{"id": "file:///Users/leipzig/Documents/dev/truwl/capanno/tools/bowtie/1.2.x/bowtie_align/bowtie-align.cwl", "doc": "Tool maps input raw reads files to reference genome using Bowtie.\n\n`default_output_filename` function returns default name for SAM output and log files. In case when `sam` and\n`output_filename` inputs are not set, default filename will have `.sam` extension but format may not correspond SAM\nspecification. To set output filename manually use `output_filename` input. Default output filename is based on\n`output_filename` or basename of `upstream_filelist`, `downstream_filelist` or `crossbow_filelist` file (if array,\nthe first file in array is taken). If function is called without argenments and `output_filename` input is set, it\nwill be returned from the function.\n\nFor single-end input data any of the `upstream_filelist` or `downstream_filelist` inputs can be used.\n\nLog filename (`log_file` output) is generated by `default_output_filename` function with ex='.bw'\n\n`indices_folder` defines folder to contain Bowtie indices. Based on the first found file with `rev.1.ebwt` or\n`rev.1.ebwtl` extension, bowtie index prefix is returned from input's `valueFrom` field.", "class": "CommandLineTool", "hints": [{"class": "DockerRequirement", "dockerPull": "truwl/bowtie:1.2.3_0.1.0"}, {"class": "SoftwareRequirement", "packages": {"bowtie": {"specs": ["http://identifiers.org/biotools/bowtie"], "version": ["1.3.0"]}}}], "inputs": [{"id": "B", "doc": "--offbase leftmost ref offset = in bowtie output (default: 0)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-B", "position": 1}}, {"id": "C", "doc": "reads and index are in colorspace\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-C", "position": 1}}, {"id": "I", "doc": "--minins minimum insert size for paired-end alignment (default: 0)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-I", "position": 1}}, {"id": "M", "doc": " like -m, but reports 1 random hit (MAPQ=0)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-M", "position": 1}}, {"id": "Q", "doc": "QV file(s) corresponding to CSFASTA inputs; use with -f -C\n", "type": ["null", "File"], "inputBinding": {"prefix": "-Q", "position": 1}}, {"id": "Q1", "doc": "--Q1/--Q2 same as -Q, but for mate files 1 and 2 respectively\n", "type": ["null", "File"], "inputBinding": {"prefix": "--Q1", "position": 1}}, {"id": "Q2", "doc": "--Q1/--Q2 same as -Q, but for mate files 1 and 2 respectively\n", "type": ["null", "File"], "inputBinding": {"prefix": "--Q2", "position": 1}}, {"id": "X", "doc": "--maxins maximum insert size for paired-end alignment (default: 250)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-X", "position": 1}}, {"id": "a", "doc": "--all report all alignments per read (much slower than low -k)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-a", "position": 1}}, {"id": "al", "doc": " write aligned reads/pairs to file(s) \n", "type": ["null", "string"], "inputBinding": {"prefix": "--al", "position": 1}}, {"id": "best", "doc": "hits guaranteed best stratum; ties broken by quality\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--best", "position": 1}}, {"id": "c", "doc": "query sequences given on cmd line (as , )\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-c", "position": 1}}, {"id": "chunkmbs", "doc": " max megabytes of RAM for best-first search frames (def: 64)\n", "type": ["null", "int"], "inputBinding": {"prefix": "--chunkmbs", "position": 1}}, {"id": "clip_3p_end", "doc": "--trim3 trim bases from 3' (right) end of reads\n", "type": ["null", "int"], "inputBinding": {"prefix": "-3", "position": 1}}, {"id": "clip_5p_end", "doc": "--trim5 trim bases from 5' (left) end of reads\n", "type": ["null", "int"], "inputBinding": {"prefix": "-5", "position": 1}}, {"id": "col_cqual", "doc": "print original colorspace quals, not decoded quals\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--col-cqual", "position": 1}}, {"id": "col_cseq", "doc": "print aligned colorspace seqs as colors, not decoded bases\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--col-cseq", "position": 1}}, {"id": "col_keepends", "doc": "keep nucleotides at extreme ends of decoded alignment\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--col-keepends", "position": 1}}, {"id": "crossbow_filelist", "doc": "Comma-separated list of files containing Crossbow-style reads.