@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: . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . 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 "Bowtie log file." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Aligned bowtie file in [SAM|BAM] format." ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.sam')" ] ; sld:type cwl:File . rdfs:comment "Read counts of the mapped BAM 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 . rdfs:comment "BED file containing the reads to be filter." ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . 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 . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . 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 "trim bases from 5' (left) end of reads" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trim5" ] ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . 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 . sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 . cwl:in , , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "Aligned file in BAM format" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bam')" ] ; sld:type cwl:File . rdfs:comment "Samtools Flagstat report file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; sld:type cwl:File . rdfs:comment "Hits guaranteed best stratum; ties broken by quality" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--best" ] ; sld:type xsd:boolean . rdfs:comment "Number of threads used" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . rdfs:comment "Filter unmapped reads in aligned file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.accepted_hits.bam')" ] ; sld:type cwl:File . 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 "Sorted bed or BAM file" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . rdfs:comment "Genome chromosome sizes file" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-g" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_basename + '.read_count.txt')" ] ; sld:type cwl:File . rdfs:comment "Number of threads used in sorting" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-sorted" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bowtie_log.path.replace(/^.*[\\\\\\/]/, '') + '.read_count.mapped')" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "\tThe input file is in BAM format.\nNote: BAM _must_ be sorted by position\n" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-ibam" ] ; 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 . 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 . sld:type xsd:string . 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 . rdfs:comment "Filtered BED file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.filtered.bed')" ] ; sld:type cwl:File . 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 . sld:type xsd:string . 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" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Extract mapped reads from BAM file using Samtools flagstat command" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 10000 ; CommandLineBinding:shellQuote false ; cwl:valueFrom " | head -n1 | cut -f 1 -d ' '" ] ) ; cwl:baseCommand ( "samtools" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_basename + '.preseq_c_curve.txt')" ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" "-b" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bam')" . 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:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "BAM files without PCR artifact reads." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 . 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 "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; sld:type cwl:File . cwl:default true . rdfs:comment "\tCalculate coverage of 3\" positions (instead of entire interval).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-3" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . a cwl:Workflow ; rdfs:comment "ChIP-seq - map - PCR Bottleneck Coefficients" ; 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:inputBinding [] ; sld:type cwl:File . 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 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.bed')" ] ; sld:type cwl:File . rdfs:comment "Write the original A and B entries plus the number of base\npairs of overlap between the two features.\n- Overlaps restricted by -f and -r.\nOnly A features with overlap are reported.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wo" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Get number of processed reads from Bowtie log." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "percent-uniq-reads-from-preseq.sh" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.preseq_c_curve_outfile.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.percentage_unique_reads.txt')" . 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 . sld:type xsd:string . cwl:source . 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 . 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 "\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" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [] ; sld:type cwl:File . 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 ; 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 ; 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: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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" . cwl:valueFrom ".mapped_and_filtered.read_count.txt" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.i.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.bam')" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:Workflow ; rdfs:comment "DNase-seq - map - Filter PCR Artifacts" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:source . rdfs:comment "When using multiple databases, show each complete filename\ninstead of a fileId when also printing the DB record.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-filenames" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Sorted aligned file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(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(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Basename for the output file" ; sld:type xsd:string . rdfs:comment "Report end-to-end hits w/ <=v mismatches; ignore qualities" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:int , sld:null . rdfs:comment "For sorted data, don't throw an error if the file has different naming conventions\nfor the same chromosome. ex. \"chr1\" vs \"chr01\".\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-nonamecheck" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Genome sizes tab-delimited file (used in samtools)" ; sld:type cwl:File . rdfs:comment "-hist input is a text file containing the observed histogram \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-H" ] ; sld:type cwl:File , sld:null . cwl:valueFrom "${return 30}" . 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" ] ; sld:type xsd:boolean , sld:null . 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 . 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 . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "File to be converted to BAM with samtools" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . rdfs:comment "Input file to be converted to BAM format" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . 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 "v1.0" ; cwl:baseCommand ( "bedtools" "genomecov" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" . a cwl:CommandLineTool ; rdfs:comment "Tool: bedtools bedtobam (aka bedToBam)\nVersion: v2.25.0\nSummary: Converts feature records to BAM format.\n\nUsage: bedtools bedtobam [OPTIONS] -i -g \n\nOptions: \n\t-mapq\tSet the mappinq quality for the BAM records.\n\t\t(INT) Default: 255\n\n\t-bed12\tThe BED file is in BED12 format. The BAM CIGAR\n\t\tstring will reflect BED \"blocks\".\n\n\t-ubam\tWrite uncompressed BAM output. Default writes compressed BAM.\n\nNotes: \n\t(1) BED files must be at least BED4 to create BAM (needs name field)." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bedtools" "bedtobam" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.i.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.bam')" . rdfs:comment "Use BAM edit distance (NM tag) for BED score.\n- Default for BED is to use mapping quality.\n- Default for BEDPE is to use the minimum of\nthe two mapping qualities for the pair.\n- When -ed is used with -bedpe, the total edit\ndistance from the two mates is reported.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-ed" ] ; sld:type xsd:boolean , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Filter out reads from a BED file that are too concentrated within a base-pair window." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "windowTrimmer.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/windowtrimmer" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.filtered.bed')" . rdfs:comment "When using multiple databases, sort the output DB hits\nfor each record.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-sortout" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Indexed BAM file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Preseq c_curve output files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] . 