mirror of
https://github.com/galaxyproject/galaxy.git
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Added Bowtie wrapper tool
This commit is contained in:
Kelly Vincent
@@ -0,0 +1,28 @@
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#This is a sample file distributed with Galaxy that enables tools
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#to use a directory of Bowtie indexed sequences data files. You will need
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#to create these data files and then create a bowtie_indices.loc file
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#similar to this one (store it in this directory ) that points to
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#the directories in which those files are stored. The bowtie_indices.loc
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#file has this format (white space characters are TAB characters):
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#
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#<build> <file_base>
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#
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#So, for example, if you had hg18 indexed stored in
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#/depot/data2/galaxy/bowtie/hg18/,
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#then the bowtie_indices.loc entry would look like this:
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#
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#hg18 /depot/data2/galaxy/bowtie/hg18/hg18
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#
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#and your /depot/data2/galaxy/bowtie/hg18/ directory
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#would contain hg18.*.ebwt files:
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#
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#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
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#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
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#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 gh18.3.ebwt
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#...etc...
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#
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#Your bowtie_indices.loc file should include an entry per line for
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#each index set you have stored. The "file" in the path does not actually
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#exist, but it is the prefix for the actual index files. For example:
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#
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#hg18 /depot/data2/galaxy/bowtie/hg18/hg18
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@@ -332,7 +332,8 @@
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<tool file="metag_tools/megablast_xml_parser.xml" />
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<tool file="metag_tools/blat_wrapper.xml" />
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<tool file="metag_tools/mapping_to_ucsc.xml" />
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</section>
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<tool file="sr_mapping/bowtie_wrapper.xml" />
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</section>
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<section name="Tracks" id="tracks">
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<tool file="visualization/genetrack.xml" />
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</section>
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@@ -0,0 +1,174 @@
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#! /usr/bin/python
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"""
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Runs Bowtie on single-end or paired-end data.
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"""
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import optparse, os, sys, tempfile
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def stop_err( msg ):
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sys.stderr.write( "%s\n" % msg )
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sys.exit()
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def __main__():
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#Parse Command Line
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parser = optparse.OptionParser()
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parser.add_option('', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format')
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parser.add_option('', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format')
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parser.add_option('', '--output', dest='output', help='The output file')
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parser.add_option('', '--paired', dest='paired', help='Whether the data is single- or paired-end')
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parser.add_option('', '--genomeSource', dest='genomeSource', help='The type of reference provided')
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parser.add_option('', '--ref', dest='ref', help='The reference genome to use or index')
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parser.add_option('', '--skip', dest='skip', help='Skip the first n reads')
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parser.add_option('', '--alignLimit', dest='alignLimit', help='Only align the first n reads')
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parser.add_option('', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment')
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parser.add_option('', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment')
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parser.add_option('', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed')
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parser.add_option('', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions')
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parser.add_option('', '--seedLen', dest='seedLen', help='Seed length')
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parser.add_option('', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30')
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parser.add_option('', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy')
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parser.add_option('', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist')
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parser.add_option('', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read')
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parser.add_option('', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read')
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parser.add_option('', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist')
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parser.add_option('', '--offbase', dest='offbase', help='Number the first base of a reference sequence as n when outputting alignments')
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parser.add_option('', '--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")
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parser.add_option('', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read')
