M/G supported.\nNote: currently has no effect with compressed files.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-iobuf" ] ; sld:type xsd:int , sld:null . rdfs:comment "Set the mappinq quality for the BAM records.\n(INT) Default: 255\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-mapq" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.preseq_c_curve_outfile.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.percentage_unique_reads.txt')" ] ; sld:type cwl:File . rdfs:comment "KEEPDUPLICATES\nIt controls the MACS behavior towards duplicate tags\nat the exact same location -- the same coordination\nand the same strand. The 'auto' option makes MACS\ncalculate the maximum tags at the exact same location\nbased on binomal distribution using 1e-5 as pvalue\ncutoff; and the 'all' option keeps every tags. If an\ninteger is given, at most this number of tags will be\nkept at the same location. The default is to keep one\ntag at the same location. Default: 1\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--keep-dup" ] ; sld:type xsd:string , sld:null . rdfs:comment "peakshift/phantomPeak results file" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . rdfs:comment "Aligned bowtie file in [SAM|BAM] format." ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.sam')" ] ; sld:type cwl:File .