@prefix LoadListingRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix InlineJavascriptRequirement: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns2: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix cwl: . rdfs:comment "All\nstring: which reads to consider for collapsed splice junctions output\nAll: all reads, unique- and multi-mappers\nUnique: uniquely mapping reads only\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterReads" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterReads" ] ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Generated bigWig file for the second strain, projected to reference genome" ; rdfs:label "II strain bigWig file" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "If true - run samtools, if false - return sort_input, previously staged into output directory\n" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${ return self ? \"true\" : \"false\" }\n" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Bash function to run samtools index with all input parameters or skip it if trigger is false\n" ; cwl:default "#!/bin/bash\nif [ \"$0\" = \"true\" ]\nthen\n echo \"Run: samtools index \" ${@:1}\n samtools index \"${@:1}\"\nelse\n echo \"Skip samtools index \" ${@:1}\nfi\n" ; cwl:inputBinding [ CommandLineBinding:position 20 ] ; cwl:inputBinding [ CommandLineBinding:position 20 ] ; sld:type xsd:string , sld:null . rdfs:comment "int: =log2(chrBin), where chrBin is the size of the bins for genome\nstorage: each chromosome will occupy an integer number of bins\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeChrBinNbits" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeChrBinNbits" ] ; sld:type xsd:int , sld:null . rdfs:comment "-2\ndeletion open penalty\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreDelOpen" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreDelOpen" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "9\nint>0: max number of bins between two anchors that allows aggregation of anchors\ninto one window\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winAnchorDistNbins" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winAnchorDistNbins" ] ; sld:type xsd:int , sld:null . a ns1:ScholarlyArticle ; ns1:name "(Li, 2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics." ; ns1:url "http://www.ncbi.nlm.nih.gov/pubmed/21903627" . rdfs:comment "float: alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMismatchNoverLmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMismatchNoverLmax" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*Aligned.out*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*Aligned.out*" ] ; sld:type cwl:File . cwl:source . rdfs:comment "Calculate genome coverage of intervals from a specific strand" ; rdfs:label "Enable strand specific genome coverage calculation" ; sld:type xsd:string , sld:null . rdfs:comment "1\nfloat: alignment will be output only if its ratio of mismatches to *read* length\nis less than this value\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMismatchNoverReadLmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMismatchNoverReadLmax" ] ; sld:type xsd:float , sld:null . rdfs:comment "Calculate 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 9 ; CommandLineBinding:prefix "-strand" ] ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "-strand" ] ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "-strand" ] ; sld:type xsd:string , sld:null . rdfs:comment "Write the final sorted output to FILE. Only out.bam|out.cram.\nIf output file extension is set to SAM, tool will fail on the index step\n" ; cwl:default "" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "-o" ; cwl:valueFrom "${\n if (self == \"\" || inputs.trigger == false){\n return default_bam();\n } else {\n return self;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "-o" ; cwl:valueFrom "${\n if (self == \"\" || inputs.trigger == false){\n return default_bam();\n } else {\n return self;\n }\n}\n" ] ; sld:type xsd:string , sld:null . rdfs:comment "If set, writes the output bigWig file to output_filename,\notherwise generates filename from default_output_filename()\n" ; cwl:default "" ; cwl:inputBinding [ CommandLineBinding:position 12 ; cwl:valueFrom "${\n if (self == \"\"){\n return default_output_filename();\n } else {\n return self;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 12 ; cwl:valueFrom "${\n if (self == \"\"){\n return default_output_filename();\n } else {\n return self;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 12 ; cwl:valueFrom "${\n if (self == \"\"){\n return default_output_filename();\n } else {\n return self;\n }\n}\n" ] ; sld:type xsd:string , sld:null . rdfs:comment "0\nint>=0: minimum total (summed) score of the chimeric segments\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimScoreMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimScoreMin" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == \"\"){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == \"\"){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == \"\"){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; sld:type cwl:File . rdfs:comment "int: maximum number of loci the read is allowed to map to. Alignments (all of them) will be output only if\nthe read maps to no more loci than this value.\nOtherwise no alignments will be output, and the read will be counted as \"mapped to too many loci\"\nin the Log.final.out.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMultimapNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMultimapNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "20\nint>=0: max drop (difference) of chimeric score (the sum of scores of all chimeric\nsegements) from the read length\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimScoreDropMax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimScoreDropMax" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "0.66\nfloat>0: alignSplicedMateMapLmin normalized to mate length\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSplicedMateMapLminOverLmate" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSplicedMateMapLminOverLmate" ] ; sld:type xsd:float , sld:null . rdfs:comment "Set minimum interval size for CSI indices to 2^INT [14]\n" ; cwl:inputBinding [ CommandLineBinding:position 24 ; CommandLineBinding:prefix "-m" ] ; cwl:inputBinding [ CommandLineBinding:position 24 ; CommandLineBinding:prefix "-m" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*Log.final.out*" ; CommandOutputBinding:outputEval "${\n let uniquelyMappedReadsNumberRegex = /Uniquely mapped reads number.*/;\n return parseInt(self[0].contents.match(uniquelyMappedReadsNumberRegex)[0].split(/\\|\\t/g)[1]);\n}\n" ; cwl:loadContents true ] ; cwl:outputBinding [ CommandOutputBinding:glob "*Log.final.out*" ; CommandOutputBinding:outputEval "${\n let uniquelyMappedReadsNumberRegex = /Uniquely mapped reads number.*/;\n return parseInt(self[0].contents.match(uniquelyMappedReadsNumberRegex)[0].split(/\\|\\t/g)[1]);\n}\n" ; cwl:loadContents true ] ; sld:type xsd:int , sld:null . rdfs:comment "bam\t convert alignment file in BAM format.\nbed\t convert genome cooridnate or annotation file in BED or BED-like format.\nbigwig\tconvert genome coordinate file in BigWig format.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . rdfs:comment "IndelSoftclipSingleend\nstring: prohibit various alignment type\nIndelSoftclipSingleend ... prohibit indels, soft clipping and single-end alignments - compatible with RSEM\nSingleend ... prohibit single-end alignments\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--quantTranscriptomeBan" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--quantTranscriptomeBan" ] ; sld:type xsd:string , sld:null . rdfs:comment "Set fixed fragment size\n" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "-fs" ] ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "-fs" ] ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "-fs" ] ; sld:type xsd:int , sld:null . rdfs:comment "User_RWX\nstring: permissions for the directories created at the run-time.\nUser_RWX ... user-read/write/execute\nAll_RWX ... all-read/write/execute (same as chmod 777)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--runDirPerm" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--runDirPerm" ] ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "string: mark duplicates in the BAM file, for now only works with (i) sorted BAM feeded with inputBAMfile, and (ii) for paired-end alignments only\n- ... no duplicate removal/marking\nUniqueIdentical ... mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical\nUniqueIdenticalNotMulti ... mark duplicate unique mappers but not multimappers.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bamRemoveDuplicatesType" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bamRemoveDuplicatesType" ] ; sld:type xsd:string , sld:null . rdfs:comment "float>=0: minimum relative coverage of the read sequence by the seeds in a window, for STARlong algorithm only.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winReadCoverageRelativeMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winReadCoverageRelativeMin" ] ; sld:type xsd:float , sld:null . cwl:in , , , ; cwl:out , , , , , ; cwl:run . rdfs:comment "Coordinate sorted BAM file mapped to the second strain genome, projected to reference genome" ; rdfs:label "II strain output BAM" ; cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.sort_output_filename == \"\" || inputs.trigger == false){\n return default_output_name();\n } else {\n return inputs.sort_output_filename;\n }\n}\n" ] ; sld:type cwl:File . a ns1:ScholarlyArticle ; ns1:author [ a ns1:Person ; ns1:name "Ira M. Hall" ] ; ns1:author [ a ns1:Person ; ns1:name "Aaron R. Quinlan" ] ; ns1:author [ a ns1:Person ; ns1:name "Ira M. Hall" ] ; ns1:author [ a ns1:Person ; ns1:name "Aaron R. Quinlan" ] ; ns1:author [ a ns1:Person ; ns1:name "Aaron R. Quinlan" ] ; ns1:author [ a ns1:Person ; ns1:name "Ira M. Hall" ] ; ns1:name "BEDTools: a flexible suite of utilities for comparing genomic features" ; ns1:url "https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btq033" . rdfs:comment "1\nint>=0: start value for the IH attribute. 0 may be required\nby some downstream software, such as Cufflinks or StringTie.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMattrIHstart" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMattrIHstart" ] ; sld:type xsd:int , sld:null . cwl:in , , , , , ; cwl:out , , , , , ; cwl:run . rdfs:comment "string(s): paths to files that contain input read1 (and, if needed, read2)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readFilesIn" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readFilesIn" ] ; sld:type cwl:File ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "50\nint>0: defines the search start point through the read - the read is split into\npieces no longer than this value\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedSearchStartLmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedSearchStartLmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "Bash function to run samtools sort with all input parameters or skip it if trigger is false\n" ; cwl:default "#!/bin/bash\nif [ \"$0\" = \"true\" ]\nthen\n echo \"Run: samtools sort \" ${@:1}\n samtools sort \"${@:1}\"\nelse\n echo \"Skip samtools sort \" ${@:1}\nfi\n" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string , sld:null . rdfs:comment "Input BAM file, sorted by coordinates" ; rdfs:label "Input BAM file" ; sld:type cwl:File . cwl:source . rdfs:comment "string: prefix for chromosome names in a GTF file (e.g. 'chr' for using\nENSMEBL annotations with UCSC geneomes)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFchrPrefix" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFchrPrefix" ] ; sld:type xsd:string , sld:null . cwl:default "cat \"$0\" | grep \"$1\" | sed \"s/$1/chr/g\" > `basename $0`" . rdfs:comment "Generate BAI-format index for BAM files [default]. If input isn't cram.\n" ; sld:type xsd:boolean , sld:null . rdfs:comment "-0.25\nextra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGenomicLengthLog2scale" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGenomicLengthLog2scale" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Chain file to project strain I to reference genome" ; rdfs:label "I strain chain file" ; sld:type cwl:File . rdfs:comment "10000\nint>0: only pieces that map fewer than this value are utilized in the stitching\nprocedure\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedMultimapNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedMultimapNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "string(s): output of unmapped reads in the SAM format\n 1st word:\n None ... no output\n Within ... output unmapped reads within the main SAM file (i.e. Aligned.out.sam)\n 2nd word:\n KeepPairs ... record unmapped mate for each alignment, and, in case of unsorted output, keep it adjacent to its mapped mate.