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parser.add_option('', '--threadMem', dest='threadMem', help='Number of megabytes of memory a given thread is given to store path descriptors in best mode')
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parser.add_option('', '--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')
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parser.add_option('', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments')
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parser.add_option('', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments')
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parser.add_option('', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand')
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parser.add_option('', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate')
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parser.add_option('', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand')
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parser.add_option('', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand')
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parser.add_option('', '--phased', dest='phased', help='Whether or not it should alternate between using the forward and mirror indexes in a series of phases so that only half of the index is resident in memory at one time')
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parser.add_option('', '--offrate', dest='offrate', help='Override the offrate of the index to n')
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parser.add_option('', '--mm', dest='mm', help='Whether or not to use memory-mapped I/O to load the index')
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parser.add_option('', '--seed', dest='seed', help='Seed for pseudo-random number generator')
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parser.add_option('', '--dbkey', dest='dbkey', help='')
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parser.add_option('', '--params', dest='params', help='Whether to use default or specified parameters')
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parser.add_option('', '--iauto_b', dest='iauto_b', help='Automatic or specified behavior')
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parser.add_option('', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings')
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parser.add_option('', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block')
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parser.add_option('', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference')
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parser.add_option('', '--idcv', dest='idcv', help='The period for the difference-cover sample')
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parser.add_option('', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample')
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parser.add_option('', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paried-end alignment')
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parser.add_option('', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows')
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parser.add_option('', '--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')
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parser.add_option('', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As')
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parser.add_option('', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file')
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parser.add_option('', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator')
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parser.add_option('', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index')
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parser.add_option('', '--ioldpmap', dest='ioldpmap', help='Use the scheme for mapping joined reference locations to original reference locations used in versions of Bowtie prior to 0.9.8')
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parser.add_option('', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set')
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(options, args) = parser.parse_args()
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# index if necessary
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if options.genomeSource == 'history':
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# set up commands
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if options.index_settings =='index_pre_set':
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indexing_cmds = ''
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else:
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try:
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indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \
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(('','--noauto')[options.iauto_b=='set'],
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('','--packed')[options.ipacked=='packed'],
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('','--bmax %s'%options.ibmax)[options.ibmax!='None' and options.ibmax>=1],
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('','--bmaxdivn %s'%options.ibmaxdivn)[options.ibmaxdivn!='None'],
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('','--dcv %s'%options.idcv)[options.idcv!='None'],
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('','--nodc')[options.inodc=='nodc'],
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('','--noref')[options.inoref=='noref'], options.ioffrate,
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('','--ftabchars %s'%options.iftab)[int(options.iftab)>=0],
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('','--ntoa')[options.intoa=='yes'],
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('--little','--big')[options.iendian=='big'],
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('','--seed %s'%options.iseed)[int(options.iseed)>0],
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('','--cutoff %s'%options.icutoff)[int(options.icutoff)>0],
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('','--oldpmap')[options.ioldpmap=='yes'])
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except ValueError:
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indexing_cmds = ''
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# make temp directory for placement of indices and copy reference file there
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tmp_dir = tempfile.gettempdir()
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try:
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os.system('cp %s %s' % (options.ref, tmp_dir))
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except Exception, erf:
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stop_err('Error creating temp directory for indexing purposes\n' + str(erf))
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options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1])
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cmd1 = 'cd %s; bowtie-build %s -f %s %s > /dev/null' % (tmp_dir, indexing_cmds, options.ref, options.ref)
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try:
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os.system(cmd1)
