Mercurial > repos > nilshomer > dwgsim
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author | nilshomer |
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date | Sun, 14 Aug 2011 20:08:09 -0400 |
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<tool id="dwgsim" name="Generate simulated reads" version="1.0.0"> <description>from a fasta sequence using dwgsim</description> <command interpreter="python">dwgsim_wrapper.py \ -e $eRateFirstread \ -E $eRateSecondread \ -d $innerDist \ -s $stDev \ -N $noReadpairs \ -1 $loFirstread \ -2 $loSecondread \ -r $rateOfMut \ -R $rateOfIndels \ -X $probExtRead \ -y $probRandRead \ -n $maxAllowN \ -S $strandDirection \ $colorSpace \ $haploMode \ -f $input \ -3 $outputSingleReads \ -4 $outputPEFirst \ -5 $outputPESecond \ -6 $outputMutations </command> <inputs> <param format="fasta" name="input" type="data" label="Select fasta file to generate reads from"/> <param name="eRateFirstread" size="4" type="text" value="0.020"> <label>base/color error rate of the first read</label> </param> <param name="eRateSecondread" size="4" type="text" value="0.020"> <label>base/color error rate of the second read</label> </param> <param name="innerDist" size="4" type="text" value="500"> <label>inner distance between the two ends</label> </param> <param name="stDev" size="4" type="text" value="50"> <label>Standard deviation</label> </param> <param name="noReadpairs" size="12" type="text" value="1000000"> <label>number of read pairs</label> </param> <param name="loFirstread" size="4" type="text" value="70"> <label>length of the first read </label> </param> <param name="loSecondread" size="4" type="text" value="70"> <label>length of the second read </label> </param> <param name="rateOfMut" size="4" type="text" value="0.0010"> <label>rate of mutations</label> </param> <param name="rateOfIndels" size="4" type="text" value="0.10"> <label>fraction of indels </label> </param> <param name="probExtRead" size="4" type="text" value="0.30"> <label>probability an indel is extended</label> </param> <param name="probRandRead" size="4" type="text" value="0.10"> <label>probability of a random DNA read</label> </param> <param name="maxAllowN" size="4" type="text" value="0"> <label>maximum number of Ns allowed in a given read</label> </param> <param name="colorSpace" type="boolean" truevalue="-c" falsevalue="" checked="False" label="generate reads in color space (SOLiD reads)"/> <param name="strandDirection" type="select" label="Direction of strand (default: opposite strand for Illumina, same for SOLiD)"> <option value="0" selected="True">Default</option> <option value="1">Same strand (mate pair)</option> <option value="2">Opposite strand (paired end)</option> </param> <param name="haploMode" type="boolean" truevalue="-H" falsevalue="" checked="False" label="Haplotype mode"/> </inputs> <outputs> <data format="fastqsanger" name="outputSingleReads"/> <data format="fastqsanger" name="outputPEFirst"/> <data format="fastqsanger" name="outputPESecond"/> <data format="text" name="outputMutations"/> </outputs> <help> This tools simulate reads from a given fasta file. For more information, please see https://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation </help> </tool>