| Previous changeset 0:ed05f8167910 (2011-08-14) |
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Commit message:
Uploaded |
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added:
dwgsim_eval_wrapper.xml |
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| diff -r ed05f8167910 -r eb58ceeedfba dwgsim_eval_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dwgsim_eval_wrapper.xml Sun Aug 14 20:09:02 2011 -0400 |
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| @@ -0,0 +1,73 @@ +<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> |