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except Exception, erf:
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stop_err('Error indexing reference sequence\n' + str(erf))
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# set up aligning and generate aligning command options
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# automatically set threads to 8 in both cases
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if options.params == 'pre_set':
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aligning_cmds = '-p 8'
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else:
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try:
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aligning_cmds = '%s %s %s %s %s %s %s %s %s %s %s %s %s %s ' \
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'%s %s %s %s %s %s %s %s %s %s %s %s %s %s -p 8' % \
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(('','-s %s'%options.skip)[options.skip!='None'],
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('','-u %s'%options.alignLimit)[int(options.alignLimit)>0],
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('','-5 %s'%options.trimH)[int(options.trimH)>=0],
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('','-3 %s'%options.trimL)[int(options.trimL)>=0],
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('','-n %s'%options.mismatchSeed)[options.mismatchSeed=='0' or options.mismatchSeed=='1' or options.mismatchSeed=='2' or options.mismatchSeed=='3'],
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('','-e %s'%options.mismatchQual)[int(options.mismatchQual)>=0],
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('','-l %s'%options.seedLen)[int(options.seedLen)>=5],
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('','--nomaqround')[options.rounding=='noRound'],
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('','-v %s'%options.maqSoapAlign)[options.maqSoapAlign!='-1'],
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('','-I %s'%options.minInsert)[options.minInsert!='None'],
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('','-X %s'%options.maxInsert)[options.maxInsert!='None'],
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('','--%s'%options.mateOrient)[options.mateOrient!='None'],
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('','--pairtries %s'%options.maxAlignAttempt)[int(options.maxAlignAttempt)>=0],
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('','--nofw')[options.forwardAlign=='noForward'],
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('','--norc')[options.reverseAlign=='noReverse'],
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('','--maxbts %s'%options.maxBacktracks)[options.maxBacktracks!='None' and (options.mismatchSeed=='2' or options.mismatchSeed=='3')],
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('','-y')[options.tryHard=='doTryHard'],
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('','--chunkmbs %s'%options.threadMem)[options.threadMem!='None' and int(options.threadMem)>=0],
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('','-k %s'%options.valAlign)[options.valAlign!='None' and int(options.valAlign)>=0],
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('','-a')[options.allValAligns=='doAllValAligns' and int(options.allValAligns)>=0],
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('','-m %s'%options.suppressAlign)[int(options.suppressAlign)>=0],
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('','--best')[options.best=='doBest'],
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('','--strata')[options.strata=='doStrata'],
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('','-B %s'%options.offbase)[int(options.offbase)>=0],
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('','-z %s'%options.phased)[options.phased!='None'],
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('','-o %s'%options.offrate)[int(options.offrate)>=0],
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('','--mm')[options.mm=='doMm'],
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('','--seed %s'%options.seed)[int(options.seed)>=0])
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except ValueError:
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aligning_cmds = '-p 8'
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tmp_out = tempfile.NamedTemporaryFile()
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# prepare actual aligning commands
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if options.paired == 'paired':
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cmd2 = 'bowtie %s %s -1 %s -2 %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, options.input2, tmp_out.name)
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else:
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cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, tmp_out.name)
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# prepare command to convert bowtie output to sam and alternative
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cmd3 = 'bowtie2sam.pl %s > %s' % (tmp_out.name, options.output)
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cmd4 = 'cp %s %s' % (tmp_out.name, options.output)
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# align
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try:
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os.system(cmd2)
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except Exception, erf:
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stop_err("Error aligning sequence\n" + str(erf))
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if len(file(tmp_out.name,'r').read()) > 0:
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#convert
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try:
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os.system(cmd3)
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except Exception, erf:
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stop_err('Error converting output to sam format\n' + str(erf))
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else:
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try:
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os.system(cmd4)
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sys.stdout.write('Alignment file contained no data')
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except Exception, erf:
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stop_err('Error producing alignment file. File contained no data.\n' + str(erf))
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if __name__=="__main__": __main__()
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@@ -0,0 +1,556 @@
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<tool id="bowtie_wrapper" name="Bowtie" version="1.0.0">
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<description> fast alignment of reads against reference sequence </description>
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<command interpreter="python">
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bowtie_wrapper.py
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--input1=$singlePaired.input1
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#if $singlePaired.sPaired == "paired":
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--input2=$singlePaired.input2
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#else:
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--input2="None"
