| Previous changeset 0:1f7032731f66 (2011-08-14) |
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Commit message:
Uploaded |
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added:
dwgsim_wrapper.xml |
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| diff -r 1f7032731f66 -r 512671604bab dwgsim_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dwgsim_wrapper.xml Sun Aug 14 20:08:09 2011 -0400 |
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| @@ -0,0 +1,84 @@ +<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> |