1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/39d41e077bca/ changeset: 39d41e077bca user: dan date: 2011-08-08 15:35:48 summary: Import patch contributed by Assaf Gordon allowing bwa_wrapper to work directly on fastqillumina formatted files. Closes #635. affected #: 2 files (633 bytes) --- a/tools/sr_mapping/bwa_wrapper.py Sat Aug 06 09:31:48 2011 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Mon Aug 08 09:35:48 2011 -0400 @@ -75,6 +75,7 @@ parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' ) parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) + parser.add_option( '-I', '--illumina1.3', dest='illumina13qual', help='Input FASTQ files have Illuina 1.3 quality scores' ) (options, args) = parser.parse_args() # output version # of tool @@ -163,10 +164,14 @@ stop_err( 'Error indexing reference sequence. ' + str( e ) ) else: ref_file_name = options.ref + if options.illumina13qual: + illumina_quals = "-I" + else: + illumina_quals = "" # set up aligning and generate aligning command options if options.params == 'pre_set': - aligning_cmds = '-t %s %s' % ( options.threads, color_space ) + aligning_cmds = '-t %s %s %s' % ( options.threads, color_space, illumina_quals ) gen_alignment_cmds = '' else: if options.maxEditDist != '0': @@ -185,11 +190,11 @@ noIterSearch = '-N' else: noIterSearch = '' - aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s' % \ + aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s %s' % \ ( editDist, options.maxGapOpens, options.maxGapExtens, options.disallowLongDel, options.disallowIndel, seed, options.maxEditDistSeed, options.threads, options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty, - suboptAlign, noIterSearch, color_space ) + suboptAlign, noIterSearch, color_space, illumina_quals ) if options.genAlignType == 'paired': gen_alignment_cmds = '-a %s -o %s' % ( options.maxInsertSize, options.maxOccurPairing ) if options.outputTopNDisc: --- a/tools/sr_mapping/bwa_wrapper.xml Sat Aug 06 09:31:48 2011 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Mon Aug 08 09:35:48 2011 -0400 @@ -5,6 +5,10 @@ bwa_wrapper.py --threads="4" + #if $input1.ext == "fastqillumina": + --illumina1.3 + #end if + ## reference source --fileSource=$genomeSource.refGenomeSource #if $genomeSource.refGenomeSource == "history": @@ -93,11 +97,11 @@ <option value="paired">Paired-end</option></param><when value="single"> - <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> + <param name="input1" type="data" format="fastqsanger,fastqillumina" label="FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" /></when><when value="paired"> - <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> - <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> + <param name="input1" type="data" format="fastqsanger,fastqillumina" label="Forward FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" /> + <param name="input2" type="data" format="fastqsanger,fastqillumina" label="Reverse FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" /></when></conditional><conditional name="params"> @@ -324,7 +328,7 @@ **Input formats** -BWA accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files. +BWA accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*) or Illumina FASTQ format (galaxy type *fastqillumina*). Use the FASTQ Groomer to prepare your files. ------ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.