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#end if
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--output=$output
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--paired=$singlePaired.sPaired
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--genomeSource=$refGenomeSource.genomeSource
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#if $refGenomeSource.genomeSource == "history":
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--ref=$refGenomeSource.ownFile
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#else:
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--ref=$refGenomeSource.indices.value
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#end if
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--params=$singlePaired.params.settings_type
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#if $singlePaired.params.settings_type == "full":
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--skip=$singlePaired.params.skip
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--alignLimit=$singlePaired.params.alignLimit
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--trimH=$singlePaired.params.trimH
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--trimL=$singlePaired.params.trimL
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--mismatchSeed=$singlePaired.params.mismatchSeed
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--mismatchQual=$singlePaired.params.mismatchQual
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--seedLen=$singlePaired.params.seedLen
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--rounding=$singlePaired.params.rounding
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--maqSoapAlign=$singlePaired.params.maqSoapAlign
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--tryHard=$singlePaired.params.tryHard
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--valAlign=$singlePaired.params.valAlign
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--allValAligns=$singlePaired.params.allValAligns
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--suppressAlign=$singlePaired.params.suppressAlign
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--offbase=$singlePaired.params.offbase
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--offrate=$singlePaired.params.offrate
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--mm=$singlePaired.params.mm
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--seed=$singlePaired.params.seed
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--best=$singlePaired.params.bestOption.best
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#if $singlePaired.params.bestOption.best == "doBest":
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--maxBacktracks=$singlePaired.params.bestOption.maxBacktracks
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--threadMem=$singlePaired.params.bestOption.threadMem
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--strata=$singlePaired.params.bestOption.strata
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--phased="None"
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#else:
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--maxBacktracks="None"
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--threadMem="None"
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--strata="None"
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#if $singlePaired.sPaired =="single":
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--phased=$singlePaired.params.bestOption.phased
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#else:
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--phased="None"
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#end if
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#end if
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#if $singlePaired.sPaired == "single":
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--minInsert="None"
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--maxInsert="None"
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--mateOrient="None"
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--maxAlignAttempt="None"
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--forwardAlign="None"
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--reverseAlign="None"
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#else:
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--minInsert=$singlePaired.params.minInsert
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--maxInsert=$singlePaired.params.maxInsert
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--mateOrient=$singlePaired.params.mateOrient
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--maxAlignAttempt=$singlePaired.params.maxAlignAttempt
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--forwardAlign=$singlePaired.params.forwardAlign
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--reverseAlign=$singlePaired.params.reverseAlign
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#end if
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#else
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--skip="None"
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--alignLimit="None"
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--trimH="None"
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--trimL="None"
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--mismatchSeed="None"
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--mismatchQual="None"
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--seedLen="None"
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--rounding="None"
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--maqSoapAlign="None"
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--tryHard="None"
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--valAlign="None"
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--allValAligns="None"
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--suppressAlign="None"
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--offbase="None"
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--best="None"
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--maxBacktracks="None"
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--threadMem="None"
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--strata="None"
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--minInsert="None"
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--maxInsert="None"
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--mateOrient="None"
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--maxAlignAttempt="None"
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--forwardAlign="None"
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--reverseAlign="None"
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--phased="None"
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--offrate="None"
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--mm="None"
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--seed="None"
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#end if
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#if $refGenomeSource.genomeSource == "history":
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--dbkey=$dbkey
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#else:
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--dbkey="None"
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#end if
