@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 ExpressionTool: . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . 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 "Output file name. If not specified, the basename of the input file with the suffix specified in the suffix argument will be used." ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "idxstats" ) ; 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:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.bam)" ] ; cwl:stdout "$(inputs.bam.basename + \".idxstats\")" . rdfs:comment "Aligned bowtie file in [SAM|BAM] format." ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.sam')" ] ; sld:type cwl:File . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Percentage of mitochondrial reads." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "-seg_len maximum segment length when merging paired end bam reads \n(default: 5000)\nHelp options:\n-?, -help print this help message\n-about print about message\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:int , sld:null . rdfs:comment "Bowtie first index files for reference genome (e.g. *1.ebwt). The rest of the files should be in the same folder." ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "trim bases from 5' (left) end of reads" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trim5" ] ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type cwl:File , xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "Print wall-clock time taken by search phases" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:boolean . cwl:source . rdfs:comment "Aligned file in BAM format" ; cwl:outputBinding [ CommandOutputBinding:glob "$(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(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; sld:type cwl:File . rdfs:comment "Number of threads used" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . rdfs:comment "Hits guaranteed best stratum; ties broken by quality" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--best" ] ; sld:type xsd:boolean . cwl:source . rdfs:comment "Filter unmapped reads in aligned file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.accepted_hits.bam')" ] ; sld:type cwl:File . cwl:source . rdfs:comment "Sorted bed or BAM file" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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 ( ) . cwl:source . rdfs:comment "Number of threads used in sorting" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . 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:source . 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 "Bowtie log file." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 "Suffix used to create the metrics output file (Default: dedup_metrics.txt)" ; cwl:default "dedup_metrics.txt" ; sld:type xsd:string . rdfs:comment "only include reads with all bits set in INT set in FLAG [0]" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; sld:type xsd:int , sld:null . sld:type xsd:string . rdfs:comment "only include reads with mapping quality >= INT [0]" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-q" ] ; sld:type xsd:int , sld:null . rdfs:comment "BAM files without duplicate reads." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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" ] ; sld:type xsd:boolean , sld:null . cwl:in , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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 cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "$(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')" . cwl:source . rdfs:comment "Number of threads used" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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:source . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" ) ; 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:inputs , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "${\n if (inputs.outfile_name) return inputs.outfile_name;\n var suffix = inputs.b ? '.bam' : '.sam';\n suffix = inputs.suffix || suffix;\n return inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + suffix\n}\n" . 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 . rdfs:comment "suffix of the transformed SAM/BAM file (including extension, e.g. .filtered.sam)" ; sld:type xsd:string , sld:null . cwl:valueFrom ".dedup.bam" . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . 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 ] . cwl:inputBinding [] ; sld:type cwl:File . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; sld:type cwl:File . cwl:source . rdfs:comment "Picard Java jar file" ; cwl:default "/usr/picard/picard.jar" ; sld:type xsd:string . rdfs:comment "Save the percentage in a file of the given name" ; sld:type xsd:string , sld:null . 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 . 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 ; 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:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "$(inputs.preseq_c_curve_outfile.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.percentage_unique_reads.txt')" . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:valueFrom "${return inputs.input_file.basename.replace('dups_marked', 'dedup')}" . 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 . rdfs:comment "Path to the picard.jar file" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-jar" ] ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:inputBinding [] ; sld:type cwl:File . cwl:source . cwl:valueFrom "bam" . rdfs:comment "only include reads with none of the bits set in INT set in FLAG [0]" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-F" ] ; sld:type xsd:int , sld:null . cwl:source . 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 . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "samtools" "sort" ) ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; 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 cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; 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:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" . rdfs:comment "PCR Bottleneck Coeficient files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:shellQuote false ] ; sld:type xsd:string , sld:null . rdfs:comment "Idxstats output file. TAB-delimited with each line consisting of reference\nsequence name, sequence length, # mapped reads and # unmapped reads\n" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename + \".idxstats\")" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . 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)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; sld:type cwl:File . 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 "If true do not write duplicates to the output file instead of writing them with appropriate flags set. (Default false)." ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$('REMOVE_DUPLICATES=' + self)" ] ; sld:type xsd:boolean . rdfs:comment "FILE only include reads overlapping this BED FILE [null]" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "-hist input is a text file containing the observed histogram \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-H" ] ; sld:type cwl:File , sld:null . rdfs:comment "\tReport the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-dz" ] ; sld:type xsd:boolean , sld:null . cwl:valueFrom ".dups_marked.bam" . cwl:valueFrom "${return 2000}" . rdfs:comment "output BAM" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-b" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "File to be converted to BAM with samtools" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; 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 ; 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.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" . cwl:source . rdfs:comment "Indexed BAM file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:valueFrom ".mapped_and_filtered.read_count.txt" . rdfs:comment "Preseq c_curve output files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:valueFrom "chrM" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Bam file (it should be indexed)" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:source . cwl:default 1 ; sld:type xsd:int . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Get number of processed reads from Bowtie log." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "read-count-from-bowtie-log.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "$(inputs.bowtie_log.path.replace(/^.*[\\\\\\/]/, '') + '.read_count.mapped')" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . rdfs:comment "Genome sizes tab-delimited file (used in samtools)" ; sld:type cwl:File . cwl:source . rdfs:comment "Include header in output" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-h" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.PBC.txt')" ] ; sld:type cwl:File . rdfs:comment "\tCalculate coverage of 5\" positions (instead of entire interval).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-5" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "If true do not write duplicates to the output file instead of writing them with appropriate flags set. (Default false)." ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "BARCODE_TAG=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . rdfs:comment "Sort by read name" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; sld:type xsd:boolean . rdfs:comment "\tReport depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bg" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "trim bases from 3' (right) end of reads" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trim3" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:valueFrom "${return 1024}" . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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 "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 "$(inputs.output_filename + '.sam')" ] ) ; cwl:baseCommand ( "bowtie" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bowtie" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$(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 . 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')" . cwl:source . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.' + inputs.metrics_suffix)" ] ; sld:type cwl:File . rdfs:comment "Hits in sub-optimal strata aren't reported (requires --best)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--strata" ] ; sld:type xsd:boolean . rdfs:comment "\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\" operations\nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-split" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Input format autodetected" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-S" ] ; sld:type xsd:boolean . rdfs:comment "Percentage of uniq reads from preseq c_curve output" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:Workflow ; rdfs:comment "ATAC-seq 03 mapping - reads: SE" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs , , , , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . rdfs:comment "-pe input is paired end read file \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-P" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.bowtie.log')" ] ; sld:type cwl:File . rdfs:comment "JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")" ; sld:type xsd:string , 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 "BAM files with marked duplicate reads." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Output filename used as basename" ; sld:type xsd:string . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-g" ] ; sld:type cwl:File . 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 ; 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 . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 3 ; cwl:valueFrom "MarkDuplicates" ] [ CommandLineBinding:position 5 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$('OUTPUT=' + inputs.output_filename + '.' + inputs.output_suffix)" ] [ CommandLineBinding:position 5 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$('METRICS_FILE='+inputs.output_filename + '.' + inputs.metrics_suffix)" ] [ CommandLineBinding:position 5 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$('TMP_DIR='+runtime.tmpdir)" ] ) ; cwl:baseCommand ( "java" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/picard" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . rdfs:comment "\tReport depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero\ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0\ncoverage by applying: \"grep -w 0$\" to the output.