\n Only affects multi-mapping reads\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMunmapped" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMunmapped" ] ; sld:type xsd:string , sld:null . rdfs:comment "1000\nint>0: max number of junctions for one read (including all multi-mappers)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitOutSJoneRead" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitOutSJoneRead" ] ; sld:type xsd:int , sld:null . rdfs:comment "10000\nint>0: max number of windows per read\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignWindowsPerReadNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignWindowsPerReadNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "Path to STAR generated indices folder for reference genome" ; rdfs:label "STAR indices folder for reference genome" ; sld:type cwl:Directory . rdfs:comment "Coordinate sorted BAM file mapped to reference genome" ; rdfs:label "Reference output BAM" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "string(s): command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout\nFor example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readFilesCommand" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readFilesCommand" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . rdfs:comment "Coefficient to scale the genome coverage by a constant factor" ; rdfs:label "Genome coverage scaling coefficient" ; sld:type xsd:float , sld:null . rdfs:comment "int>0: number of bases from the 5' of mate 2 to use in collapsing (e.g. for\nRAMPAGE)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bamRemoveDuplicatesMate2basesN" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bamRemoveDuplicatesMate2basesN" ] ; sld:type xsd:int , sld:null . rdfs:comment "Optional parameter to calculate scale as 1000000/mapped_reads_number if inputs.scale is not provided\n" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-scale" ; cwl:valueFrom "${\n if (inputs.scale){\n return null;\n } else if (inputs.mapped_reads_number) {\n return 1000000/inputs.mapped_reads_number;\n } else {\n return null;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-scale" ; cwl:valueFrom "${\n if (inputs.scale){\n return null;\n } else if (inputs.mapped_reads_number) {\n return 1000000/inputs.mapped_reads_number;\n } else {\n return null;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-scale" ; cwl:valueFrom "${\n if (inputs.scale){\n return null;\n } else if (inputs.mapped_reads_number) {\n return 1000000/inputs.mapped_reads_number;\n } else {\n return null;\n }\n}\n" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:comment "Tool calculates genome coverage from input bam/bed/gff/vcf using `bedtools genomecov`\n\nDepending on `input_file` extension additional prefix is used: if `*.bam` use `-ibam`, else use `-i`.\n\n`scale` and `mapped_reads_number` inputs result in the same parameter `-scale`. If `scale` is not provided, check if\n`mapped_reads_number` is not null and calculate `-scale` as `1000000/mapped_reads_number`. If both inputs are\nnull, `bedtools genomecov` will use its default scaling value.\n\n`default_output_filename` function returns default output filename and is used when `output_filename` is not provided.\nDefault output file extention is `.tab`. If bedGraph should be generated (check flags `inputs.depth`), extension is\nupdated to `.bedGraph`. Default basename of the output file is generated on the base of `input_file` basename.\n" ; ns2:original_cwlVersion "v1.2" ; ns1:about "Usage: 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-pc\t\tCalculate coverage of pair-end fragments.\n\t\t\tWorks for BAM files only\n\t-fs\t\tForce to use provided fragment size instead of read length\n\t\t\tWorks for BAM files only\n\t-du\t\tChange strand af the mate read (so both reads from the same strand) useful for strand specific\n\t\t\tWorks for BAM files only\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\n" ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/bedtools-genomecov.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:mainEntity ; ns1:name "bedtools-genomecov" ; cwl:baseCommand ( "bedtools" "genomecov" ) ; cwl:baseCommand ( "bedtools" "genomecov" ) ; cwl:baseCommand ( "bedtools" "genomecov" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/bedtools2:v2.26.0" ] ; 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 "biowardrobe2/bedtools2:v2.26.0" ] ; 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 "biowardrobe2/bedtools2:v2.26.0" ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { let ext = (inputs.depth == \"-bg\" || inputs.depth == \"-bga\")?\".bedGraph\":\".tab\"; return inputs.input_file.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.') + ext; };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { let ext = (inputs.depth == \"-bg\" || inputs.depth == \"-bga\")?\".bedGraph\":\".tab\"; return inputs.input_file.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.') + ext; };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { let ext = (inputs.depth == \"-bg\" || inputs.depth == \"-bga\")?\".bedGraph\":\".tab\"; return inputs.input_file.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.') + ext; };" ] ; cwl:stdout "${\n if (inputs.output_filename == null){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" . rdfs:comment "-k, --key=POS1[,POS2]\nstart a key at POS1, end it at POS2 (origin 1)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:default "cat \"$0\" | grep \"$1\" | sed \"s/$1/chr/g\" > `basename $0`" . rdfs:comment "16\nint>0: =log2(winBin), where winBin is the size of the bin for the windows/clustering,\neach window will occupy an integer number of bins.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winBinNbits" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winBinNbits" ] ; sld:type xsd:int , sld:null . rdfs:comment "Stranded\nstring: strandedness of wiggle/bedGraph output\nStranded ... separate strands, str1 and str2\nUnstranded ... collapsed strands\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outWigStrand" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outWigStrand" ] ; sld:type xsd:string , sld:null . cwl:default "1,1" , "2,2n" . cwl:outputBinding [ CommandOutputBinding:glob "*Unmapped.out.mate1*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*Unmapped.out.mate1*" ] ; sld:type cwl:File , sld:null . rdfs:comment "-\nstrings: extra @PG (software) line of the SAM header (in addition to STAR)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMheaderPG" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMheaderPG" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "-2\ndeletion extension penalty per base (in addition to scoreDelOpen)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreDelBase" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreDelBase" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Normal\nstring: type of filtering\nNormal ... standard filtering using only current alignment\nBySJout ... keep only those reads that contain junctions that passed filtering into SJ.out.tab\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterType" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterType" ] ; sld:type xsd:string , sld:null . a ns1:SoftwareSourceCode ; ns1:about "Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.\nSTAR has a potential for accurately aligning long (several kilobases) reads that\nare emerging from the third-generation sequencing technologies\n" ; ns1:codeRepository "https://github.com/alexdobin/STAR" ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "main author" ; ns1:name "Alexander Dobin" ] ; ns1:name "Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "main author" ; ns1:name "Alexander Dobin" ] ; ns1:name "Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA" ] ; ns1:discussionUrl "https://github.com/alexdobin/STAR/issues" ; ns1:license "https://opensource.org/licenses/GPL-3.0" ; ns1:name "STAR" ; ns1:programmingLanguage "C++" ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "command line tool" ; ns1:softwareVersion "v2.5.3a" ] ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "command line tool" ; ns1:softwareVersion "v2.5.3a" ] ; ns1:url "https://github.com/alexdobin/STAR" . rdfs:comment "Bash function to run samtools sort with all input parameters or skip it if trigger is false\n" ; cwl:default "#!/bin/bash\nif [ \"$0\" = \"true\" ]\nthen\n samtools sort \"${@:1}\"\nelse\n echo \"Skip samtools sort \" ${@:1}\nfi\n" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string , sld:null . rdfs:comment "banGenomicN\nstring(s): different filters for chimeric alignments\nNone ... no filtering\nbanGenomicN ... Ns are not allowed in the genome sequence around the chimeric junction\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimFilter" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimFilter" ] ; sld:type xsd:string , sld:null . rdfs:comment "int>0: suffux array sparsity, i.e. distance between indices: use bigger\nnumbers to decrease needed RAM at the cost of mapping speed reduction\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeSAsparseD" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeSAsparseD" ] ; sld:type xsd:int , sld:null . rdfs:comment "Chain file\n" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source , ; cwl:valueFrom "${\n return (Array.isArray(self[0]) && self[0].length>1)?2*self[1]:self[1];\n}\n" . cwl:outputBinding [ CommandOutputBinding:glob "*Unmapped.out.mate2*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*Unmapped.out.mate2*" ] ; sld:type cwl:File , sld:null . rdfs:comment "0\nint: alignment will be output only if the number of matched bases is higher\nthan this value\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMatchNmin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMatchNmin" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:comment "Runs CrossMap.py script to project input BAM, BED, BIGWIG file based on input chain file.\nNot supported input file types: SAM, GFF, VCF, WIG\n\nIf `output_basename` is not set, call get_output_filename() and get_log_filename() functions to\nget default output and log filenames. Input `output_basename` should not include extension.\n" ; ns2:original_cwlVersion "v1.2" ; ns1:about "Description:\n CrossMap is a program for convenient conversion of genome coordinates and\n genomeannotation files between assemblies (eg. lift from human hg18 to hg19 or\n vice versa).It supports file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF and VCF\n format.\n\nUsage: CrossMap.py [options]\n\n bam\tconvert alignment file in BAM or SAM format.\n bed\tconvert genome cooridnate or annotation file in BED or BED-like format.\n bigwig\tconvert genome coordinate file in BigWig format.\n gff\tconvert genome cooridnate or annotation file in GFF or GTF format.\n vcf\tconvert genome coordinate file in VCF format.\n wig\tconvert genome coordinate file in Wiggle, or bedGraph format.\n\nUsage: CrossMap.py bam input_chain_file input_bam_file output_file [options]\nNote: If output_file == STDOUT or -, CrossMap will write BAM file to the screen\n\nOptions:\n -m INSERT_SIZE, --mean=INSERT_SIZE\n Average insert size of pair-end sequencing (bp).\n [default=200.0]\n -s INSERT_SIZE_STDEV, --stdev=INSERT_SIZE_STDEV\n Stanadard deviation of insert size. [default=30.0]\n -t INSERT_SIZE_FOLD, --times=INSERT_SIZE_FOLD\n A mapped pair is considered as \"proper pair\" if both\n ends mapped to different strand and the distance\n between them is less then '-t' * stdev from the mean.\n [default=3.0]\n -a, --append-tags Add tag to each alignment.\n" ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/crossmap.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:mainEntity ; ns1:name "crossmap" ; cwl:baseCommand ( "CrossMap.py" ) ; cwl:baseCommand ( "CrossMap.py" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/crossmap:0.2.7--py27_0" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/crossmap:0.2.7--py27_0" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var get_log_filename = function() { var ext = \".log\"; if (inputs.output_basename == \"\"){ let root = inputs.input_file.basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.input_file.basename+ext:root+ext; } else { return inputs.output_basename+ext; } };" , "var get_output_filename = function(ext) { var alt_ext = \"\"; if (inputs.input_file_type == \"bam\") { alt_ext = \".sorted.bam\"; } else if (inputs.input_file_type == \"bigwig\") { alt_ext = \".bw\"; } else if (inputs.input_file_type == \"bed\") { ext = \".bedGraph\"; } else { alt_ext = \"\"; } ext = (ext || ext==\"\")?ext:alt_ext; if (inputs.output_basename == \"\"){ let root = inputs.input_file.basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.input_file.basename+ext:root+ext; } else { return inputs.output_basename+ext; } };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var get_log_filename = function() { var ext = \".log\"; if (inputs.output_basename == \"\"){ let root = inputs.input_file.basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.input_file.basename+ext:root+ext; } else { return inputs.output_basename+ext; } };" , "var get_output_filename = function(ext) { var alt_ext = \"\"; if (inputs.input_file_type == \"bam\") { alt_ext = \".sorted.bam\"; } else if (inputs.input_file_type == \"bigwig\") { alt_ext = \".bw\"; } else if (inputs.input_file_type == \"bed\") { ext = \".bedGraph\"; } else { alt_ext = \"\"; } ext = (ext || ext==\"\")?ext:alt_ext; if (inputs.output_basename == \"\"){ let root = inputs.input_file.basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.input_file.basename+ext:root+ext; } else { return inputs.output_basename+ext; } };" ] ; cwl:stdout "$(get_log_filename())" . rdfs:comment "0\nint: splice junction penalty (independent on intron motif)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGap" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGap" ] ; sld:type xsd:int , sld:null . rdfs:comment "STAR Log.std.out for reference genome" ; rdfs:label "STAR stdout log for reference genome" ; cwl:outputSource ; sld:type cwl:File , sld:null . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "-4\nGC/AG and CT/GC junction penalty (in addition to scoreGap)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGapGCAG" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGapGCAG" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "0\nint>=0: defines the maximum length of the seeds, if =0 max seed lengthis infinite\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedSearchLmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedSearchLmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "int: add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outQSconversionAdd" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outQSconversionAdd" ] ; sld:type xsd:int , sld:null . rdfs:comment "0\nint>=0: maximum gap in the read sequence between chimeric segments\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimSegmentReadGapMax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimSegmentReadGapMax" ] ; sld:type xsd:int , sld:null . rdfs:comment "string: path to the GTF file with annotations\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFfile" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFfile" ] ; sld:type cwl:File , sld:null . rdfs:comment "double(s): max proportion of mismatches for 3p adpater clipping for each\nmate. If one value is given, it will be assumed the same for both mates.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip3pAdapterMMp" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip3pAdapterMMp" ] ; sld:type xsd:float , sld:null . rdfs:comment "Report the depth type. By default, bedtools genomecov will compute a histogram of coverage\nfor the genome file provided (intputs.chrom_length_file)\n" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*Log.out*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*Log.out*" ] ; sld:type cwl:File , sld:null . cwl:in , , ; cwl:out ; cwl:run . a cwl:Workflow ; rdfs:comment "Workflow converts input BAM file into bigWig and bedGraph files\n" ; ns2:original_cwlVersion "v1.2" ; ns1:about "Workflow converts input BAM file into bigWig and bedGraph files.\n\nInput BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step).\n\nIf `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split`\ninput inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs.\n\n`scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for\n`bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is\nimplemented inside `bedtools-genomecov.cwl`.\n\n`bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name\nfor generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided.\n\nAll workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used\nas subworkflow." ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/workflows/bam-bedgraph-bigwig.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:name "bam-bedgraph-bigwig" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . rdfs:comment "30 12 12 12\n4 integers: minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif\ndoes not apply to annotated junctions\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterOverhangMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterOverhangMin" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "0\nint: alignment will be output only if its score is higher than or equal to this value\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterScoreMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterScoreMin" ] ; sld:type xsd:int , sld:null . cwl:source ; cwl:valueFrom "$(self+\"_\")" . rdfs:comment "int: 0 to 65535: sam FLAG will be bitwise OR'd with this value, i.e.\nFLAG=FLAG | outSAMflagOR. This is applied after all flags have been set by\nSTAR, and after outSAMflagAND. Can be used to set specific bits that are\nnot set otherwise.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMflagOR" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMflagOR" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "exon\nstring: feature type in GTF file to be used as exons for building\ntranscripts\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFfeatureExon" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFfeatureExon" ] ; sld:type xsd:string , sld:null . rdfs:comment "Log file\n" ; cwl:outputBinding [ CommandOutputBinding:glob "$(get_log_filename())" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(get_log_filename())" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Tool to sort BAM/SAM file (set as input `sort_input`).\nIf input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `samtools sort`, return\nnewly generated sorted BAM/SAM/CRAM file (the actual format of the output file depends on `out_format` value and\nextension of a filename set in `sort_output_filename`).\nIf input `trigger` is set to `false`, return unchanged BAM/SAM file, previously staged into output directory.\n\nBefore `baseCommand` is executed, input BAM/SAM file is staged into output directory (docker parameter `--workdir`),\nusing `InitialWorkDirRequirement`. Setting `writable: true` makes cwl-runner to copy input BAM/SAM file and\nmount it to docker container with `rw` mode as part of `--workdir` (if set to false, the file staged into output\ndirectory will be mounted to docker container separately with `ro` mode). Because `samtools sort` can overwrite input\nBAM/SAM file and save output with the same name, we don't need to rename it (as we did for samtools rmdup).\n\nTrigger logic is implemented in bash script set by default in input `bash_script`. If first argment $0 (which is `trigger` input)\nis true, run `samtools sort` with the rest of the arguments. If $0 is not true, skip `samtools sort` and return\ninput BAM/SAM file, previously staged into output directory.\n\nInput `trigger` is Boolean, but returns String, because of `valueFrom` field. The `valueFrom` is used, because if `trigger`\nis false, cwl-runner doesn't append this argument at all to the the `baseCommand` - new feature of CWL v1.0.2. Alternatively,\n`prefix` field could be used, but it causes changing logic in bash script saved in `bash_script` input.\n\n`default_output_name` function is used for generating output filename if input `sort_output_filename` is not set or in\ncase when `trigger` is false and we need to return original BAM/SAM file staged into output directory.\n\n`ext` function returns output filename extension on the base of `out_format` value. If input `out_format` is not set,\nuse `.bam` by default. If input `trigger` is false, `out_format` is ignored.\n\nIf `trigger` is set to true (or true is used by default), but both `sort_output_filename` and `out_format` are not set,\nthe output file format will be BAM by default.\n\nIf `trigger` is set to true (or true is used by default) and `sort_output_filename` is set to some value, but `out_format`\nis not set, the actual format of output file will be defined on the filename extension set in `sort_output_filename`\n(if filename doesn't have any extension, BAM is used by default). When `out_format` is also set, it overwrites extension\ngenerated on the base of `sort_output_filename` value.\n" ; ns2:original_cwlVersion "v1.0" ; ns1:about "Usage: samtools sort [options...] [in.bam]\nOptions:\n -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n -n Sort by read name\n -o FILE Write final output to FILE rather than standard output\n -T PREFIX Write temporary files to PREFIX.nnnn.bam\n --input-fmt-option OPT[=VAL]\n Specify a single input file format option in the form\n of OPTION or OPTION=VALUE\n -O, --output-fmt FORMAT[,OPT[=VAL]]...\n Specify output format (SAM, BAM, CRAM)\n --output-fmt-option OPT[=VAL]\n Specify a single output file format option in the form\n of OPTION or OPTION=VALUE\n --reference FILE\n Reference sequence FASTA FILE [null]\n -@, --threads INT\n Number of additional threads to use [0]\n" ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:michael.kotliar@cchmc.org" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/samtools-sort.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:mainEntity ; ns1:name "samtools-sort" ; cwl:baseCommand ( "bash" "-c" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/samtools:v1.4" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${\n return [\n {\n \"entry\": inputs.sort_input,\n \"entryname\": inputs.sort_input.basename,\n \"writable\": true\n }\n ]\n}\n" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_name = function() { if (inputs.trigger == true){ return inputs.sort_input.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.') + ext(); } else { return inputs.sort_input.location.split('/').slice(-1)[0]; } };" , "var ext = function() { if (inputs.out_format && inputs.out_format == 'SAM'){ return '.sam'; } else if (inputs.out_format && inputs.out_format == 'CRAM') { return '.cram'; } else { return '.bam'; } };" ] . a ns1:SoftwareSourceCode ; ns1:about "A suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools (Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format), BCFtools (Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants) and HTSlib (A C library for reading/writing high-throughput sequencing data).\n" ; ns1:codeRepository "https://github.com/samtools/samtools.git" ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "wrote most of the initial source codes of SAMtools and various converters." ; ns1:name "Heng Li" ] ; ns1:name "Sanger Institute" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "Designed and implemented the\nRAZF format, an alternative indexable compression format. RAZF is no longer\nused by or provided with SAMtools. Source code remains available in older\nSAMtools 0.1.x releases and from the standalone branch in the repository.\n" ; ns1:name "Jue Ruan" ] ; ns1:name "Beijing Genome Institute" ] ; ns1:creator [ a ns1:Person ; ns1:description "updated novo2sam.pl to support gapped alignment by novoalign." ; ns1:name "Colin Hercus" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "Designed and implemented the\nRAZF format, an alternative indexable compression format. RAZF is no longer\nused by or provided with SAMtools. Source code remains available in older\nSAMtools 0.1.x releases and from the standalone branch in the repository.\n" ; ns1:name "Jue Ruan" ] ; ns1:name "Beijing Genome Institute" ] ; ns1:creator [ a ns1:Person ; ns1:description "contributed the header parsing library sam_header.c and sam2vcf.pl script." ; ns1:name "Petr Danecek" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "A major contributor to the\nSAM/BAM specification. He designed and implemented the BGZF format, the\nunderlying indexable compression format for the BAM format. BGZF does\nnot support arithmetic between file offsets.\n" ; ns1:name "Bob Handsaker" ] ; ns1:name "Broad Institute" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "wrote most of the initial source codes of SAMtools and various converters." ; ns1:name "Heng Li" ] ; ns1:name "Sanger Institute" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "A major contributor to the\nSAM/BAM specification. He designed and implemented the BGZF format, the\nunderlying indexable compression format for the BAM format. BGZF does\nnot support arithmetic between file offsets.\n" ; ns1:name "Bob Handsaker" ] ; ns1:name "Broad Institute" ] ; ns1:creator [ a ns1:Person ; ns1:description "contributed the header parsing library sam_header.c and sam2vcf.pl script." ; ns1:name "Petr Danecek" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "Designed and implemented the\nRAZF format, an alternative indexable compression format. RAZF is no longer\nused by or provided with SAMtools. Source code remains available in older\nSAMtools 0.1.x releases and from the standalone branch in the repository.\n" ; ns1:name "Jue Ruan" ] ; ns1:name "Beijing Genome Institute" ] ; ns1:creator [ a ns1:Person ; ns1:description "contributed the header parsing library sam_header.c and sam2vcf.pl script." ; ns1:name "Petr Danecek" ] ; ns1:creator [ a ns1:Person ; ns1:description "updated novo2sam.pl to support gapped alignment by novoalign." ; ns1:name "Colin Hercus" ] ; ns1:creator [ a ns1:Person ; ns1:description "updated novo2sam.pl to support gapped alignment by novoalign." ; ns1:name "Colin Hercus" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "wrote most of the initial source codes of SAMtools and various converters." ; ns1:name "Heng Li" ] ; ns1:name "Sanger Institute" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "A major contributor to the\nSAM/BAM specification. He designed and implemented the BGZF format, the\nunderlying indexable compression format for the BAM format. BGZF does\nnot support arithmetic between file offsets.