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#if $refGenomeSource.genomeSource == "history":
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--indexSettings=$refGenomeSource.indexParams.index_settings
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#else:
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--indexSettings="None"
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#end if
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#if $refGenomeSource.genomeSource == "history" and $refGenomeSource.indexParams.index_settings == "index_full":
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--iauto_b=$refGenomeSource.indexParams.auto_behavior.auto_b
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#if $refGenomeSource.indexParams.auto_behavior.auto_b == "set":
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--ipacked=$refGenomeSource.indexParams.auto_behavior.packed
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--ibmax=$refGenomeSource.indexParams.auto_behavior.bmax
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--ibmaxdivn=$refGenomeSource.indexParams.auto_behavior.bmaxdivn
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--idcv=$refGenomeSource.indexParams.auto_behavior.dcv
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#else:
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--ipacked="None"
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--ibmax="None"
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||||
--ibmaxdivn="None"
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||||
--idcv="None"
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||||
#end if
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--inodc=$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=$refGenomeSource.indexParams.cutoff
|
||||
--ioldpmap=$refGenomeSource.indexParams.oldpmap
|
||||
#else:
|
||||
--iauto_b="None"
|
||||
--ipacked="None"
|
||||
--ibmax="None"
|
||||
--ibmaxdivn="None"
|
||||
--idcv="None"
|
||||
--inodc="None"
|
||||
--inoref="None"
|
||||
--ioffrate="None"
|
||||
--iftab="None"
|
||||
--intoa="None"
|
||||
--iendian="None"
|
||||
--iseed="None"
|
||||
--icutoff="None"
|
||||
--ioldpmap="None"
|
||||
#end if
|
||||
</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="indices" type="select" label="Select a reference genome">
|
||||
<options from_file="bowtie_indices.loc">
|
||||
<column name="value" index="1" />
|
||||
<column name="name" index="0" />
|
||||
<filter type="sort_by" column="0" />
|
||||
</options>
|
||||
</param>
|
||||
</when>
|
||||
<when value="history">
|
||||
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />
|
||||
<conditional name="indexParams">
|
||||
<param name="index_settings" type="select" label="Choose whether to use default options or to set your own">
|
||||
<option value="index_pre_set">Commonly Used</option>
|
||||
<option value="index_full">Full Parameter List</option>
|
||||
</param>
|
||||
<when value="index_pre_set" />
|
||||
<when value="index_full">
|
||||
<conditional name="auto_behavior">
|
||||
<param name="auto_b" 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 (-p)">
|
||||
<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 (a very repetetive 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" />
|
||||
<param name="oldpmap" type="select" label="Use the scheme for mapping joined reference locations to original reference locations used in versions of Bowtie prior to 0.9.8 (--oldpmap)" help="The old scheme uses padding and the new one doesn't">
|
||||
<option value="no">Use the new scheme</option>
|
||||
<option value="yes">Use the old scheme</option>
|
||||
</param>
|
||||
</when> <!-- index_full -->
|
||||
</conditional>
|
||||
</when>
|
||||
</conditional> <!-- refGenomeSource -->
|
||||
<conditional name="singlePaired">
|
||||
<param name="sPaired" type="select" label="Is this library mate-paired?">
|
||||
<option value="single">Single-end</option>
|
||||
<option value="paired">Paired-end</option>
|
||||
</param>
|
||||
<when value="single">
|
||||
<param name="input1" type="data" format="fastqsanger" label="FASTQ file" />
|
||||
<conditional name="params">
|
||||
<param name="settings_type" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
|
||||
<option value="pre_set">Commonly used</option>
|
||||
<option value="full">Full parameter list</option>
|
||||
</param>
|
||||
<when value="pre_set" />
|
||||
<when value="full">
|
||||
<param name="skip" type="integer" value="0" label="Skip the first n reads (-s)" />
|
||||
<param name="alignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
|
||||
<param name="trimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
|
||||
<param name="trimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
|
||||
<param name="mismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
|
||||
<param name="mismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
|
||||
<param name="seedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
|
||||
<param name="rounding" 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="maqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
|
||||
<param name="tryHard" 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="valAlign" type="integer" value="1" label="Report up to n valid arguments per read (-k)" />
|
||||
<param name="allValAligns" 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="suppressAlign" 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="offbase" type="integer" value="0" label="Number the first base of a reference sequence as n when outputting alignments (-B)" />
|
||||
<conditional name="bestOption">
|
||||
<param name="best" 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="maxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
|
||||
<param name="phased" type="select" label="Whether or not it should alternate between using the forward and mirror indexes in a series of phases so that only half of the index is resident in memory at one time (-z)">
|
||||
<option value="noPhased">Don't alternate</option>
|
||||
<option value="doPhased">Do alternate</option>
|
||||
</param>
|
||||
</when>
|
||||
<when value="doBest">
|
||||
<param name="maxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
|
||||
<param name="threadMem" type="integer" value="32" label="Number of megabytes of memory a given thread is given to store path descriptors in best mode (--chunkmbs)" help="If running in best mode, and you run out of memory, try adjusting this" />
|
||||
<param name="strata" 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="offrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
|
||||
<param name="mm" type="select" label="Whether or not to use memory-mapped I/O to load the index (--m)">
|
||||
<option value="noMm">Use POSIX/C file I/O</option>
|
||||
<option value="doMm">Use memory-mapped I/O</option>
|
||||
</param>
|
||||
<param name="seed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
|
||||
</when> <!-- full -->
|
||||
</conditional> <!-- params -->
|
||||
</when> <!-- single -->
|
||||
<when value="paired">
|
||||
<param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" />
|
||||
<param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" />
|
||||
<conditional name="params">
|
||||
<param name="settings_type" type="select" label="BWA settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
|
||||
<option value="pre_set">Commonly used</option>
|
||||
<option value="full">Full parameter list</option>
|
||||
</param>
|
||||
<when value="pre_set" />
|
||||
<when value="full">