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 . 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 "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 . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Bedfile containing ENCODE consensus blacklist regions to be excluded." ; sld:type cwl:File . rdfs:comment "Percentage of uniq reads from preseq c_curve output" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "$(inputs.bowtie_log.path.replace(/^.*[\\\\\\/]/, '') + '.read_count.mapped')" . cwl:source . rdfs:comment "Disable buffered output. Using this option will cause each line\nof output to be printed as it is generated, rather than saved\nin a buffer. This will make printing large output files\nnoticeably slower, but can be useful in conjunction with\nother software tools and scripts that need to process one\nline of bedtools output at a time.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-nobuf" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.PBC.txt')" ] ; sld:type cwl:File . rdfs:comment "\tCalculate coverage of 5\" positions (instead of entire interval).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-5" ] ; sld:type xsd:boolean , sld:null . cwl:source . 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:source . 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 . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bedtools" "bamtobed" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.bam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.bed')" . 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" ] ; sld:type xsd:boolean , 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 . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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 "trim bases from 3' (right) end of reads" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trim3" ] ; sld:type xsd:int , sld:null . rdfs:comment "Read counts of the mapped and filtered BAM files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . 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" ] ; sld:type xsd:string , sld:null . 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 . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:valueFrom "${return 1}" . rdfs:comment "max mismatches in seed (between [0, 3], default: 2)" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedmms" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 11 ; cwl:valueFrom "$(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:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$(inputs.output_filename + '.bowtie.log')" . rdfs:comment "Input format autodetected" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-S" ] ; sld:type xsd:boolean . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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 - $2} END {print N1/Nd}" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:stdout "$(inputs.output_filename + '.PBC.txt')" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 . 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" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . 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 . rdfs:comment "Input fastq files" ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "-pe input is paired end read file \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-P" ] ; sld:type xsd:boolean , sld:null . 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 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.bowtie.log')" ] ; sld:type cwl:File . rdfs:comment "Write the original entry in A for each overlap.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wa" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "\tScale the coverage by a constant factor.\nEach coverage value is multiplied by this factor before being reported.\nUseful for normalizing coverage by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-scale" ] ; sld:type xsd:float , sld:null . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-g" ] ; sld:type cwl:File . rdfs:comment "CUTOFF\n threshold for concentration at a single base\n within a window to cutoff\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-c" ] ; sld:type xsd:float , sld:null . cwl:source . rdfs:comment "\tReport depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero\ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0\ncoverage by applying: \"grep -w 0$\" to the output.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bga" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Suppress all alignments if > exist (def: 1)" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-m" ] ; sld:type xsd:int . rdfs:comment "Read counts of the (unprocessed) input fastq files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_basename_file + '.masked.bam')" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Usage: c_curve [OPTIONS] \n\nOptions:\n -o, -output yield output file (default: stdout) \n -s, -step step size in extrapolations (default: 1e+06) \n -v, -verbose print more information \n -P, -pe input is paired end read file \n -H, -hist input is a text file containing the observed histogram \n -V, -vals input is a text file containing only the observed counts \n -B, -bam input is in BAM format \n -l, -seg_len maximum segment length when merging paired end bam reads \n (default: 5000) \n\nHelp options:\n -?, -help print this help message \n -about print about message" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "preseq" "c_curve" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/preseq:2.0" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_file_basename + '.preseq_c_curve.txt')" . cwl:source . cwl:source . 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 . cwl:source . cwl:in , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . 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 "Input file" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-a" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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 01 mapping - 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" "-F" "4" "-b" "-h" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_filename + '.accepted_hits.bam')" . rdfs:comment "Specify amount of memory to use for input buffer.\nTakes an integer argument. Optional suffixes K/M/G supported.\nNote: currently has no effect with compressed files.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-iobuf" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:in , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "-verbose print more information \n" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:boolean . rdfs:comment "Write uncompressed BAM output. Default writes compressed BAM.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-ubam" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Number of threads used in sorting" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . rdfs:comment "Aligned BAM file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" ] ; sld:type cwl:File . rdfs:comment "Minimum overlap required as a fraction of B.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-F" ] ; sld:type xsd:float , sld:null . rdfs:comment "Write hits in SAM format (default: BAM)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--sam" ] ; sld:type xsd:boolean . sld:type xsd:string . cwl:valueFrom "${return 20}" . rdfs:comment "seed length for -n (default: 28)" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedlen" ] ; sld:type xsd:int , sld:null . cwl:default true . 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 "$(self.path.split('.').splice(0,self.path.split('.').length-2).join(\".\"))" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.preseq_c_curve_outfile.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.percentage_unique_reads.txt')" ] ; sld:type cwl:File . 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 . 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 "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 "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 . 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" ] ; sld:type xsd:boolean , sld:null . 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 cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . 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 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:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_basename + '.read_count.txt')" . 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 " 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 "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" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; 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 "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 . sld:type xsd:string . cwl:default 1 ; sld:type xsd:int . rdfs:comment "suffix of the transformed SAM/BAM file (including extension, e.g. .filtered.sam)" ; cwl:default ".sorted.bam" ; sld:type xsd:string . 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 . rdfs:comment "Query input FASTQ file." ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-b" ] ; sld:type cwl:File . 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 .