\n" ; ns1:name "Bob Handsaker" ] ; ns1:name "Broad Institute" ] ; ns1:discussionUrl "https://lists.sourceforge.net/lists/listinfo/samtools-help" , "https://lists.sourceforge.net/lists/listinfo/samtools-devel" ; ns1:license "https://opensource.org/licenses/BSD-3-Clause" , "https://opensource.org/licenses/MIT" ; ns1:name "samtools" ; ns1:programmingLanguage "C, Perl" ; ns1:publication , , ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "commandline tool" ; ns1:softwareVersion "1.4" ] ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "commandline tool" ; ns1:softwareVersion "1.4" ] ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "commandline tool" ; ns1:softwareVersion "1.4" ] ; ns1:url "http://www.htslib.org/" . rdfs:comment "int>=0: minimum difference (separation) between the best chimeric score and\nthe next one\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimScoreSeparation" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimScoreSeparation" ] ; sld:type xsd:int , sld:null . cwl:default "-bg" . rdfs:comment "Number of items to bundle in r-tree. Default 256\n" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-blockSize=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-blockSize=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-blockSize=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . rdfs:comment "0\nint>=0: minimum length of chimeric segment length, if ==0, no chimeric output\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimSegmentMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimSegmentMin" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*Log.std.out*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*Log.std.out*" ] ; sld:type cwl:File , sld:null . rdfs:comment "4\nint>0: log2(winFlank), where win Flank is the size of the left and right flanking\nregions for each window\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winFlankNbins" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winFlankNbins" ] ; sld:type xsd:int , sld:null . rdfs:comment "Log\nstring: which output will be directed to stdout (standard out)\nLog ... log messages\nSAM ... alignments in SAM format (which normally are output to Aligned.out.sam file), normal standard output will go into Log.std.out\nBAM_Unsorted ... alignments in BAM format, unsorted. Requires --outSAMtype BAM Unsorted\nBAM_SortedByCoordinate ... alignments in BAM format, unsorted. Requires --outSAMtype BAM SortedByCoordinate\nBAM_Quant ... alignments to transcriptome in BAM format, unsorted. Requires --quantMode TranscriptomeSAM\n" ; cwl:default "Log" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outStd" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outStd" ] ; sld:type xsd:string . rdfs:comment "STAR Log.final.out for reference genome" ; rdfs:label "STAR final log for reference genome" ; cwl:outputSource ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "int(s): number of bases to clip from 3p of each mate after the adapter\nclipping. If one value is given, it will be assumed the same for both\nmates.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip3pAfterAdapterNbases" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip3pAfterAdapterNbases" ] ; sld:type xsd:int , sld:null . rdfs:comment "0 ConcordantPair\nint, string:\nallow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate\n 1st word: int: maximum number of protrusion bases allowed\n 2nd word: string:\n ConcordantPair ... report alignments with non-zero protrusion as concordant pairs\n DiscordantPair ... report alignments with non-zero protrusion as discordant pairs\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignEndsProtrude" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignEndsProtrude" ] ; sld:type xsd:string , sld:null . rdfs:comment "Calculate coverage of 3\" positions (instead of entire interval)\n" ; cwl:inputBinding [ CommandLineBinding:position 15 ; CommandLineBinding:prefix "-3" ] ; cwl:inputBinding [ CommandLineBinding:position 15 ; CommandLineBinding:prefix "-3" ] ; cwl:inputBinding [ CommandLineBinding:position 15 ; CommandLineBinding:prefix "-3" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "For BAM only: Average insert size of pair-end sequencing (bp). [default=200.0]\n" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-m" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-m" ] ; sld:type xsd:int , sld:null . rdfs:comment "65535\nint: 0 to 65535: sam FLAG will be bitwise AND''d with this value, i.e. FLAG=FLAG\n& outSAMflagOR. This is applied after all flags have been set by STAR, but before\noutSAMflagOR. Can be used to unset specific bits that are not set otherwise.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMflagAND" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMflagAND" ] ; sld:type xsd:int , sld:null . rdfs:comment "-8\nAT/AC and GT/AT junction penalty (in addition to scoreGap)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGapATAC" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGapATAC" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Standard\nstring: read ID record type\nStandard ... first word (until space) from the FASTx read ID line, removing /1,/2 from the end\nNumber ... read number (index) in the FASTx file\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMreadID" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMreadID" ] ; sld:type xsd:string , sld:null . rdfs:comment "string: path to the directory where genome files are stored\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeDir" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeDir" ] ; sld:type cwl:Directory . cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Name for the generated output file\n" ; cwl:default "" ; cwl:inputBinding [ CommandLineBinding:position 4 ; cwl:valueFrom "$(get_output_filename(\"\"))" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; cwl:valueFrom "$(get_output_filename(\"\"))" ] ; sld:type xsd:string , sld:null . rdfs:comment "1000\nint>0: max number of seeds per read\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedPerReadNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedPerReadNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "Generated bigWig file for the first strain, projected to reference genome" ; rdfs:label "I strain bigWig file" ; cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Tool to run custom script set as `script` input with arguments from `param`.\nDefault script runs sed command over the input file and exports results to the file with the same name as input's basename\n" ; ns2:original_cwlVersion "v1.2" ; ns1:about "Custom bash script runner" ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:michael.kotliar@cchmc.org" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:michael.kotliar@cchmc.org" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/custom-bash.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:name "custom-bash" ; cwl:baseCommand ( "bash" "-c" ) ; cwl:baseCommand ( "bash" "-c" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.3" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.3" ] ; cwl:inputs , , ; cwl:outputs . cwl:in , , ; cwl:out ; cwl:run . cwl:default "bam" . rdfs:comment "STAR Log.out for reference genome" ; rdfs:label "STAR log out for reference genome" ; cwl:outputSource ; sld:type cwl:File , sld:null . cwl:in , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:comment "Tool runs STAR alignReads.\n\n`default_output_name_prefix` function returns output files prefix if `outFileNamePrefix` is not set. By default prefix\nis equal to basename of `readFilesIn`.\n" ; ns2:original_cwlVersion "v1.2" ; ns1:about "Usage: STAR [options]... --genomeDir REFERENCE --readFilesIn R1.fq R2.fq\n" ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/star-alignreads.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:mainEntity ; ns1:name "star-alignreads" ; cwl:arguments ( "--runMode" "alignReads" ) ; cwl:arguments ( "--runMode" "alignReads" ) ; cwl:baseCommand ( "STAR" ) ; cwl:baseCommand ( "STAR" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/star:v2.5.3a" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/star:v2.5.3a" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_name_prefix = function() { if (Array.isArray(inputs.readFilesIn) && inputs.readFilesIn.length > 0){ return inputs.readFilesIn[0].location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\".\"; } else { return inputs.readFilesIn.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\".\"; } };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_name_prefix = function() { if (Array.isArray(inputs.readFilesIn) && inputs.readFilesIn.length > 0){ return inputs.readFilesIn[0].location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\".\"; } else { return inputs.readFilesIn.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\".\"; } };" ] . rdfs:comment "Input only in.sam|in.bam|in.cram. Optionally could be supplemented with index file in secondaryFiles\n" ; cwl:inputBinding [ CommandLineBinding:position 16 ] ; cwl:inputBinding [ CommandLineBinding:position 16 ] ; sld:type cwl:File . rdfs:comment "0\nint>0: minimum mapped length for a read mate that is spliced\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSplicedMateMapLmin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSplicedMateMapLmin" ] ; sld:type xsd:int , sld:null . rdfs:comment "20\nint>=0: minimum overhang for a chimeric junction\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimJunctionOverhangMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimJunctionOverhangMin" ] ; sld:type xsd:int , sld:null . rdfs:comment "0 -1 0 0\n4*int>=0: maximum number of mismatches for stitching of the splice junctions (-1: no limit).\n(1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSJstitchMismatchNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSJstitchMismatchNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "Parameter to calculate scale as 1000000/mapped_reads_number. Ignored by bedtools-genomecov.cwl in\nbam_to_bedgraph step if scale is provided\n" ; rdfs:label "Mapped reads number" ; sld:type xsd:int , sld:null . rdfs:comment "string: Equal/NotEqual - lengths of names,sequences,qualities for both\nmates are the same / not the same. NotEqual is safe in all situations.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readMatesLengthsIn" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readMatesLengthsIn" ] ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "0.66\nfloat: outFilterScoreMin normalized to read length (sum of mates'' lengths for\npaired-end reads)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterScoreMinOverLread" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterScoreMinOverLread" ] ; sld:type xsd:float , sld:null . rdfs:comment "0\nmaximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignIntronMax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignIntronMax" ] ; sld:type xsd:boolean , sld:null . a ns1:SoftwareSourceCode ; ns1:about "A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.\n" ; ns1:codeRepository "https://github.com/arq5x/bedtools2" ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "Main author" ; ns1:name "Neil Kindlon" ] ; ns1:member [ a ns1:Person ; ns1:description "Main author" ; ns1:name "Aaron Quinlan" ] ; ns1:name "University of Utah" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "Main author" ; ns1:name "Neil Kindlon" ] ; ns1:member [ a ns1:Person ; ns1:description "Main author" ; ns1:name "Aaron Quinlan" ] ; ns1:name "University of Utah" ] ; ns1:creator [ a ns1:Organization ; ns1:member [ a ns1:Person ; ns1:description "Main author" ; ns1:name "Neil Kindlon" ] ; ns1:member [ a ns1:Person ; ns1:description "Main author" ; ns1:name "Aaron Quinlan" ] ; ns1:name "University of Utah" ] ; ns1:discussionUrl "https://github.com/arq5x/bedtools2/issues" , "https://groups.google.com/forum/#!forum/bedtools-discuss" ; ns1:license "https://opensource.org/licenses/GPL-2.0" ; ns1:name "bowtie2" ; ns1:programmingLanguage "C++" ; ns1:publication ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "command line tool" ; ns1:softwareVersion "2.26.0" ] ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "command line tool" ; ns1:softwareVersion "2.26.0" ] ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "command line tool" ; ns1:softwareVersion "2.26.0" ] ; ns1:url "http://bedtools.readthedocs.org" . cwl:default 1 . rdfs:comment "treat \"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 8 ; CommandLineBinding:prefix "-split" ] ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-split" ] ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-split" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "10\nnint>0: max number of one seed loci per window\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedNoneLociPerWindow" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedNoneLociPerWindow" ] ; sld:type xsd:int , sld:null . rdfs:comment "Second strain name" ; rdfs:label "II strain name" ; sld:type xsd:string . rdfs:comment "Two-column chromosome length file: \n" ; cwl:inputBinding [ CommandLineBinding:position 11 ] ; cwl:inputBinding [ CommandLineBinding:position 11 ] ; cwl:inputBinding [ CommandLineBinding:position 11 ] ; sld:type cwl:File . rdfs:comment "-2\ninsertion open penalty\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreInsOpen" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreInsOpen" ] ; sld:type xsd:boolean , sld:null . a ns1:ScholarlyArticle ; ns1:name "(Li et al., 2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics." ; ns1:url "http://www.ncbi.nlm.nih.gov/pubmed/19505943" . cwl:source ; cwl:valueFrom "$(self+\"_\")" . rdfs:comment "Four column bedGraph file: \n" ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File . rdfs:comment "string: mode of SAM output\nNone ... no SAM output\nFull ... full SAM output\nNoQS ... full SAM but without quality scores\n" ; cwl:default "Full" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMmode" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMmode" ] ; sld:type xsd:string . rdfs:comment "Yes\nstring: allow the soft-clipping of the alignments past the end of the chromosomes\nYes ... allow\nNo ... prohibit, useful for compatibility with Cufflinks\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSoftClipAtReferenceEnds" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSoftClipAtReferenceEnds" ] ; sld:type xsd:string , sld:null . rdfs:comment "string: output files name prefix (including full or relative path). Can\nonly be defined on the command line.