Mercurial > repos > nilshomer > dwgsim_eval
view dwgsim_eval_wrapper.xml @ 1:eb58ceeedfba default tip
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author | nilshomer |
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date | Sun, 14 Aug 2011 20:09:02 -0400 |
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<tool id="dwgsim" name="Evaluate simulated reads" version="1.0.0"> <description>from a SAM/BAM file using dwgsim_eval</description> <command interpreter="python"> if 'sam' == input.ext: dwgsim_wrapper.py \ $alignmentScore \ $bwa \ $colorSpace \ -d $scoreFactor \ -g $wiggle \ -n $numReads \ -q $minMapq \ $singleEnd \ $printIncorrect \ -s $numSnps \ -e $numErrors \ $indels \ -s $input \ -o $output else: dwgsim_wrapper.py \ $alignmentScore \ $bwa \ $colorSpace \ -d $scoreFactor \ -g $wiggle \ -n $numReads \ -q $minMapq \ $singleEnd \ $printIncorrect \ -s $numSnps \ -e $numErrors \ $indels \ -b $input \ -o $output </command> <inputs> <param format="sam,bam" name="input" type="data" label="SAM/BAM file to evaluate"/> <param name="alignmentScore" type="boolean" truevalue="-a" falsevalue="" checked="False" label="split alignments by alignment score instead of mapping quality"/> <param name="bwa" type="boolean" truevalue="-b" falsevalue="" checked="False" label="alignments are from BWA"/> <param name="colorSpace" type="boolean" truevalue="-c" falsevalue="" checked="False" label="color space alignments"/> <param name="scoreFactor" size="4" type="text" value="1"> <label>divide quality/alignment score by this factor</label> </param> <param name="wiggle" size="4" type="text" value="5"> <label>gap "wiggle"</label> </param> <param name="numReads" size="4" type="text" value="-1"> <label>number of raw input paired-end reads (otherwise, inferred from all SAM records present)</label> </param> <param name="minMapq" size="4" type="text" value="0"> <label>consider only alignments with this mapping quality or greater</label> </param> <param name="singleEnd" type="boolean" truevalue="-z" falsevalue="" checked="False" label="input contains only single end reads"/> <param name="printIncorrect" type="boolean" truevalue="-p" falsevalue="" checked="False" label="print incorrect alignments"/> <param name="numSnps" size="4" type="text" value="-1"> <label>consider only alignments with the number of specified SNPs</label> </param> <param name="numErrors" size="4" type="text" value="-1"> <label>consider only alignments with the number of specified errors</label> </param> <param name="indels" type="boolean" truevalue="-i" falsevalue="" checked="False" label="consider only alignments with indels"/> </inputs> <outputs> <data format="text" name="output"/> </outputs> <help> This tool evaluates simulated reads from DWGSIM. For more information, please see https://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation#Evaluating_mapping_-_dwgsim_eval </help> </tool>