\nCan be a mixture of paired and unpaired. Specify \"-\"for stdin.\n", "type": ["null", "File", {"name": "_:0308ba20-8126-42f4-a2d1-19067eafe9b7", "type": "array", "items": "File"}], "inputBinding": {"prefix": "-12", "position": 86, "itemSeparator": ","}}, {"id": "downstream_filelist", "doc": "Comma-separated list of files containing downstream mates (or the\nsequences themselves if -c is set) paired with mates in \n", "type": ["null", "File", {"name": "_:00e731ec-2c1c-449e-8391-1dae419d05d9", "type": "array", "items": "File"}], "inputBinding": {"position": 85, "itemSeparator": ","}}, {"id": "e", "doc": "--maqerr max sum of mismatch quals across alignment for -n (def: 70)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-e", "position": 1}}, {"id": "f", "doc": "query input files are (multi-)FASTA .fa/.mfa\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-f", "position": 1}}, {"id": "ff", "doc": "--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--ff", "position": 1}}, {"id": "fr", "doc": "--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--fr", "position": 1}}, {"id": "fullref", "doc": "write entire ref name (default: only up to 1st space)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--fullref", "position": 1}}, {"id": "indices_folder", "doc": "Folder with Bowtie indices\n", "type": "Directory", "inputBinding": {"position": 81, "valueFrom": "${\n for (var i = 0; i < self.listing.length; i++) {\n if (self.listing[i].path.split('.').slice(-3).join('.') == 'rev.1.ebwt' ||\n self.listing[i].path.split('.').slice(-3).join('.') == 'rev.1.ebwtl'){\n return self.listing[i].path.split('.').slice(0,-3).join('.');\n }\n }\n return null;\n}\n"}}, {"id": "integer_quals", "doc": "qualities are given as space-separated integers (not ASCII)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--integer-quals", "position": 1}}, {"id": "k", "doc": " report up to good alignments per read (default: 1)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-k", "position": 1}}, {"id": "l", "doc": "--seedlen seed length for -n (default: 28)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-l", "position": 1}}, {"id": "large_index", "doc": "force usage of a 'large' index, even if a small one is present\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--large-index", "position": 1}}, {"id": "m", "doc": " suppress all alignments if > exist (def: no limit)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-m", "position": 1}}, {"id": "mapq", "doc": " default mapping quality (MAPQ) to print for SAM alignments\n", "type": ["null", "int"], "inputBinding": {"prefix": "--mapq", "position": 1}}, {"id": "max", "doc": " write reads/pairs over -m limit to file(s) \n", "type": ["null", "string"], "inputBinding": {"prefix": "--max", "position": 1}}, {"id": "maxbts", "doc": " max # backtracks for -n 2/3 (default: 125, 800 for --best)\n", "type": ["null", "int"], "inputBinding": {"prefix": "--maxbts", "position": 1}}, {"id": "mm", "doc": "use memory-mapped I/O for index; many 'bowtie's can share\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--mm", "position": 1}}, {"id": "n", "doc": "--seedmms max mismatches in seed (can be 0-3, default: -n 2)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-n", "position": 1}}, {"id": "nofw", "doc": "--norc do not align to forward/reverse-complement reference strand\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--nofw", "position": 1}}, {"id": "nomaqround", "doc": "disable Maq-like quality rounding for -n (nearest 10 <= 30)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--nomaqround", "position": 1}}, {"id": "o", "doc": "--offrate override offrate of index; must be >= index's offrate\n", "type": ["null", "int"], "inputBinding": {"prefix": "-o", "position": 1}}, {"id": "output_filename", "doc": "Generates default output filename on the base of upstream_filelist/downstream_filelist files\n", "type": ["null", "string"], "inputBinding": {"position": 