\n" ; cwl:default "" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFileNamePrefix" ; cwl:valueFrom "${\n if (self == \"\"){\n return default_output_name_prefix();\n } else {\n return self;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFileNamePrefix" ; cwl:valueFrom "${\n if (self == \"\"){\n return default_output_name_prefix();\n } else {\n return self;\n }\n}\n" ] ; sld:type xsd:string , sld:null . rdfs:comment "Combine all positions with a depth >= max into\na single bin in the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n" ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "-max" ] ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "-max" ] ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "-max" ] ; sld:type xsd:int , sld:null . rdfs:comment "Sorted file\n" ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == null){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == null){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == null){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "${\n if (self == null){\n return true;\n } else {\n return self;\n }\n}\n" . rdfs:comment "string: path to the shell binary, preferrably bash, e.g. /bin/bash.\n- ... the default shell is executed, typically /bin/sh. This was reported to fail on some Ubuntu systems - then you need to specify path to bash.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sysShell" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sysShell" ] ; sld:type xsd:string , sld:null . cwl:default "bam" . cwl:outputBinding [ CommandOutputBinding:glob "*SJ.out.tab*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*SJ.out.tab*" ] ; sld:type cwl:File , sld:null . cwl:source , ; cwl:valueFrom "$(default_output_name(self[0], \"_\"+self[1], \".bam\"))" . rdfs:comment "Write the final sorted output to FILE, rather than to standard output\n" ; cwl:default "" ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "-o" ; cwl:valueFrom "${\n if (self == \"\" || inputs.trigger == false){\n return default_output_name();\n } else {\n return self;\n }\n}\n" ] ; sld:type xsd:string , sld:null . rdfs:comment "Unmap output file\n" ; cwl:outputBinding [ CommandOutputBinding:glob "*.unmap" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.unmap" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:comment "Tool converts bedGraph to bigWig file.\n\n`default_output_filename` function returns filename for generated bigWig if `output_filename` is not provided.\nDefault filename is generated on the base of `bedgraph_file` basename with the updated to `*.bigWig` extension.\n" ; ns2:original_cwlVersion "v1.2" ; ns1:about "usage:\n bedGraphToBigWig in.bedGraph chrom.sizes out.bw\nwhere in.bedGraph is a four column file in the format:\n \nand chrom.sizes is a two-column file/URL: \nand out.bw is the output indexed big wig file.\nIf the assembly is hosted by UCSC, chrom.sizes can be a URL like\n http://hgdownload.cse.ucsc.edu/goldenPath//bigZips/.chrom.sizes\nor you may use the script fetchChromSizes to download the chrom.sizes file.\nIf not hosted by UCSC, a chrom.sizes file can be generated by running\ntwoBitInfo on the assembly .2bit file.\nThe input bedGraph file must be sorted, use the unix sort command:\n sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph\noptions:\n -blockSize=N - Number of items to bundle in r-tree. Default 256\n -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024\n -unc - If set, do not use compression.\n" ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/ucsc-bedgraphtobigwig.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:mainEntity ; ns1:name "ucsc-bedgraphtobigwig" ; cwl:baseCommand ( "bedGraphToBigWig" ) ; cwl:baseCommand ( "bedGraphToBigWig" ) ; cwl:baseCommand ( "bedGraphToBigWig" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/ucscuserapps:v358" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/ucscuserapps:v358" ] ; 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 "biowardrobe2/ucscuserapps:v358" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { let basename = inputs.bedgraph_file.location.split('/').slice(-1)[0]; let root = basename.split('.').slice(0,-1).join('.'); let ext = \".bigWig\"; return (root == \"\")?basename+ext:root+ext; };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { let basename = inputs.bedgraph_file.location.split('/').slice(-1)[0]; let root = basename.split('.').slice(0,-1).join('.'); let ext = \".bigWig\"; return (root == \"\")?basename+ext:root+ext; };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { let basename = inputs.bedgraph_file.location.split('/').slice(-1)[0]; let root = basename.split('.').slice(0,-1).join('.'); let ext = \".bigWig\"; return (root == \"\")?basename+ext:root+ext; };" ] . rdfs:comment "Path to STAR generated indices folder for insilico genome" ; rdfs:label "STAR indices folder for insilico genome" ; sld:type cwl:Directory . rdfs:comment "2\nint: extra alignment score for alignmets that cross database junctions\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbScore" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbScore" ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:comment "Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and\ninsilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains).\nFor both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads.\nFor insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted\nby coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.\n" ; ns2:original_cwlVersion "v1.0" ; ns1:about "Workflow corresponds to MEA alignReads command from\nhttps://github.com/julienrichardalbert/MEA/blob/e3de228734bafd957cc2072dd8a6a0e84d554724/src/scripts/alignReads.sh\nSamtools quality and flag filtering of generated SAM/BAM files are replaced by outFilterMultimapNmax=1 parameter on\nmapping stage. Flag filtering 1540 should be clarified as long as it's not absolutely the same as STAR's implementation\nof outFilterMultimapNmax=1." ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/workflows/allele-vcf-alignreads-se-pe.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:name "allele-vcf-alignreads-se-pe" ; 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_name = function(named_input, suffix, ext) { if (Array.isArray(named_input) && named_input.length > 0){ return named_input[0].location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+suffix+ext; } else { return named_input.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+suffix+ext; } };" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . rdfs:comment "5\nint>0: minimum overhang (i.e. block size) for spliced alignments\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSJoverhangMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSJoverhangMin" ] ; sld:type xsd:int , sld:null . rdfs:comment "3 1 1 1 \\n4 integers: minimum uniquely mapping read count per junction\nfor: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC\nmotif, (4) AT/AC and GT/AT motif. -1 means no output for that motif\\nJunctions\nare output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin\nconditions are satisfied\\ndoes not apply to annotated junctions\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterCountUniqueMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterCountUniqueMin" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "string: name of a user-defined parameters file, \"-\": none. Can only be\ndefined on the command line.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--parametersFiles" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--parametersFiles" ] ; sld:type xsd:string , sld:null . cwl:source , ; cwl:valueFrom "${\n return (Array.isArray(self[0]) && self[0].length>1)?2*self[1]:self[1];\n}\n" . a ns1:SoftwareSourceCode ; ns1:about "CrossMap is a program for convenient conversion of genome coordinates and\ngenomeannotation files between assemblies (eg. lift from human hg18 to hg19 or\nvice versa).It supports file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF and VCF\nformat" ; ns1:name "CrossMap" . rdfs:comment "50\nint>0: max number of loci anchors are allowed to map to\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winAnchorMultimapNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winAnchorMultimapNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "Generate CSI-format index for BAM files. If input isn't cram.\n" ; sld:type xsd:boolean , sld:null . rdfs:comment "int>=1: maximum number of multi-alignments for the main chimeric segment. =1 will prohibit multimapping main segments.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimMainSegmentMultNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimMainSegmentMultNmax" ] ; sld:type xsd:int , sld:null . cwl:source ; cwl:valueFrom "$(default_output_name(self, \"\", \".bam\"))" . rdfs:comment "3 1 1 1 \\n4 integers: minimum total (multi-mapping+unique) read count\nper junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3)\nGC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that\nmotif\\nJunctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin\nconditions are satisfied\\ndoes not apply to annotated junctions\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterCountTotalMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterCountTotalMin" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . rdfs:comment "int: -1 to 10 BAM compression level, -1=default compression (6?), 0=no\ncompression, 10=maximum compression\n" ; cwl:default 10 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outBAMcompression" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outBAMcompression" ] ; sld:type xsd:int . rdfs:comment "bigWig output file" ; rdfs:label "bigWig output file" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "For BAM only: A mapped pair is considered as \"proper pair\" if both\n ends mapped to different strand and the distance\n between them is less then '-t' * stdev from the mean.\n [default=3.0]\n" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . rdfs:comment "Change strand af the mate read, so both reads come from the same strand" ; rdfs:label "Enable dUTP" ; sld:type xsd:boolean , sld:null . rdfs:comment "1\nmaximum score reduction while searching for SJ boundaries inthe stitching step\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreStitchSJshift" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreStitchSJshift" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "gene_id\nstring: tag name to be used as exons'' gene-parents (default \"gene_id\" works\nfor GTF files)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFtagExonParentGene" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFtagExonParentGene" ] ; sld:type xsd:string , sld:null . rdfs:comment "Calculate coverage of 5\" positions (instead of entire interval)\n" ; cwl:inputBinding [ CommandLineBinding:position 14 ; CommandLineBinding:prefix "-5" ] ; cwl:inputBinding [ CommandLineBinding:position 14 ; CommandLineBinding:prefix "-5" ] ; cwl:inputBinding [ CommandLineBinding:position 14 ; CommandLineBinding:prefix "-5" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "10 0 5 10\n4 integers>=0: minimum allowed distance to other junctions' donor/acceptor\ndoes not apply to annotated junctions\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterDistToOtherSJmin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterDistToOtherSJmin" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "10\nint: alignment will be output only if it has no more mismatches than this value\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMismatchNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMismatchNmax" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "string: path to BAM input file, to be used with --runMode\ninputAlignmentsFromBAM\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--inputBAMfile" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--inputBAMfile" ] ; sld:type cwl:File , sld:null . cwl:default "SAM" . rdfs:comment "For BAM only: Stanadard deviation of insert size. [default=30.0]\n" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:float , sld:null . rdfs:comment "RPM\nstring: type of normalization for the signal\nRPM ... reads per million of mapped reads\nNone ... no normalization, \"raw\" counts\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outWigNorm" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outWigNorm" ] ; sld:type xsd:string , sld:null . rdfs:comment "Local\nstring: type of read ends alignment\nLocal ... standard local alignment with soft-clipping allowed\nEndToEnd ... force end-to-end read alignment, do not soft-clip\nExtend5pOfRead1 ... fully extend only the 5p of the read1, all other ends: local alignment\nExtend5pOfReads12 ... fully extend only the 5p of the both read1 and read2, all other ends: local alignment\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignEndsType" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignEndsType" ] ; sld:type xsd:string , sld:null . rdfs:comment "STAR Log.final.out for insilico genome" ; rdfs:label "STAR final log for insilico genome" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "0.66\nfloat: outFilterMatchNmin normalized to read length (sum of mates'' lengths\nfor paired-end reads)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMatchNminOverLread" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMatchNminOverLread" ] ; sld:type xsd:float , sld:null . rdfs:comment "int: >=0: number of threads for BAM sorting. 