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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 (SOLiD only)"/>
<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>
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