Mercurial > repos > qfab > bowtie_for_fasta
changeset 0:c9d76b53903a draft
Uploaded
| author | qfab |
|---|---|
| date | Wed, 19 Mar 2014 21:35:16 -0400 |
| parents | |
| children | fc523597d86d |
| files | bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.py bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.xml bowtie_for_fasta-254d8bd5d21a/bowtie_indices.loc.sample bowtie_for_fasta-254d8bd5d21a/tool_data_table_conf.xml.sample bowtie_for_fasta-254d8bd5d21a/tool_dependencies.xml |
| diffstat | 5 files changed, 621 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.py Wed Mar 19 21:35:16 2014 -0400 @@ -0,0 +1,324 @@ +#!/usr/bin/env python + +import optparse, os, shutil, subprocess, sys, tempfile + +#Allow more than Sanger encoded variants +DEFAULT_ASCII_ENCODING = '--phred33-quals' +GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' } +#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' ) + parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) + parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' ) + parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' ) + parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' ) + parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' ) + parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' ) + parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' ) + parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' ) + parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' ) + parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' ) + parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' ) + parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' ) + parser.add_option( '-P', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy' ) + parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' ) + parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read' ) + parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read' ) + parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' ) + parser.add_option( '-b', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions" ) + parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' ) + parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' ) + parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' ) + parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' ) + parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' ) + parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' ) + parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' ) + parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' ) + parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' ) + parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' ) + parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' ) + parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' ) + parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' ) + parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' ) + parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' ) + parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' ) + parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' ) + parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference') + parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' ) + parser.add_option( '-O', '--seed', dest='seed', help='Seed for pseudo-random number generator' ) + parser.add_option( '-S', '-S', dest='samformat', help='The output format' ) + parser.add_option( '-o', '--output', dest='output', help='The output file' ) + parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fasta", help='galaxy input format' ) + (options, args) = parser.parse_args() + stdout = '' + + # make temp directory for placement of indices and copy reference file there if necessary + tmp_index_dir = tempfile.mkdtemp() + # get type of data (solid or solexa) + if options.dataType == 'solid': + colorspace = '-C' + else: + colorspace = '' + + # get type of data (solid or solexa) + if options.samformat == 'true': + format = '-S' + else: + format = '' + + # index if necessary + if options.genomeSource == 'history' and not options.do_not_build_index: + # set up commands + if options.index_settings =='indexPreSet': + indexing_cmds = '%s' % colorspace + else: + try: + if options.iautoB and options.iautoB == 'set': + iautoB = '--noauto' + else: + iautoB = '' + if options. ipacked and options.ipacked == 'packed': + ipacked = '--packed' + else: + ipacked = '' + if options.ibmax and int( options.ibmax ) >= 1: + ibmax = '--bmax %s' % options.ibmax + else: + ibmax = '' + if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0: + ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn + else: + ibmaxdivn = '' + if options.idcv and int( options.idcv ) > 0: + idcv = '--dcv %s' % options.idcv + else: + idcv = '' + if options.inodc and options.inodc == 'nodc': + inodc = '--nodc' + else: + inodc = '' + if options.inoref and options.inoref == 'noref': + inoref = '--noref' + else: + inoref = '' + if options.iftab and int( options.iftab ) >= 0: + iftab = '--ftabchars %s' % options.iftab + else: + iftab = '' + if options.intoa and options.intoa == 'yes': + intoa = '--ntoa' + else: + intoa = '' + if options.iendian and options.iendian == 'big': + iendian = '--big' + else: + iendian = '--little' + if options.iseed and int( options.iseed ) > 0: + iseed = '--seed %s' % options.iseed + else: + iseed = '' + if options.icutoff and int( options.icutoff ) > 0: + icutoff = '--cutoff %s' % options.icutoff + else: + icutoff = '' + indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \ + ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc, + inoref, options.ioffrate, iftab, intoa, iendian, + iseed, icutoff, colorspace ) + except ValueError, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) ) + ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) + ref_file_name = ref_file.name + ref_file.close() + os.symlink( options.ref, ref_file_name ) + + cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name ) + + try: + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Error indexing reference sequence\n' + str( e ) ) + stdout += 'File indexed. ' + else: + + ref_file_name = options.ref + # set up aligning and generate aligning command options + # automatically set threads in both cases + tmp_suppressed_file_name = None + tmp_unmapped_file_name = None + quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING ) + + try: + if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ + or options.mismatchSeed == '2' or options.mismatchSeed == '3'): + mismatchSeed = '-n %s' % options.mismatchSeed + else: + mismatchSeed = '' + if options.mismatchQual and int( options.mismatchQual ) >= 0: + mismatchQual = '-e %s' % options.mismatchQual + else: + mismatchQual = '' + print "seedLen is %s" % options.seedLen + if options.seedLen and int( options.seedLen ) >= 5: + print "seedLen1 is %s" % options.seedLen + seedLen = '-l %s' % options.seedLen + else: + print "seedLen2 is %s" % options.seedLen + seedLen = '' + if options.valAlign and int( options.valAlign ) >= 0: + valAlign = '-k %s' % options.valAlign + else: + valAlign = '' + if options.suppressAlign and int( options.suppressAlign ) >= 0: + suppressAlign = '-m %s' % options.suppressAlign + else: + suppressAlign = '' + except ValueError, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Something is wrong \n' + str( e ) ) + if options.params: + aligning_cmds = '-f -p %s -S %s %s %s %s %s %s ' % \ + (options.threads, mismatchSeed,mismatchQual,seedLen,valAlign,suppressAlign, + quality_score_encoding ) + else: + try: + if options.skip and int( options.skip ) > 0: + skip = '-s %s' % options.skip + else: + skip = '' + if options.alignLimit and int( options.alignLimit ) >= 0: + alignLimit = '-u %s' % options.alignLimit + else: + alignLimit = '' + if options.trimH and int( options.trimH ) > 0: + trimH = '-5 %s' % options.trimH + else: + trimH = '' + if options.trimL and int( options.trimL ) > 0: + trimL = '-3 %s' % options.trimL + else: + trimL = '' + if int(options.maqSoapAlign) != '-1' and int(options.maqSoapAlign) >= '0': + maqSoapAlign = '-v %s' % options.maqSoapAlign + else: + maqSoapAlign = '' + if options.rounding == 'noRound': + rounding = '--nomaqround' + else: + rounding = '' + if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \ + ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ): + maxBacktracks = '--maxbts %s' % options.maxBacktracks + else: + maxBacktracks = '' + if options.tryHard == 'doTryHard': + tryHard = '-y' + else: + tryHard = '' + if options.valAlign and int( options.valAlign ) >= 0: + valAlign = '-k %s' % options.valAlign + else: + valAlign = '' + if options.allValAligns == 'doAllValAligns': + allValAligns = '-a' + else: + allValAligns = '' + if options.best == 'doBest': + best = '--best' + else: + best = '' + if options.strata == 'doStrata': + strata = '--strata' + else: + strata = '' + if options.offrate and int( options.offrate ) >= 0: + offrate = '-o %s' % options.offrate + else: + offrate = '' + if options.seed and int( options.seed ) > 0: + seed = '--seed %s' % options.seed + else: + iseed = '' + aligning_cmds = '-f -p %s %s %s %s %s %s %s %s %s %s %s %s ' \ + '%s %s %s %s %s %s %s %s' % \ + ( options.threads, skip, alignLimit, + trimH, trimL, maqSoapAlign,mismatchSeed, mismatchQual, seedLen, rounding, + maxBacktracks,tryHard, valAlign, allValAligns, suppressAlign, best, + strata, offrate,seed, quality_score_encoding ) + except ValueError, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) + + # have to nest try-except in try-finally to handle 2.4 + try: + # prepare actual mapping commands + cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output) + print(cmd2) + # align + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + # check that there are results in the output file + if os.path.getsize( options.output ) == 0: + raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + except Exception, e: + stop_err( 'Error aligning sequence. ' + str( e ) ) + finally: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stdout += 'Sequence file aligned.\n' + sys.stdout.write( stdout ) + +if __name__=="__main__": __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.xml Wed Mar 19 21:35:16 2014 -0400 @@ -0,0 +1,248 @@ +<tool id="bowtie_for_fasta_wrapper" name="Map with Bowtie for Fasta" version="1.1.2"> + <requirements> + <requirement type='package' version="0.12.7">bowtie</requirement> + </requirements> + <description>Fasta File</description> + <parallelism method="basic"></parallelism> + <command interpreter="python"> + bowtie_for_fasta_wrapper.py + ## Hackish setting of number of threads + --threads="4" + ## Output + #if str( $outformat) == "sam": + -S "true" + --output "${samoutput}" + #else: + -S "false" + --output "${taboutput}" + #end if + + +## #if $output_unmapped_reads_l +## --output_unmapped_reads="${output_unmapped_reads_l}" +## #end if +## #if $output_suppressed_reads_l +## --output_suppressed_reads="${output_suppressed_reads_l}" +## #end if +## --galaxy_input_format="${singlePaired.sInput1.ext}" + ## Inputs + --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper +## --suppressHeader="${suppressHeader}" + --genomeSource="${refGenomeSource.genomeSource}" + #if $refGenomeSource.genomeSource == "history": + ##index already exists + #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): + ##user previously built + --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" + --do_not_build_index + #else: + ##build index on the fly + --ref="${refGenomeSource.ownFile}" + --indexSettings="${refGenomeSource.indexParams.indexSettings}" + #if $refGenomeSource.indexParams.indexSettings == "indexFull": + --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}" + #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": + --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}" + --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}" + --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}" + --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}" + #end if + --inodc="${refGenomeSource.indexParams.nodc}" + --inoref="${refGenomeSource.indexParams.noref}" + --ioffrate="${refGenomeSource.indexParams.offrate}" + --iftab="${refGenomeSource.indexParams.ftab}" + --intoa="${refGenomeSource.indexParams.ntoa}" + --iendian="${refGenomeSource.indexParams.endian}" + --iseed="${refGenomeSource.indexParams.seed}" + --icutoff="${refGenomeSource.indexParams.cutoff}" + #end if + #end if + #else + ##use pre-built index + --ref="${refGenomeSource.index.fields.path}" + #end if + --input1="${sInput1}" + --params="${Params.sSettingsType}" + --mismatchQual="${sMismatchQual}" + --mismatchSeed="${sMismatchSeed}" + --seedLen="${sSeedLen}" + --suppressAlign="${sSuppressAlign}" + --valAlign="${sValAlign}" + #unless $Params.sSettingsType: + --skip="${Params.sSkip}" + --alignLimit="${Params.sAlignLimit}" + --trimH="${Params.sTrimH}" + --trimL="${Params.sTrimL}" + --rounding="${Params.sRounding}" + --maqSoapAlign="${Params.sMaqSoapAlign}" + --tryHard="${Params.sTryHard}" + --best="${Params.sBestOption.sBest}" + #if $Params.sBestOption.sBest == "doBest": + --maxBacktracks="${Params.sBestOption.sdMaxBacktracks}" + --strata="${Params.sBestOption.sdStrata}" + #else: + --maxBacktracks="${Params.sBestOption.snMaxBacktracks}" + #end if + --offrate="${Params.sOffrate}" + --seed="${Params.sSeed}" + #end unless + </command> + <inputs> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> + <options from_data_table="bowtie_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" /> + <conditional name="indexParams"> + <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> + <option value="indexPreSet">Default</option> + <option value="indexFull">Set your own</option> + </param> + <when value="indexPreSet" /> + <when value="indexFull"> + <conditional name="autoBehavior"> + <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> + <option value="auto">Automatic behavior</option> + <option value="set">Set values (sets --noauto and allows others to be set)</option> + </param> + <when value="auto" /> + <when value="set"> + <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)"> + <option value="unpacked">Use regular representation</option> + <option value="packed">Use packed representation</option> + </param> + <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> + <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> + <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> + </when> + </conditional> + <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)"> + <option value="dc">Use difference-cover sample</option> + <option value="nodc">Disable difference-cover sample</option> + </param> + <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> + <option value="ref">Build all index files</option> + <option value="noref">Do not build paired-end alignment index files</option> + </param> + <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" /> + <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" /> + <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> + <option value="no">Do not convert Ns</option> + <option value="yes">Convert Ns to As</option> + </param> + <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> + <option value="little">Little</option> + <option value="big">Big</option> + </param> + <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> + <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" /> + </when> <!-- indexFull --> + </conditional> <!-- indexParams --> + </when> <!-- history --> + </conditional> <!-- refGenomeSource --> + <param name="sInput1" type="data" format="fasta" label="FASTA file" /> + <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> + <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> + <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> + <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> + <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> + <param name="outformat" size="" type="select" label="Output format"> + <option value="tab">TABULAR</option> + <option value="sam">SAM</option> + </param> + + <conditional name="Params"> + <param name="sSettingsType" type="boolean" checked="true" label="Default settings to use" help="For most mapping needs use Commonly used settings. If you want full control uncheck this box"/> + <when value="true"></when> + <when value="false"> + <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> + <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> + <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> + <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> + <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> + <option value="round">Round to nearest 10</option> + <option value="noRound">Do not round to nearest 10</option> + </param> + <param name="sMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> + <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> + <option value="noTryHard">Do not try hard</option> + <option value="doTryHard">Try hard</option> + </param> + <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> + <option value="noAllValAligns">Do not report all valid alignments</option> + <option value="doAllValAligns">Report all valid alignments</option> + </param> + <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> + <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> + <conditional name="sBestOption"> + <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> + <option value="noBest">Do not use best</option> + <option value="doBest">Use best</option> + </param> + <when value="noBest"> + <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + </when> + <when value="doBest"> + <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> + <option value="noStrata">Do not use strata option</option> + <option value="doStrata">Use strata option</option> + </param> + </when> + </conditional> <!-- bestOption --> + <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> + <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> + </when> <!-- full --> + </conditional> + </inputs> + <outputs> + <data format="sam" name="samoutput" label="${tool.name} on ${on_string}: SAM"> + <filter>outformat == "sam"</filter> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="tabular" name="taboutput" label="${tool.name} on ${on_string}: TAB"> + <filter>outformat == "tab"</filter> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </data> + </outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_for_fasta-254d8bd5d21a/bowtie_indices.loc.sample Wed Mar 19 21:35:16 2014 -0400 @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, +#then the bowtie_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_for_fasta-254d8bd5d21a/tool_data_table_conf.xml.sample Wed Mar 19 21:35:16 2014 -0400 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_for_fasta-254d8bd5d21a/tool_dependencies.xml Wed Mar 19 21:35:16 2014 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Bowtie for fasta requieres Bowtie to be installed."> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="bowtie" owner="devteam" changeset_revision="e1c59c194b7b" /> +</repositories>