0 will default to\nmin(6,--runThreadN).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outBAMsortingThreadN" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outBAMsortingThreadN" ] ; sld:type xsd:int , sld:null . rdfs:comment "1000000\nint>0: max number of collapsed junctions\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitOutSJcollapsed" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitOutSJcollapsed" ] ; sld:type xsd:int , sld:null . rdfs:comment "Set number of sorting and compression threads [1] (Only for sorting)\n" ; sld:type xsd:int , sld:null . rdfs:comment "Paired\nstring: type of sorting for the SAM output\nPaired: one mate after the other for all paired alignments\nPairedKeepInputOrder: one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMorder" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMorder" ] ; sld:type xsd:string , sld:null . rdfs:comment "-\nstring(s): types of quantification requested\n- ... none\nTranscriptomeSAM ... output SAM/BAM alignments to transcriptome into a separate file\nGeneCounts ... count reads per gene\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--quantMode" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--quantMode" ] ; sld:type xsd:string , sld:null . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "Output filename for generated bedGraph" ; rdfs:label "bedGraph output filename" ; sld:type xsd:string , sld:null . rdfs:comment "Specify output format (SAM, BAM, CRAM)\n" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-O" ] ; sld:type xsd:string , sld:null . rdfs:comment "OneBestScore\nstring: which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG\nOneBestScore ... only one alignment with the best score is primary\nAllBestScore ... all alignments with the best score are primary\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMprimaryFlag" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMprimaryFlag" ] ; sld:type xsd:string , sld:null . rdfs:comment "-2\ninsertion extension penalty per base (in addition to scoreInsOpen)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreInsBase" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreInsBase" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "transcript_id\nstring: tag name to be used as exons' transcript-parents (default\n\"transcript_id\" works for GTF files)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFtagExonParentTranscript" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbGTFtagExonParentTranscript" ] ; sld:type xsd:string , sld:null . rdfs:comment "777\nint: random number generator seed.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--runRNGseed" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--runRNGseed" ] ; sld:type xsd:int , sld:null . cwl:source . a ns1:SoftwareSourceCode ; ns1:about "UCSC genome browser bioinformatic utilities\n" ; ns1:license "https://opensource.org/licenses/GPL-3.0" ; ns1:name "UCSC userApps" ; ns1:programmingLanguage "C++" ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "commandline tool" ; ns1:downloadURL "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v358.src.tgz" ; ns1:softwareVersion "v358" ] ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "commandline tool" ; ns1:downloadURL "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v358.src.tgz" ; ns1:softwareVersion "v358" ] ; ns1:targetProduct [ a ns1:SoftwareApplication ; ns1:applicationCategory "commandline tool" ; ns1:downloadURL "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v358.src.tgz" ; ns1:softwareVersion "v358" ] ; ns1:url "https://genome.ucsc.edu/util.html" . cwl:source . cwl:source . rdfs:comment "STAR Log.progress.out for insilico genome" ; rdfs:label "STAR progress log for insilico genome" ; cwl:outputSource ; sld:type cwl:File , sld:null . rdfs:comment "-1\nint: max number of multiple alignments for a read that will be output to the\nSAM/BAM files. -1 ... all alignments (up to --outFilterMultimapNmax) will be\noutput\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMmultNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMmultNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "31000000000\nint>0: maximum available RAM (bytes) for genome generation\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitGenomeGenerateRAM" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitGenomeGenerateRAM" ] ; sld:type xsd:int , sld:null . rdfs:comment "100\nint>0: max number of transcripts per window\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignTranscriptsPerWindowNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignTranscriptsPerWindowNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "Input FASTQ file or array of files" ; rdfs:label "Input FASTQ file(s)" ; sld:type cwl:File ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:comment "Tool sorts data from `unsorted_file` by key\n\n`default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.\n" ; ns2:original_cwlVersion "v1.2" ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:Andrey.Kartashov@cchmc.org" ; ns1:name "Andrey Kartashov" ; ns1:sameAs ] ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/linux-sort.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:name "linux-sort" ; cwl:baseCommand ( "sort" ) ; cwl:baseCommand ( "sort" ) ; cwl:baseCommand ( "sort" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.2" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.2" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.2" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { return inputs.unsorted_file.location.split('/').slice(-1)[0]; };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { return inputs.unsorted_file.location.split('/').slice(-1)[0]; };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_output_filename = function() { return inputs.unsorted_file.location.split('/').slice(-1)[0]; };" ] ; cwl:stdout "${\n if (inputs.output_filename == null){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" . rdfs:comment "int: number of reads to process for the 1st step. Use very large number (or\ndefault -1) to map all reads in the first step.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--twopass1readsN" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--twopass1readsN" ] ; sld:type xsd:int , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Tool to sort and index input BAM/SAM/CRAM.\nIf input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `samtools sort` and\n`samtools index`, return sorted BAM and BAI/CSI index file.\nIf input `trigger` is set to `false`, return unchanged `sort_input` (BAM/SAM/CRAM) and index (BAI/CSI, if provided in\n`secondaryFiles`) files, previously staged into output directory.\n\nBefore execution `baseCommand`, `sort_input` and `secondaryFiles` (if provided) are staged into directory\nset as docker parameter `--workdir` (tool's output directory), using `InitialWorkDirRequirement`. Setting\n`writable: true` makes cwl-runner to make copies of the `sort_input` and `secondaryFiles` (if provided) and mount\nthem to docker container with `rw` mode as part of `--workdir` (if set to false, the files staged into output\ndirectory will be mounted to docker container separately with `ro` mode). Because both `samtools sort` and\n`samtools index` can overwrite files with the same names (and in case of `samtools sort` even the input file can be\noverwritten), we don't need to rename any of the staged files.\n\nTrigger logic is implemented in two bash scripts set by default as `bash_script_sort` and `bash_script_index` inputs.\nFor both of then, if the first argument $0 (which is `trigger` input) is true, run `samtools sort/index` with the rest\nof the arguments. If $0 is not true, skip `samtools sort/index` and return `sort_input` and `secondaryFiles`\n(if provided) staged into output directory.\n\nInput `trigger` is Boolean, but returns String, because of `valueFrom` field. The `valueFrom` is used, because if `trigger`\nis false, cwl-runner doesn't append this argument at all to the the `baseCommand` - new feature of CWL v1.0.2. Alternatively,\n`prefix` field could be used, but it causes changing in script logic.\n\nIf using `sort_output_filename`, the output file extension should be `*.bam`, because `samtools sort` defines the output\nfile format on the base of the file extension. If `*.sam` is sed as output filename, it cannot be usefully indexed\nby `samtools index`.\n\n`default_bam` function is used to generate output filename for `samtools sort` if input `sort_output_filename` is not\nset or when `trigger` is false and we need to return `sort_input` and `secondaryFiles` (if provided) files staged into\noutput directory. Output filename is generated on the base of `sort_input` basename with `.bam` extension by default.\n\n`ext` function is used to return the index file extension (BAI/CSI) based on `csi` and `bai` inputs according to the\nfollowing logic\n `csi` && `bai` => BAI\n !`csi` && !`bai ` => BAI\n `csi` && !`bai ` => CSI\n" ; ns2:original_cwlVersion "v1.2" ; ns1:about "Usage: samtools sort [options...] [in.bam]\nOptions:\n -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n -n Sort by read name\n -o FILE Write final output to FILE rather than standard output\n -T PREFIX Write temporary files to PREFIX.nnnn.bam\n --input-fmt-option OPT[=VAL]\n Specify a single input file format option in the form\n of OPTION or OPTION=VALUE\n -O, --output-fmt FORMAT[,OPT[=VAL]]...\n Specify output format (SAM, BAM, CRAM)\n --output-fmt-option OPT[=VAL]\n Specify a single output file format option in the form\n of OPTION or OPTION=VALUE\n --reference FILE\n Reference sequence FASTA FILE [null]\n -@, --threads INT\n Number of additional threads to use [0]\n\nUsage: samtools index [-bc] [-m INT] [out.index]\nOptions:\n -b Generate BAI-format index for BAM files [default]\n -c Generate CSI-format index for BAM files\n -m INT Set minimum interval size for CSI indices to 2^INT [14]\n -@ INT Sets the number of threads [none]\n" ; ns1:codeRepository "https://github.com/Barski-lab/workflows" ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:creator [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:department [ a ns1:Organization ; ns1:legalName "Barski Research Lab" ; ns1:member [ a ns1:Person ; ns1:email "mailto:misha.kotliar@gmail.com" ; ns1:name "Michael Kotliar" ; ns1:sameAs ] ] ; ns1:legalName "Allergy and Immunology" ] ; ns1:legalName "Cincinnati Children's Hospital Medical Center" ; ns1:location [ a ns1:PostalAddress ; ns1:addressCountry "USA" ; ns1:addressLocality "Cincinnati" ; ns1:addressRegion "OH" ; ns1:postalCode "45229" ; ns1:streetAddress "3333 Burnet Ave" ; ns1:telephone "+1(513)636-4200" ] ; ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" ] ; ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/samtools-sort-index.cwl" ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:isPartOf [ a ns1:CreativeWork ; ns1:name "Common Workflow Language" ; ns1:url "http://commonwl.org/" ] ; ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ; ns1:mainEntity ; ns1:name "samtools-sort-index" ; cwl:arguments ( [ CommandLineBinding:position 6 ; cwl:valueFrom "${ return inputs.trigger ? \"true\" : \"false\" }\n" ] [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "-O" ; cwl:valueFrom "bam" ] [ CommandLineBinding:position 15 ; CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(inputs.threads?inputs.threads:1)" ] [ CommandLineBinding:position 17 ; CommandLineBinding:shellQuote false ; cwl:valueFrom ";" ] [ CommandLineBinding:position 18 ; cwl:valueFrom "bash" ] [ CommandLineBinding:position 19 ; cwl:valueFrom "-c" ] [ CommandLineBinding:position 21 ; cwl:valueFrom "${ return inputs.trigger ? \"true\" : \"false\" }\n" ] [ CommandLineBinding:position 23 ; cwl:valueFrom "$(inputs.bai?'-b':inputs.csi?'