90, "valueFrom": "$(default_output_filename())"}}, {"id": "pairtries", "doc": " max # attempts to find mate for anchor hit (default: 100)\n", "type": ["null", "int"], "inputBinding": {"prefix": "--pairtries", "position": 1}}, {"id": "phred33_quals", "doc": "input quals are Phred+33 (default)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--phred33-quals", "position": 1}}, {"id": "phred64_quals", "doc": "input quals are Phred+64 (same as --solexa1.3-quals)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--phred64-quals", "position": 1}}, {"id": "q", "doc": "query input files are FASTQ .fq/.fastq (default)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-q", "position": 1}}, {"id": "quiet", "doc": "print nothing but the alignments\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--quiet", "position": 1}}, {"id": "r", "doc": "query input files are raw one-sequence-per-line\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-r", "position": 1}}, {"id": "reads_per_batch", "doc": "# of reads to read from input file at once (default: 16)\n", "type": ["null", "int"], "inputBinding": {"prefix": "--reads-per-batch", "position": 1}}, {"id": "refidx", "doc": "refer to ref. seqs by 0-based index rather than name\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--refidx", "position": 1}}, {"id": "refout", "doc": "write alignments to files refXXXXX.map, 1 map per reference\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--refout", "position": 1}}, {"id": "rf", "doc": "--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--rf", "position": 1}}, {"id": "s", "doc": "--skip skip the first reads/pairs in the input\n", "type": ["null", "int"], "inputBinding": {"prefix": "-s", "position": 1}}, {"id": "sam", "doc": "--sam write hits in SAM format\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-S", "position": 1}}, {"id": "sam_RG", "doc": " add (usually \"lab=value\") to @RG line of SAM header\n", "type": ["null", "string"], "inputBinding": {"prefix": "--sam-RG", "position": 1}}, {"id": "sam_nohead", "doc": "supppress header lines (starting with @) for SAM output\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--sam-nohead", "position": 1}}, {"id": "sam_nosq", "doc": "supppress @SQ header lines for SAM output\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--sam-nosq", "position": 1}}, {"id": "seed", "doc": " seed for random number generator\n", "type": ["null", "int"], "inputBinding": {"prefix": "--seed", "position": 1}}, {"id": "shmem", "doc": "use shared mem for index\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--shmem", "position": 1}}, {"id": "snpfrac", "doc": " approx. fraction of SNP bases (e.g. 0.001); sets --snpphred\n", "type": ["null", "float"], "inputBinding": {"prefix": "--snpfrac", "position": 1}}, {"id": "snpphred", "doc": " Phred penalty for SNP when decoding colorspace (def: 30)\n", "type": ["null", "int"], "inputBinding": {"prefix": "--snpphred", "position": 1}}, {"id": "solexa1.3_quals", "doc": "input quals are from GA Pipeline ver. >= 1.3\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--solexa1.3-quals", "position": 1}}, {"id": "solexa_quals", "doc": "input quals are from GA Pipeline ver. < 1.3\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--solexa-quals", "position": 1}}, {"id": "strata", "doc": "hits in sub-optimal strata aren't reported (requires --best)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--strata", "position": 1}}, {"id": "suppress", "doc": " suppresses given columns (comma-delim'ed) in default output\n", "type": ["null", "string"], "inputBinding": {"prefix": "--suppress", "position": 1}}, {"id": "t", "doc": "--time print wall-clock time taken by search phases\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-t", "position": 1}}, {"id": "threads", "doc": "--threads number of alignment threads to launch (default: 1)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-p", "position": 1}}, {"id": "u", "doc": "--qupto stop after first reads/pairs (excl. skipped reads)\n", "type": ["null", "int"], "inputBinding": {"prefix": "-u", "position": 1}}, {"id": "un", "doc": " write unaligned reads/pairs to