|
||||
<param name="skip" type="integer" value="0" label="Skip the first n pairs (-s)" />
|
||||
<param name="alignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
|
||||
<param name="trimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
|
||||
<param name="trimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
|
||||
<param name="mismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
|
||||
<param name="mismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
|
||||
<param name="seedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
|
||||
<param name="rounding" 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="maqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
|
||||
<param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
|
||||
<param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments (-X)" />
|
||||
<param name="mateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
|
||||
<option value="fr">FR (for Illumina)</option>
|
||||
<option value="rf">RF</option>
|
||||
<option value="ff">FF</option>
|
||||
</param>
|
||||
<param name="maxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
|
||||
<param name="forwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)">
|
||||
<option value="forward">Align against the forward reference strand</option>
|
||||
<option value="noForward">Do not align against the forward reference strand</option>
|
||||
</param>
|
||||
<param name="reverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)">
|
||||
<option value="reverse">Align against the reverse-complement reference strand</option>
|
||||
<option value="noReverse">Do not align against the reverse-complement reference strand</option>
|
||||
</param>
|
||||
<param name="tryHard" 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="valAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
|
||||
<param name="allValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
|
||||
<option value="noAllValAligns">Do not report all valid alignments</option>
|
||||
<option value="doAllValAligns">Report all valid alignments</option>
|
||||
</param>
|
||||
<param name="suppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" />
|
||||
<param name="offbase" type="integer" value="0" label="Number the first base of a reference sequence as n when outputting alignments (-B)" />
|
||||
<conditional name="bestOption">
|
||||
<param name="best" 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="maxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
|
||||
</when>
|
||||
<when value="doBest">
|
||||
<param name="maxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
|
||||
<param name="threadMem" type="integer" value="32" label="Number of megabytes of memory a given thread is given to store path descriptors in best mode (--chunkmbs)" help="If running in best mode, and you run out of memory, try adjusting this" />
|
||||
<param name="strata" 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>
|
||||
<param name="offrate" type="integer" value="-1" label="Override the offrate of the index to n -o)" help="-1 for default" />
|
||||
<param name="mm" type="select" label="Whether or not to use memory-mapped I/O to load the index (--mm)">
|
||||
<option value="noMm">Use POSIX/C file I/O</option>
|
||||
<option value="doMm">Use memory-mapped I/O</option>
|
||||
</param>
|
||||
<param name="seed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
|
||||
</when> <!-- full -->
|
||||
</conditional> <!-- params -->
|
||||
</when> <!-- paired -->
|
||||
</conditional> <!-- singlePaired -->
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="sam" name="output" />
|
||||
</outputs>
|
||||
<tests>
|
||||
<test>
|
||||
<param name="genomeSource" value="indexed" />
|
||||
<param name="indices" value="chrM" />
|
||||
<param name="sPaired" value="single" />
|
||||
<param name="input1" ftype="fastqsanger" value="bowtie_in1.fastq" />
|
||||
<param name="settings_type" value="pre_set" />
|
||||
<output name="output" ftype="sam" file="bowtie_out1.sam" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="genomeSource" value="history" />
|
||||
<param name="ownFile" value="chrM.fa" />
|
||||
<param name="index_settings" value="index_pre_set" />
|
||||
<param name="sPaired" value="paired" />
|
||||
<param name="input1" ftype="fastqsanger" value="bowtie_in2.fastq" />
|
||||
<param name="input2" ftype="fastqsanger" value="bowtie_in3.fastq" />
|
||||
<param name="settings_type" value="pre_set" />
|
||||
<output name="output" ftype="sam" file="bowtie_out2.sam" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="genomeSource" value="history" />
|
||||
<param name="ownFile" value="chrM.fa" />
|
||||
<param name="index_settings" value="index_full" />
|
||||
<param name="auto_b" value="set" />
|
||||
<param name="packed" value="unpacked" />
|
||||
<param name="bmax" value="-1" />
|
||||
<param name="bmaxdivn" value="4" />
|
||||
<param name="dcv" value="2048" />
|
||||
<param name="nodc" value="dc" />
|
||||
<param name="noref" value="noref" />
|
||||
<param name="offrate" value="6" />
|
||||
<param name="ftab" value="10" />
|
||||
<param name="ntoa" value="yes" />
|
||||
<param name="endian" value="little" />
|
||||
<param name="seed" value="-1" />
|
||||
<param name="cutoff" value="-1" />
|
||||
<param name="oldpmap" value="no" />
|
||||
<param name="sPaired" value="single" />
|
||||
<param name="input1" ftype="fastqsanger" value="bowtie_in1.fastq" />
|
||||
<param name="settings_type" value="pre_set" />
|
||||
<output name="output" ftype="sam" file="bowtie_out1.sam" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="genomeSource" value="indexed" />
|
||||
<param name="indices" value="chrM" />
|
||||
<param name="sPaired" value="paired" />
|
||||
<param name="input1" ftype="fastqsanger" value="bowtie_in2.fastq" />
|
||||
<param name="input2" ftype="fastqsanger" value="bowtie_in3.fastq" />
|
||||
<param name="settings_type" value="full" />
|
||||
<param name="skip" value="0" />
|
||||
<param name="alignLimit" value="-1" />
|
||||
<param name="trimL" value="0" />
|
||||
<param name="trimH" value="0" />
|
||||
<param name="mismatchSeed" value="3" />
|
||||
<param name="mismatchQual" value="50" />
|
||||
<param name="seedLen" value="10" />
|
||||
<param name="rounding" value="round" />
|
||||
<param name="maqSoapAlign" value="-1" />
|
||||
<param name="minInsert" value="0" />
|
||||
<param name="maxInsert" value="250" />
|
||||
<param name="mateOrient" value="fr" />
|
||||
<param name="maxAlignAttempt" value="100" />
|
||||
<param name="forwardAlign" value="forward" />
|
||||
<param name="reverseAlign" value="reverse" />
|
||||
<param name="tryHard" value="doTryHard" />
|
||||
<param name="valAlign" value="1" />
|
||||
<param name="allValAligns" value="noAllValAligns" />
|
||||
<param name="suppressAlign" value="-1" />
|
||||
<param name="offbase" value="0" />
|
||||
<param name="best" value="doBest" />
|
||||
<param name="maxBacktracks" value="800" />
|
||||
<param name="threadMem" value="32" />
|
||||
<param name="strata" value="noStrata" />
|
||||
<param name="offrate" value="-1" />
|
||||
<param name="mm" value="noMm" />
|
||||
<param name="seed" value="403" />
|
||||
<output name="output" ftype="sam" file="bowtie_out2.sam" />
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
|
||||
**What it does**
|
||||
|
||||
Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. Reads can be as long as 1024 base pairs, though shorter is better. Bowtie produces a specific output format which is converted to SAM by this tool.