-c':[])" ] [ CommandLineBinding:position 25 ; CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(inputs.threads?inputs.threads:1)" ] [ CommandLineBinding:position 26 ; cwl:valueFrom "${\n if (inputs.sort_output_filename == \"\" || inputs.trigger == false){\n return default_bam();\n } else {\n return inputs.sort_output_filename;\n }\n}\n" ] [ CommandLineBinding:position 27 ; cwl:valueFrom "${\n if (inputs.sort_output_filename == \"\" || inputs.trigger == false){\n return default_bam() + ext();\n } else {\n return inputs.sort_output_filename + ext();\n }\n}\n" ] ) ; cwl:arguments ( [ CommandLineBinding:position 6 ; cwl:valueFrom "${ return inputs.trigger ? \"true\" : \"false\" }\n" ] [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "-O" ; cwl:valueFrom "bam" ] [ CommandLineBinding:position 15 ; CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(inputs.threads?inputs.threads:1)" ] [ CommandLineBinding:position 17 ; CommandLineBinding:shellQuote false ; cwl:valueFrom ";" ] [ CommandLineBinding:position 18 ; cwl:valueFrom "bash" ] [ CommandLineBinding:position 19 ; cwl:valueFrom "-c" ] [ CommandLineBinding:position 21 ; cwl:valueFrom "${ return inputs.trigger ? \"true\" : \"false\" }\n" ] [ CommandLineBinding:position 23 ; cwl:valueFrom "$(inputs.bai?'-b':inputs.csi?'-c':[])" ] [ CommandLineBinding:position 25 ; CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(inputs.threads?inputs.threads:1)" ] [ CommandLineBinding:position 26 ; cwl:valueFrom "${\n if (inputs.sort_output_filename == \"\" || inputs.trigger == false){\n return default_bam();\n } else {\n return inputs.sort_output_filename;\n }\n}\n" ] [ CommandLineBinding:position 27 ; cwl:valueFrom "${\n if (inputs.sort_output_filename == \"\" || inputs.trigger == false){\n return default_bam() + ext();\n } else {\n return inputs.sort_output_filename + ext();\n }\n}\n" ] ) ; cwl:baseCommand ( "bash" "-c" ) ; cwl:baseCommand ( "bash" "-c" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/samtools:v1.4" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "biowardrobe2/samtools:v1.4" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_bam = function() { if (inputs.trigger == true){ return inputs.sort_input.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\".bam\"; } else { return inputs.sort_input.location.split('/').slice(-1)[0]; } };" , "var ext = function() { if (inputs.csi && !inputs.bai){ return '.csi'; } else { return '.bai'; } };" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "var default_bam = function() { if (inputs.trigger == true){ return inputs.sort_input.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\".bam\"; } else { return inputs.sort_input.location.split('/').slice(-1)[0]; } };" , "var ext = function() { if (inputs.csi && !inputs.bai){ return '.csi'; } else { return '.bai'; } };" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${\n return [\n {\n \"entry\": inputs.sort_input,\n \"entryname\": inputs.sort_input.basename,\n \"writable\": true\n }\n ]\n}\n" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${\n return [\n {\n \"entry\": inputs.sort_input,\n \"entryname\": inputs.sort_input.basename,\n \"writable\": true\n }\n ]\n}\n" ] . rdfs:comment "0\nmaximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignMatesGapMax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignMatesGapMax" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "SORT: desired compression level for the final output file, ranging from 0 (uncompressed)\nor 1 (fastest but minimal compression) to 9 (best compression but slowest to write),\nsimilarly to gzip(1)'s compression level setting.\nIf -l is not used, the default compression level will apply.\n" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . rdfs:comment "50\nint>0: max number of seeds per window\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedPerWindowNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedPerWindowNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "int(s): number(s) of bases to clip from 3p of each mate. If one value is\ngiven, it will be assumed the same for both mates.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip3pNbases" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip3pNbases" ] ; sld:type xsd:int , sld:null . rdfs:comment "1\nint: the score range below the maximum score for multimapping alignments\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMultimapScoreRange" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterMultimapScoreRange" ] ; sld:type xsd:int , sld:null . rdfs:comment "Input file BAM(+bai), BED, BigWig.\n" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; sld:type cwl:File . rdfs:comment "STAR Log.progress.out for reference genome" ; rdfs:label "STAR progress log for reference genome" ; cwl:outputSource ; sld:type cwl:File , sld:null . rdfs:comment "Name for generated output file\n" ; sld:type xsd:string , sld:null . rdfs:comment "-\nstring: path to the file with @CO (comment) lines of the SAM header\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMheaderCommentFile" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMheaderCommentFile" ] ; sld:type xsd:string , sld:null . rdfs:comment "Output filename for generated bigWig" ; rdfs:label "bigWig output filename" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*Log.progress.out*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*Log.progress.out*" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "string(s): path to the files with genomic coordinates (chr start \nend strand) for the splice junction introns. Multiple files can be supplied\nwand will be concatenated.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbFileChrStartEnd" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbFileChrStartEnd" ] ; sld:type xsd:string , sld:null . rdfs:comment "int>=0: maximum available RAM for sorting BAM. If =0, it will be set to the\ngenome index size. 0 value can only be used with --genomeLoad\nNoSharedMemory option.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitBAMsortRAM" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitBAMsortRAM" ] ; sld:type xsd:int , sld:null . rdfs:comment "21\nminimum intron size: genomic gap is considered intron if its length>=alignIntronMin,\notherwise it is considered Deletion\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignIntronMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignIntronMin" ] ; sld:type xsd:boolean , sld:null . cwl:source , ; cwl:valueFrom "$(default_output_name(self[0], \"_\"+self[1], \".bam\"))" . rdfs:comment "SORT: desired compression level for the final output file, ranging from 0 (uncompressed)\nor 1 (fastest but minimal compression) to 9 (best compression but slowest to write),\nsimilarly to gzip(1)'s compression level setting.\nIf -l is not used, the default compression level will apply.\n" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Set number of sorting and compression threads\n" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int , sld:null . rdfs:comment "Chromosome length file for reference genome" ; rdfs:label "Chromosome length file for reference genome" ; sld:type cwl:File . rdfs:comment "50000 100000 200000\nN integers>=0: maximum gap allowed for junctions supported by 1,2,3,,,N reads\ni.e. by default junctions supported by 1 read can have gaps <=50000b, by 2 reads: <=100000b, by 3 reads: <=200000. by >=4 reads any gap <=alignIntronMax\ndoes not apply to annotated junctions\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterIntronMaxVsReadN" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSJfilterIntronMaxVsReadN" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Generated genome coverage output file\n" ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == null){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == null){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_filename == null){\n return default_output_filename();\n } else {\n return inputs.output_filename;\n }\n}\n" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Coordinate sorted BAM file mapped to the first strain genome, projected to reference genome" ; rdfs:label "I strain output BAM" ; cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "-8\nint: non-canonical junction penalty (in addition to scoreGap)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGapNoncan" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--scoreGapNoncan" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "STAR Log.std.out for insilico genome" ; rdfs:label "STAR stdout log for insilico genome" ; cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Chain file to project strain II to reference genome" ; rdfs:label "II strain chain file" ; sld:type cwl:File . rdfs:comment "1\nint: number of threads to run STAR\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--runThreadN" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--runThreadN" ] ; sld:type xsd:int , sld:null . rdfs:comment "NoSharedMemory\nstring: mode of shared memory usage for the genome files\nLoadAndKeep ... load genome into shared and keep it in memory after run\nLoadAndRemove ... load genome into shared but remove it after run\nLoadAndExit ... load genome into shared memory and exit, keeping the genome in memory for future runs\nRemove ... do not map anything, just remove loaded genome from memory\nNoSharedMemory ... do not use shared memory, each job will have its own private copy of the genome\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeLoad" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeLoad" ] ; sld:type xsd:string , sld:null . rdfs:comment "1.0\nfloat: seedSearchStartLmax normalized to read length (sum of mates'' lengths\nfor paired-end reads)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedSearchStartLmaxOverLread" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedSearchStartLmaxOverLread" ] ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.sort_output_filename == \"\" || inputs.trigger == false){\n return default_bam();\n } else {\n return inputs.sort_output_filename;\n }\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.sort_output_filename == \"\" || inputs.trigger == false){\n return default_bam();\n } else {\n return inputs.sort_output_filename;\n }\n}\n" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "int>0: minimum number of bases covered by the seeds in a window , for STARlong algorithm only.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winReadCoverageBasesMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--winReadCoverageBasesMin" ] ; sld:type xsd:int , sld:null . rdfs:comment "Old_2.4\nstring: order of multimapping alignments in the output files\nOld_2.4 ... quasi-random order used before 2.5.0\nRandom ... random order of alignments for each multi-mapper. Read mates (pairs) are always adjacent, all alignment for each read stay together. This option will become default in the future releases.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outMultimapperOrder" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outMultimapperOrder" ] ; sld:type xsd:string , sld:null . rdfs:comment "3\nint>0: minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSJDBoverhangMin" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignSJDBoverhangMin" ] ; sld:type xsd:int , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:source , ; cwl:valueFrom "$(default_output_name(inputs.readFilesIn, \"_\"+self.join(\"_\"), \".\"))" . rdfs:comment "Enable paired-end genome coverage calculation" ; rdfs:label "Enable paired-end genome coverage calculation" ; sld:type xsd:boolean , sld:null . sld:symbols , ; sld:type sld:enum . rdfs:comment "Scale 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 6 ; CommandLineBinding:prefix "-scale" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-scale" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-scale" ] ; sld:type xsd:float , sld:null . rdfs:comment "Change strand af the mate read (so both reads from the same strand) useful for strand specific.\nWorks for BAM files only\n" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "-du" ] ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "-du" ] ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "-du" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Calculate genome coverage for each part of the splitted by 'N' and 'D' read" ; rdfs:label "Split reads by 'N' and 'D'" ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Standard\nstring: a string of desired SAM attributes, in the order desired for the output SAM\nNH HI AS nM NM MD jM jI XS ch ... any combination in any order\nStandard ... NH HI AS nM\nAll ... NH HI AS nM NM MD jM jI ch\nNone ... no attributes\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMattributes" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMattributes" ] ; sld:type xsd:string , sld:null . rdfs:comment "-\nstring(s): SAM/BAM read group line. The first word contains the read group identifier and must start with \"ID:\", e.g. --outSAMattrRGline ID:xxx CN:yy \"DS:z z z\".\nxxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted.\nComma separated RG lines correspons to different (comma separated) input files in --readFilesIn. Commas have to be surrounded by spaces, e.g.