file(s) \n", "type": ["null", "string"], "inputBinding": {"prefix": "--un", "position": 1}}, {"id": "upstream_filelist", "doc": "Comma-separated list of files containing upstream mates (or the\nsequences themselves, if -c is set) paired with mates in \n", "type": ["null", "File", {"name": "_:0deb7310-e407-4917-a504-7ab27912d38a", "type": "array", "items": "File"}], "inputBinding": {"position": 83, "itemSeparator": ","}}, {"id": "v", "doc": "report end-to-end hits w/ <=v mismatches; ignore qualities\n", "type": ["null", "int"], "inputBinding": {"prefix": "-v", "position": 1}}, {"id": "verbose", "doc": "verbose output (for debugging)\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "--verbose", "position": 1}}, {"id": "y", "doc": "--tryhard try hard to find valid alignments, at the expense of speed\n", "type": ["null", "boolean"], "inputBinding": {"prefix": "-y", "position": 1}}], "outputs": [{"id": "aligned_file", "type": ["null", "File"], "outputBinding": {"glob": "$(inputs.al)"}}, {"id": "log_file", "type": "File", "outputBinding": {"glob": "$(default_output_filename(\".bw\"))"}}, {"id": "mapped_reads_number", "type": "int", "outputBinding": {"glob": "$(default_output_filename(\".bw\"))", "outputEval": "${\n var mappedRegex = /alignment\\:.*/;\n return parseInt(self[0].contents.match(mappedRegex)[0].split(\" \")[1]);\n}\n", "loadContents": true}}, {"id": "multimapped_file", "type": ["null", "File"], "outputBinding": {"glob": "$(inputs.max)"}}, {"id": "refout_file", "type": ["null", {"name": "_:1eb0197b-84eb-4851-819e-2d89bf0946ed", "type": "array", "items": "File"}], "outputBinding": {"glob": "*ref*.map*"}}, {"id": "sam_file", "type": ["null", "File"], "outputBinding": {"glob": "$(default_output_filename())"}}, {"id": "total_reads_number", "type": "int", "outputBinding": {"glob": "$(default_output_filename(\".bw\"))", "outputEval": "${\n var totalRegex = /processed\\:.*/;\n return parseInt(self[0].contents.match(totalRegex)[0].split(\" \")[1]);\n}\n", "loadContents": true}}, {"id": "unaligned_file", "type": ["null", "File"], "outputBinding": {"glob": "$(inputs.un)"}}, {"id": "unmapped_reads_number", "type": "int", "outputBinding": {"glob": "$(default_output_filename(\".bw\"))", "outputEval": "${\n var unmappedRegex = /align\\:.*/;\n return parseInt(self[0].contents.match(unmappedRegex)[0].split(\" \")[1]);\n}\n", "loadContents": true}}], "arguments": [], "cwlVersion": "v1.0", "baseCommand": ["bowtie"], "requirements": [{"class": "ShellCommandRequirement"}, {"class": "InlineJavascriptRequirement", "expressionLib": ["var default_output_filename = function(ext) { if (inputs.output_filename != \"\" && !ext){ return inputs.output_filename; } ext = ext || \".sam\"; var root = \"\"; if (inputs.output_filename != \"\"){ root = inputs.output_filename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.output_filename+ext:root+ext; } else if (Array.isArray(inputs.upstream_filelist) && inputs.upstream_filelist.length > 0){ root = inputs.upstream_filelist[0].basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.upstream_filelist[0].basename+ext:root+ext; } else if (inputs.upstream_filelist != null){ root = inputs.upstream_filelist.basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.upstream_filelist.basename+ext:root+ext; } else if (Array.isArray(inputs.downstream_filelist) && inputs.downstream_filelist.length > 0){ root = inputs.downstream_filelist[0].basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.downstream_filelist[0].basename+ext:root+ext; } else if (inputs.downstream_filelist != null){ root = inputs.downstream_filelist.basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.downstream_filelist.basename+ext:root+ext; } else if (Array.isArray(inputs.crossbow_filelist) && inputs.crossbow_filelist.length > 0){ root = inputs.crossbow_filelist[0].basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.crossbow_filelist[0].basename+ext:root+ext; } else if (inputs.crossbow_filelist != null){ root = inputs.crossbow_filelist.basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.crossbow_filelist.basename+ext:root+ext; } else { return null; } };"]}]}

bowtie align

Version:1.2.0

Identifier: TL_af1548_f7.62

Tool

Version:
1.2.0