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<tool id="dwgsim" name="Generate simulated reads" version="1.1.0">
<description>from a fasta sequence using dwgsim</description>
<command interpreter="python">
#if $outputFormat.splitOutput == "two" #dwgsim_wrapper.py \
-4 $outputPEFirst \
-5 $outputPESecond \
#else if $outputFormat.splitOutput == "one" #dwgsim_wrapper.py \
-3 $outputSingleReads \
#else #dwgsim_wrapper.py \
-3 $outputSingleReads \
-4 $outputPEFirst \
-5 $outputPESecond \
#end if
-6 $outputMutations \
-e $eRateFirstread \
-E $eRateSecondread \
-d $innerDist \
-s $stDev \
-N $noReadpairs \
-1 $loFirstread \
-2 $loSecondread \
-r $rateOfMut \
-R $rateOfIndels \
-X $probExtRead \
-y $probRandRead \
-n $maxN \
-S $strandDirection \
-c $platform.platformType \
#if $platform.platformType == "2" #
-f $platform.flowOrder
#end if
$haploMode \
-O $outputFormat.splitOutput \
-i $input \
</command>
<inputs>
<param format="fasta" name="input" type="data" label="Select fasta file to generate reads from"/>
<conditional name="platform">
<param name="platformType" type="select" label="Select the platform to simulate reads for">
<option value="0" selected="True">Illumina</option>
<option value="1" >SOLiD (Color space)</option>
<option value="2" >Ion Torrent</option>
</param>
<when value="0"/>
<when value="1"/>
<when value="2">
<param name="flowOrder" type="text" size="12" value="2">
<label> Flow order for Ion Torrent data </label>
</param>
</when>
</conditional>
<conditional name="outputFormat">
<param name="splitOutput" type="select" label="Output mate reads in">
<option value="two" selected="True">Two separate files</option>
<option value="one" >In a single file (~bfast)</option>
<option value="all" >Both output options</option>
</param>
<when value="two"/>
<when value="one"/>
<when value="all"/>
</conditional>
<param name="noReadpairs" size="12" type="text" value="1000000">
<label>number of read pairs</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="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 on the inner distance between two ends</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 mutations that are 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="maxN" size="4" type="text" value="0">
<label>maximum number of Ns allowed in a given read</label>
</param>
<param name="strandDirection" type="select" label="Direction of strand (default: opposite strand for Illumina, same strand for SOLiD?Ion Torrent)">
<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" label="Simulated reads from ${on_string}">
<filter>(outputFormat['splitOutput'] == 'one') | (outputFormat['splitOutput'] == 'all')</filter>
</data>
<data format="fastqsanger" name="outputPEFirst" label="Simulated forw reads from ${on_string}">
<filter>(outputFormat['splitOutput'] == 'two') | (outputFormat['splitOutput'] == 'all') </filter>
</data>
<data format="fastqsanger" name="outputPESecond" label="Simulated rev reads from ${on_string}">
<filter>(outputFormat['splitOutput'] == 'two') | (outputFormat['splitOutput'] == 'all')</filter>
</data>
<data format="text" name="outputMutations" label="Mutation report of reads from ${on_string}"/>
</outputs>
<help>
This tool 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>
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