\n--outSAMattrRGline ID:xxx , ID:zzz \"DS:z z\" , ID:yyy DS:yyyy\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMattrRGline" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMattrRGline" ] ; sld:type xsd:string , sld:null . rdfs:comment "-1\nint: penalty for a non-GT/AG chimeric junction\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimScoreJunctionNonGTAG" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimScoreJunctionNonGTAG" ] ; sld:type xsd:int , sld:null . rdfs:comment "255\nint: 0 to 255: the MAPQ value for unique mappers\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMmapqUnique" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMmapqUnique" ] ; sld:type xsd:int , sld:null . rdfs:comment "100000\nint>0: max size of the SAM record for one read. Recommended value: >(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitOutSAMoneReadBytes" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitOutSAMoneReadBytes" ] ; sld:type xsd:int , sld:null . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "None\nstring(s): filter the output into main SAM/BAM files\nKeepOnlyAddedReferences ... only keep the reads for which all alignments are to the extra reference sequences added with --genomeFastaFiles at the mapping stage.\nKeepAllAddedReferences ... keep all alignments to the extra reference sequences added with --genomeFastaFiles at the mapping stage.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMfilter" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMfilter" ] ; sld:type xsd:string , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "First strain name" ; rdfs:label "I strain name" ; sld:type xsd:string . rdfs:comment "10000\nint>0: max number of different alignments per read to consider\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignTranscriptsPerReadNmax" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--alignTranscriptsPerReadNmax" ] ; sld:type xsd:int , sld:null . rdfs:comment "The input file can be in BAM format (Note: BAM must be sorted by position) or .\nPrefix is selected on the base of input file extension\n" ; cwl:inputBinding [ CommandLineBinding:position 16 ; cwl:valueFrom "${\n var prefix = ((/.*\\.bam$/i).test(inputs.input_file.path))?'-ibam':'-i';\n return [prefix, inputs.input_file.path];\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 16 ; cwl:valueFrom "${\n var prefix = ((/.*\\.bam$/i).test(inputs.input_file.path))?'-ibam':'-i';\n return [prefix, inputs.input_file.path];\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 16 ; cwl:valueFrom "${\n var prefix = ((/.*\\.bam$/i).test(inputs.input_file.path))?'-ibam':'-i';\n return [prefix, inputs.input_file.path];\n}\n" ] ; sld:type cwl:File . rdfs:comment "1000000\nint>=0: maximum number of junction to be inserted to the genome on the fly at\nthe mapping stage, including those from annotations and those detected in the\n1st step of the 2-pass run\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitSjdbInsertNsj" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitSjdbInsertNsj" ] ; sld:type xsd:int , sld:null . rdfs:comment "-\nstrings: @HD (header) line of the SAM header\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMheaderHD" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMheaderHD" ] ; sld:type xsd:boolean , sld:null . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "-1\nint: number of reads to map from the beginning of the file\n-1: map all reads\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readMapNumber" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readMapNumber" ] ; sld:type xsd:int , sld:null . rdfs:comment "150000000\nint>0: max available buffers size (bytes) for input/output, per thread\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitIObufferSize" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limitIObufferSize" ] ; sld:type xsd:int , sld:null . rdfs:comment "Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates\n" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-n" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "pair-end chip seq experiment\n" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-pc" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-pc" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-pc" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Basic\nstring: which files to save when sjdb junctions are inserted on the fly at the mapping step\nBasic ... only small junction / transcript files\nAll ... all files including big Genome, SA and SAindex - this will create a complete genome directory\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbInsertSave" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbInsertSave" ] ; sld:type xsd:string , sld:null . rdfs:comment "Name for generated output file\n" ; sld:type xsd:string , sld:null . rdfs:comment "int: -1 to 10 transcriptome BAM compression level, -1=default compression\n(6?), 0=no compression, 10=maximum compression\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--quantTranscriptomeBAMcompression" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--quantTranscriptomeBAMcompression" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "100\nint>0: length of the donor/acceptor sequence on each side of the junctions,\nideally = (mate_length - 1)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbOverhang" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--sjdbOverhang" ] ; sld:type xsd:int , sld:null . rdfs:comment "Number of data points bundled at lowest level. Default 1024\n" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-itemsPerSlot=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-itemsPerSlot=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-itemsPerSlot=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*Log.final.out*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*Log.final.out*" ] ; sld:type cwl:File , sld:null . rdfs:comment "string: path to a directory that will be used as temporary by STAR. All contents of this directory will be removed!\n- the temp directory will default to outFileNamePrefix_STARtmp\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outTmpDir" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outTmpDir" ] ; sld:type xsd:string , sld:null . cwl:source , ; cwl:valueFrom "${\n return (Array.isArray(self[0]) && self[0].length>1)?2*self[1]:self[1];\n}\n" . rdfs:comment "Input genome file. Needed only when -i flag. The genome file is tab delimited \n" ; cwl:inputBinding [ CommandLineBinding:position 17 ; CommandLineBinding:prefix "-g" ] ; cwl:inputBinding [ CommandLineBinding:position 17 ; CommandLineBinding:prefix "-g" ] ; cwl:inputBinding [ CommandLineBinding:position 17 ; CommandLineBinding:prefix "-g" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "None\nstring: 2-pass mapping mode.\nNone ... 1-pass mapping\nBasic ... basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--twopassMode" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--twopassMode" ] ; sld:type xsd:string , sld:null . rdfs:comment "int: length (bases) of the SA pre-indexing string. Typically between 10 and\n15. Longer strings will use much more memory, but allow faster searches.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeSAindexNbases" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genomeSAindexNbases" ] ; sld:type xsd:int , sld:null . rdfs:comment "If true - run samtools, if false - return sort_input and optional index file in secondaryFiles, previously staged\ninto output directory.\n" ; cwl:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "None\nstring: Cufflinks-like strand field flag\nNone ... not used\nintronMotif ... strand derived from the intron motif. Reads with inconsistent and/or non-canonical introns are filtered out.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMstrandField" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMstrandField" ] ; sld:type xsd:string , sld:null . rdfs:comment "Number of threads for those steps that support multithreading" ; rdfs:label "Number of threads" ; cwl:default 2 ; sld:type xsd:int , sld:null . rdfs:comment "strings: type of SAM/BAM output\n1st word:\nBAM ... output BAM without sorting\nSAM ... output SAM without sorting\nNone ... no SAM/BAM output\n2nd, 3rd:\nUnsorted ... standard unsorted\nSortedByCoordinate ... sorted by coordinate. This option will allocate extra memory for sorting which can be specified by --limitBAMsortRAM.\n" ; cwl:default "BAM" , "Unsorted" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMtype" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outSAMtype" ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Disable compression\n" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-unc" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-unc" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-unc" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "string(s): type of chimeric output\n1st word:\nSeparateSAMold ... output old SAM into separate Chimeric.out.sam file\nWithinBAM ... output into main aligned BAM files (Aligned.*.bam)\n2nd word:\nWithinBAM HardClip ... hard-clipping in the CIGAR for supplemental chimeric alignments (defaultif no 2nd word is present)\nWithinBAM SoftClip ... soft-clipping in the CIGAR for supplemental chimeric alignments\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimOutType" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--chimOutType" ] ; sld:type xsd:string , sld:null . rdfs:comment "Projected output file\n" ; cwl:outputBinding [ CommandOutputBinding:glob "${\n return get_output_filename();\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n return get_output_filename();\n}\n" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "string(s): character(s) separating the part of the read names that will be\ntrimmed in output (read name after space is always trimmed)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readNameSeparator" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--readNameSeparator" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . rdfs:comment "For BAM only: Add tag to each alignment\n" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-a" ] ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-a" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "int(s): number(s) of bases to clip from 5p of each mate. If one value is\ngiven, it will be assumed the same for both mates.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip5pNbases" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip5pNbases" ] ; sld:type xsd:int , sld:null . rdfs:comment "Tab delimited chromosome length file: " ; rdfs:label "Chromosome length file" ; sld:type cwl:File . rdfs:comment "Set fixed fragment size for genome coverage calculation" ; rdfs:label "Fixed fragment size" ; sld:type xsd:int , sld:null . rdfs:comment "None\nstring: filter alignment using their motifs\nNone ... no filtering\nRemoveNoncanonical ... filter out alignments that contain non-canonical junctions\nRemoveNoncanonicalUnannotated ... filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterIntronMotifs" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outFilterIntronMotifs" ] ; sld:type xsd:string , sld:null . cwl:default "cat \"$0\" | grep \"$1\" | sed \"s/$1//g\" > `basename $0`\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string , sld:null . rdfs:comment "bedGraph output file" ; rdfs:label "bedGraph output file" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "STAR Log.out for insilico genome" ; rdfs:label "STAR log out for insilico genome" ; cwl:outputSource ; sld:type cwl:File , sld:null . rdfs:comment "string: prefix matching reference names to include in the output wiggle\nfile, e.g. \"chr\", default \"-\" - include all references\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outWigReferencesPrefix" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outWigReferencesPrefix" ] ; sld:type xsd:string , sld:null . rdfs:comment "Generated BigWig file for the reference genome" ; rdfs:label "Reference bigWig file" ; cwl:outputSource ; sld:type cwl:File . cwl:default 1 . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "string(s): adapter sequences to clip from 3p of each mate. If one value is\ngiven, it will be assumed the same for both mates.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip3pAdapterSeq" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--clip3pAdapterSeq" ] ; sld:type xsd:string , sld:null . sld:symbols , , , ; sld:type sld:enum . rdfs:comment "None\nstring: output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s).\nNone ... no output\nFastx ... output in separate fasta/fastq files, Unmapped.out.mate1/2\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outReadsUnmapped" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outReadsUnmapped" ] ; sld:type , sld:null . a ns1:ScholarlyArticle ; ns1:name "(Li, 2011) Improving SNP discovery by base alignment quality. Bioinformatics." ; ns1:url "http://www.ncbi.nlm.nih.gov/pubmed/21320865" . rdfs:comment "None\nstring(s): type of signal output, e.g. \"bedGraph\" OR \"bedGraph read1_5p\". Requires sorted BAM: --outSAMtype BAM SortedByCoordinate .\n1st word:\nNone ... no signal output\nbedGraph ... bedGraph format\nwiggle ... wiggle format\n2nd word:\nread1_5p ... signal from only 5' of the 1st read, useful for CAGE/RAMPAGE etc\nread2 ... signal from only 2nd read\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outWigType" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outWigType" ] ; sld:type xsd:string , sld:null . rdfs:comment "Input only in.sam|in.bam\n" ; cwl:inputBinding [ CommandLineBinding:position 12 ] ; sld:type cwl:File .