|
||||
|
||||
.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
|
||||
|
||||
------
|
||||
|
||||
**Input formats**
|
||||
|
||||
Bowtie accepts files in Sanger FASTQ format.
|
||||
|
||||
------
|
||||
|
||||
**Outputs**
|
||||
|
||||
The output is in SAM format, and has the following columns::
|
||||
|
||||
1 QNAME - Query (pair) NAME
|
||||
2 FLAG - bitwise FLAG
|
||||
3 RNAME - Reference sequence NAME
|
||||
4 POS - 1-based leftmost POSition/coordinate of clipped sequence
|
||||
5 MAPQ - MAPping Quality (Phred-scaled)
|
||||
6 CIGAR - extended CIGAR string
|
||||
7 MRNM - Mate Reference sequence NaMe ('=' if same as RNAME)
|
||||
8 MPOS - 1-based Mate POSition
|
||||
9 ISIZE - Inferred insert SIZE
|
||||
10 SEQ - query SEQuence on the same strand as the reference
|
||||
11 QUAL - query QUALity (ASCII-33 gives the Phred base quality)
|
||||
12 OPT - variable OPTional fields in the format TAG:VTYPE:VALU
|
||||
|
||||
The flags are as follows::
|
||||
|
||||
Flag - Description
|
||||
0x0001 - the read is paired in sequencing
|
||||
0x0002 - the read is mapped in a proper pair
|
||||
0x0004 - the query sequence itself is unmapped
|
||||
0x0008 - the mate is unmapped
|
||||
0x0010 - strand of the query (1 for reverse)
|
||||
0x0020 - strand of the mate
|
||||
0x0040 - the read is the first read in a pair
|
||||
0x0080 - the read is the second read in a pair
|
||||
0x0100 - the alignment is not primary
|
||||
|
||||
It looks like this (scroll sideways to see the entire example)::
|
||||
|
||||
QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
|
||||
HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
|
||||
HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
|
||||
|
||||
-------
|
||||
|
||||
**Bowtie settings**
|
||||
|
||||
All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
|
||||
|
||||
------
|
||||
|
||||
**Bowtie parameter list**
|
||||
|
||||
This is an exhaustive list of Bowtie options:
|
||||
|
||||
For indexing (bowtie-build)::
|
||||
-a No auto behavior. Disable the default behavior where bowtie automatically selects values for --bmax/--dcv/--packed parameters according to the memory available. [off]
|
||||
-p Packing. Use a packed representation for DNA strings. [auto]
|
||||
--bmax <int> Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
|
||||
--bmaxdivn <int> Suffix maximum fraction. The maximum number of suffixes allowed in a block expressed as a fraction of the length of the reference. [4]
|
||||
--dcv <int> Difference-cover sample. Use <int> as the period for the difference-cover sample. [1024]
|
||||
--nodc <int> No difference-cover sample. Disable the difference-cover sample. [off]
|
||||
-r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions of the index, used only for paired-end alignment. [off]
|
||||
-o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The indexer will mark every 2^<int> rows. The marked rows correspond to rows on the genome. [5]
|
||||
-t <int> Ftab. The lookup table used to calculate an initial Burrows-Wheeler range with respect to the first <int> characters of the query. Ftab is 4^<int>+1 bytes. [10]
|
||||
--ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are simply excluded from the index and Bowtie will not find alignments that overlap them. [off]
|
||||
--big Endianness. Endianness to use when serializing integers to the index file. [off]
|
||||
--little Endianness. [--little]
|
||||
--seed <int> Random seed. Use <int> as the seed for the pseudo-random number generator. [off]
|
||||
--cutoff <int> Cutoff. Index only the first <int> bases of the reference sequences (cumulative across sequences) and ignore the rest. [off]
|
||||
--oldpmap Use old mapping scheme. Use the padding-based scheme from Bowtie versions before 0.9.8 instead of the current scheme. [off]
|
||||
|
||||
For aligning (bowtie)::
|
||||
-s <int> Skip. Do not align the first <int> reads or pairs in the input. [off]
|
||||
-u <int> Align limit. Only align the first <int> reads/pairs from the input. [no limit]
