example of auto-detected arguments for bowtie1 using chain's program_parser.rb

bowtie_arguments.rb

{:arg=>["-q"], :desc=>"query input files are FASTQ .fq/.fastq (default)"}
{:arg=>["-f"], :desc=>"query input files are (multi-)FASTA .fa/.mfa"}
{:arg=>["-r"], :desc=>"query input files are raw one-sequence-per-line"}
{:arg=>["-c"], :desc=>"query sequences given on cmd line (as <mates>, <singles>)"}
{:arg=>["-C"], :desc=>"reads and index are in colorspace"}
{:arg=>["-Q", "--quals"], :type=>:string, :desc=>"QV file(s) corresponding to CSFASTA inputs; use with -f -C"}
{:arg=>["--Q1", "--Q2"], :type=>:string, :desc=>"same as -Q, but for mate files 1 and 2 respectively"}
{:arg=>["-s", "--skip"], :type=>:integer, :desc=>"skip the first <int> reads/pairs in the input"}
{:arg=>["-u", "--qupto"], :type=>:integer, :desc=>"stop after first <int> reads/pairs (excl. skipped reads)"}
{:arg=>["-5", "--trim5"], :type=>:integer, :desc=>"trim <int> bases from 5' (left) end of reads"}
{:arg=>["-3", "--trim3"], :type=>:integer, :desc=>"trim <int> bases from 3' (right) end of reads"}
{:arg=>["--phred33-quals"], :desc=>"input quals are Phred+33 (default)"}
{:arg=>["--phred64-quals"], :desc=>"input quals are Phred+64 (same as --solexa1.3-quals)"}
{:arg=>["--solexa-quals"], :desc=>"input quals are from GA Pipeline ver. < 1.3"}
{:arg=>["--solexa1.3-quals"], :desc=>"input quals are from GA Pipeline ver. >= 1.3"}
{:arg=>["--integer-quals"], :desc=>"qualities are given as space-separated integers (not ASCII)"}
{:arg=>["-v"], :type=>:integer, :desc=>"report end-to-end hits w/ <=v mismatches; ignore qualities"}
{:arg=>["-e", "--maqerr"], :type=>:integer, :desc=>"max sum of mismatch quals across alignment for -n (def: 70)"}
{:arg=>["--nomaqround"], :desc=>"disable Maq-like quality rounding for -n (nearest 10 <= 30)"}
{:arg=>["-I", "--minins"], :type=>:integer, :desc=>"minimum insert size for paired-end alignment (default: 0)"}
{:arg=>["-X", "--maxins"], :type=>:integer, :desc=>"maximum insert size for paired-end alignment (default: 250)"}
{:arg=>["--fr", "--rf", "--ff"]}
{:arg=>["--nofw", "--norc"], :desc=>"do not align to forward/reverse-complement reference strand"}
{:arg=>["--maxbts"], :type=>:integer, :desc=>"max # backtracks for -n 2/3 (default: 125, 800 for --best)"}
{:arg=>["--pairtries"], :type=>:integer, :desc=>"max # attempts to find mate for anchor hit (default: 100)"}
{:arg=>["-y", "--tryhard"], :desc=>"try hard to find valid alignments, at the expense of speed"}
{:arg=>["--chunkmbs"], :type=>:integer, :desc=>"max megabytes of RAM for best-first search frames (def: 64)"}
{:arg=>["-k"], :type=>:integer, :desc=>"report up to <int> good alignments per read (default: 1)"}
{:arg=>["-a", "--all"], :desc=>"report all alignments per read (much slower than low -k)"}
{:arg=>["-m"], :type=>:integer, :desc=>"suppress all alignments if > <int> exist (def: no limit)"}
{:arg=>["-M"], :type=>:integer, :desc=>"like -m, but reports 1 random hit (MAPQ=0); requires --best"}
{:arg=>["--best"], :desc=>"hits guaranteed best stratum; ties broken by quality"}
{:arg=>["--strata"], :desc=>"hits in sub-optimal strata aren't reported (requires --best)"}
{:arg=>["-t", "--time"], :desc=>"print wall-clock time taken by search phases"}
{:arg=>["--quiet"], :desc=>"print nothing but the alignments"}
{:arg=>["--refout"], :desc=>"write alignments to files refXXXXX.map, 1 map per reference"}
{:arg=>["--refidx"], :desc=>"refer to ref. seqs by 0-based index rather than name"}
{:arg=>["--al"], :type=>:string, :desc=>"write aligned reads/pairs to file(s) <fname>"}
{:arg=>["--un"], :type=>:string, :desc=>"write unaligned reads/pairs to file(s) <fname>"}
{:arg=>["--max"], :type=>:string, :desc=>"write reads/pairs over -m limit to file(s) <fname>"}
{:arg=>["--suppress"], :desc=>"suppresses given columns (comma-delim'ed) in default output"}
{:arg=>["--fullref"], :desc=>"write entire ref name (default: only up to 1st space)"}
{:arg=>["--snpphred"], :type=>:integer, :desc=>"Phred penalty for SNP when decoding colorspace (def: 30)"}
{:arg=>["--snpfrac"], :desc=>"approx. fraction of SNP bases (e.g. 0.001); sets --snpphred"}
{:arg=>["--col-cseq"], :desc=>"print aligned colorspace seqs as colors, not decoded bases"}
{:arg=>["--col-cqual"], :desc=>"print original colorspace quals, not decoded quals"}
{:arg=>["--col-keepends"], :desc=>"keep nucleotides at extreme ends of decoded alignment"}
{:arg=>["-S", "--sam"], :desc=>"write hits in SAM format"}
{:arg=>["--mapq"], :type=>:integer, :desc=>"default mapping quality (MAPQ) to print for SAM alignments"}
{:arg=>["--sam-nohead"], :desc=>"supppress header lines (starting with @) for SAM output"}
{:arg=>["--sam-nosq"], :desc=>"supppress @SQ header lines for SAM output"}
{:arg=>["--sam-RG"], :type=>:string, :desc=>"add <text> (usually \"lab=value\") to @RG line of SAM header"}
{:arg=>["--mm"], :desc=>"use memory-mapped I/O for index; many 'bowtie's can share"}
{:arg=>["--shmem"], :desc=>"use shared mem for index; many 'bowtie's can share"}
{:arg=>["--seed"], :type=>:integer, :desc=>"seed for random number generator"}
{:arg=>["--verbose"], :desc=>"verbose output (for debugging)"}
{:arg=>["--version"], :desc=>"print version information and quit"}
{:arg=>["-h", "--help"], :desc=>"print this usage message"}