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bga" ] ; sld:type xsd:boolean , sld:null . 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:valueFrom "${return true}" . rdfs:comment "Samtools idxstats file" ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Usage: c_curve [OPTIONS] \n\nOptions:\n -o, -output yield output file (default: stdout) \n -s, -step step size in extrapolations (default: 1e+06) \n -v, -verbose print more information \n -P, -pe input is paired end read file \n -H, -hist input is a text file containing the observed histogram \n -V, -vals input is a text file containing only the observed counts \n -B, -bam input is in BAM format \n -l, -seg_len maximum segment length when merging paired end bam reads \n (default: 5000) \n\nHelp options:\n -?, -help print this help message \n -about print about message" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "preseq" "c_curve" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/preseq:2.0" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_file_basename + '.preseq_c_curve.txt')" . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:valueFrom "${return inputs.idxstats.basename.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '').replace(/\\.[^/.]+$/, '').replace(/\\.[^/.]+$/, '.mitochondrial_percentage.txt')}" . cwl:source . cwl:source . cwl:source . rdfs:comment "Read counts of the mapped BAM files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . 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 "$(inputs.output_filename + '.accepted_hits.bam')" . cwl:source . rdfs:comment "-verbose print more information \n" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:boolean . rdfs:comment "Number of threads used in sorting" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . rdfs:comment "Aligned BAM file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" ] ; sld:type cwl:File . rdfs:comment "Write hits in SAM format (default: BAM)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--sam" ] ; sld:type xsd:boolean . sld:type xsd:string . rdfs:comment "Input fastq files" ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "seed length for -n (default: 28)" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedlen" ] ; sld:type xsd:int , sld:null . cwl:default true . rdfs:comment "First file (extension .1.ebwt) of the Bowtie index files generated for the reference genome (see http://bowtie-bio.sourceforge.net/tutorial.shtml#newi)" ; cwl:inputBinding [ CommandLineBinding:position 9 ; cwl:valueFrom "$(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 . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var regExp = new RegExp(inputs.chrom + \"\\\\s\\\\d+\\\\s(\\\\d+)\\\\s(\\\\d+)\");\n var match = inputs.idxstats.contents.match(regExp);\n if (match){\n var chrom_mapped_reads = match[1];\n var total_reads = inputs.idxstats.contents.split(\"\\n\")\n .map(function(x){\n var rr = x.match(/.*\\s\\d+\\s(\\d+)\\s\\d+/);\n return (rr ? rr[1] : 0);\n })\n .reduce(function(a, b) { return Number(a) + Number(b); });\n\n var output = (100*chrom_mapped_reads/total_reads).toFixed(4) + \"%\" + \"\\n\";\n\n if (inputs.output_filename){\n return {\n percent_map : {\n \"class\": \"File\",\n \"basename\" : inputs.output_filename,\n \"contents\" : output,\n }\n }\n }\n return output;\n }\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:comment "Suffix used to identify the output file (Default: dedup.bam)" ; cwl:default "dedup.bam" ; sld:type xsd:string . rdfs:comment "Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\nhttp://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\nuploaded to the Genome Browser as a custom track,\nBUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-trackline" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "uncompressed BAM output (implies -b)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-u" ] ; sld:type xsd:boolean . cwl:valueFrom "${return 2}" . 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.file_path.replace(/\\.[^/.]+$/, \"\"))" ] ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.input_file.path.substr(inputs.input_file.path.lastIndexOf('/') + 1, inputs.input_file.path.lastIndexOf('.') - (inputs.input_file.path.lastIndexOf('/') + 1)))" ] ; sld:type xsd:string . rdfs:comment " number of alignment threads to launch (default: 1)" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--threads" ] ; sld:type xsd:int . rdfs:comment "Writes additional track line definition parameters in the first line.\n- Example:\n-trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\nNote the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-trackopts" ] ; sld:type xsd:string , sld:null . rdfs:comment "Picard MarkDuplicates metrics files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Query chromosome used to calculate percentage" ; sld:type xsd:string . rdfs:comment "maximum insert size for paired-end alignment (default: 250)" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-X" ] ; sld:type xsd:int , sld:null . rdfs:comment "One or more input SAM or BAM files to analyze. Must be coordinate sorted." ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$('INPUT=' + self.path)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.' + inputs.output_suffix)" ] ; sld:type cwl:File . sld:type xsd:string . rdfs:comment "suffix of the transformed SAM/BAM file (including extension, e.g. .filtered.sam)" ; cwl:default ".sorted.bam" ; sld:type xsd:string . rdfs:comment "Query input FASTQ file." ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File . sld:type xsd:string . rdfs:comment "Aligned file in SAM or BAM format" ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.outfile_name) return inputs.outfile_name;\n var suffix = inputs.b ? '.bam' : '.sam';\n suffix = inputs.suffix || suffix;\n return inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + suffix\n}\n" ] ; sld:type cwl:File .