|
||||
-5 <int> High-quality trim. Trim <int> bases from the high-quality (left) end of each read before alignment. [0]
|
||||
-3 <int> Low-quality trim. Trim <int> bases from the low-quality (right) end of each read before alignment. [0]
|
||||
-n <int> Mismatch seed. Maximum number of mismatches permitted in the seed (defined with seed length option). Can be 0, 1, 2, or 3. [2]
|
||||
-e <int> Mismatch quality. Maximum permitted total of quality values at mismatched read positions. Bowtie rounds quality values to the nearest 10 and saturates at 30. [70]
|
||||
-l <int> Seed length. The number of bases on the high-quality end of the read to which the -n ceiling applies. Must be at least 5. [28]
|
||||
--nomaqround Suppress MAQ rounding. Values are internally rounded to the nearest 10 and saturate at 30. This options turns off that rounding. [off]
|
||||
-v <int> MAQ- or SOAP-like alignment policy. This option turns off the default MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments with at most <int> mismatches. [off]
|
||||
-I <int> Minimum insert. The minimum insert size for valid paired-end alignments. Does checking on untrimmed reads if -5 or -3 is used. [0]
|
||||
--fr Mate orientation. The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. [--fr]
|
||||
--rf Mate orientation. [off]
|
||||
--ff Mate orientation. [off]
|
||||
-X <int> Maximum insert. The maximum insert size for valid paired-end alignments. Does checking on untrimmed reads if -5 or -3 is used. [250]
|
||||
--pairtries <int> Maximum alignment attempts for paired-end data. [100]
|
||||
--nofw No forward aligning. Choosing this option means that Bowtie will not attempt to align against the forward reference strand. [off]
|
||||
--norc No reverse-complement aligning. Setting this will mean that Bowtie will not attempt to align against the reverse-complement reference strand. [off]
|
||||
--maxbts <int> Maximum backtracks. The maximum number of backtracks permitted when aligning a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
|
||||
-y Try hard. Try as hard as possible to find valid alignments when they exist, including paired-end alignments. [off]
|
||||
--chunkmbs <int> Thread memory. The number of megabytes of memory a given thread is given to store path descriptors in --best mode. [32]
|
||||
-k <int> Valid alignments. The number of valid alignments per read or pair. [off]
|
||||
-a All valid alignments. Choosing this means that all valid alignments per read or pair will be reported. [off]
|
||||
-m <int> Suppress alignments. Suppress all alignments for a particular read or pair if more than <int> reportable alignments exist for it. [no limit]
|
||||
--best Best mode. Make Bowtie guarantee that reported singleton alignments are "best" in terms of stratum (the number of mismatches) and quality values at mismatched position. [off]
|
||||
--strata Best strata. When running in best mode, report alignments that fall into the best stratum if there are ones falling into more than one. [off]
|
||||
-B <int> First base number. When outputting alignments, number the first base of a reference sequence as <int>. [0]
|
||||
-z <int> Phased. Alternate between using the forward and mirror indexes in a series of phases such that only one half of the index is resident in memory at one time. Cannot be used with paired-end alignment. [off]
|
||||
-o <int> Offrate override. Override the offrate of the index with <int>. Some row markings are discarded when index read into memory. <int> must be greater than the value used to build the index (default: 5). [off]
|
||||
--mm I/O for index loading. Choosing this option means that memory-mapped I/O will be used to load the index instead of the normal POSIX/C file I/O. Allows memory-efficient parallelization where using -p is not desirable. [off]
|
||||
--seed <int> Random seed. Use <int> as the seed for the pseudo-random number generator. [off]
|
||||
|
||||
</help>
|
||||
</tool>
|
||||
Reference in New Issue
Block a user