1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e5182b8038e8/ changeset: e5182b8038e8 user: dan date: 2012-04-10 15:24:25 summary: Fix for BWA -R option. affected #: 3 files
diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_color_wrapper.xml --- a/tools/sr_mapping/bwa_color_wrapper.xml +++ b/tools/sr_mapping/bwa_color_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.1"> +<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.2"><description></description><parallelism method="basic"></parallelism><command interpreter="python"> @@ -42,7 +42,7 @@ --mismatchPenalty=$params.mismatchPenalty --gapOpenPenalty=$params.gapOpenPenalty --gapExtensPenalty=$params.gapExtensPenalty - --suboptAlign=$params.suboptAlign + --suboptAlign="${params.suboptAlign}" --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN --outputTopNDisc=$params.outputTopNDisc @@ -125,7 +125,7 @@ <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /><param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /><param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" /> - <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> + <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /><param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /><param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /><param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" /> @@ -249,7 +249,7 @@ <param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="true" /> + <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" /> @@ -300,7 +300,7 @@ <param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="true" /> + <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" />
diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py +++ b/tools/sr_mapping/bwa_wrapper.py @@ -54,7 +54,7 @@ parser.add_option( '-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' ) parser.add_option( '-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' ) parser.add_option( '-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' ) - parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat' ) + parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', default=None, help='Proceed with suboptimal alignments even if the top hit is a repeat' ) parser.add_option( '-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search' ) parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Maximum number of alignments to output in the XA tag for reads paired properly' ) parser.add_option( '', '--outputTopNDisc', dest='outputTopNDisc', help='Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)' ) @@ -182,8 +182,8 @@ seed = '-l %s' % options.seed else: seed = '' - if options.suboptAlign == 'true': - suboptAlign = '-R' + if options.suboptAlign: + suboptAlign = '-R "%s"' % ( options.suboptAlign ) else: suboptAlign = '' if options.noIterSearch == 'true':
diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.2"> +<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.3"><description></description><parallelism method="basic"></parallelism><command interpreter="python"> @@ -45,7 +45,7 @@ --mismatchPenalty=$params.mismatchPenalty --gapOpenPenalty=$params.gapOpenPenalty --gapExtensPenalty=$params.gapExtensPenalty - --suboptAlign=$params.suboptAlign + --suboptAlign="${params.suboptAlign}" --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN --outputTopNDisc=$params.outputTopNDisc @@ -122,7 +122,7 @@ <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /><param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /><param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" /> - <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> + <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /><param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /><param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /><param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" /> @@ -226,7 +226,7 @@ <param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="true" /> + <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" /> @@ -263,7 +263,7 @@ <param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="true" /> + <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" />
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