Mercurial > repos > nilshomer > dwgsim_eval
comparison dwgsim_eval_wrapper.xml @ 1:eb58ceeedfba default tip
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| author | nilshomer |
|---|---|
| date | Sun, 14 Aug 2011 20:09:02 -0400 |
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| 0:ed05f8167910 | 1:eb58ceeedfba |
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| 1 <tool id="dwgsim" name="Evaluate simulated reads" version="1.0.0"> | |
| 2 <description>from a SAM/BAM file using dwgsim_eval</description> | |
| 3 <command interpreter="python"> | |
| 4 if 'sam' == input.ext: | |
| 5 dwgsim_wrapper.py \ | |
| 6 $alignmentScore \ | |
| 7 $bwa \ | |
| 8 $colorSpace \ | |
| 9 -d $scoreFactor \ | |
| 10 -g $wiggle \ | |
| 11 -n $numReads \ | |
| 12 -q $minMapq \ | |
| 13 $singleEnd \ | |
| 14 $printIncorrect \ | |
| 15 -s $numSnps \ | |
| 16 -e $numErrors \ | |
| 17 $indels \ | |
| 18 -s $input \ | |
| 19 -o $output | |
| 20 else: | |
| 21 dwgsim_wrapper.py \ | |
| 22 $alignmentScore \ | |
| 23 $bwa \ | |
| 24 $colorSpace \ | |
| 25 -d $scoreFactor \ | |
| 26 -g $wiggle \ | |
| 27 -n $numReads \ | |
| 28 -q $minMapq \ | |
| 29 $singleEnd \ | |
| 30 $printIncorrect \ | |
| 31 -s $numSnps \ | |
| 32 -e $numErrors \ | |
| 33 $indels \ | |
| 34 -b $input \ | |
| 35 -o $output | |
| 36 | |
| 37 </command> | |
| 38 <inputs> | |
| 39 <param format="sam,bam" name="input" type="data" label="SAM/BAM file to evaluate"/> | |
| 40 <param name="alignmentScore" type="boolean" truevalue="-a" falsevalue="" checked="False" label="split alignments by alignment score instead of mapping quality"/> | |
| 41 <param name="bwa" type="boolean" truevalue="-b" falsevalue="" checked="False" label="alignments are from BWA"/> | |
| 42 <param name="colorSpace" type="boolean" truevalue="-c" falsevalue="" checked="False" label="color space alignments"/> | |
| 43 <param name="scoreFactor" size="4" type="text" value="1"> | |
| 44 <label>divide quality/alignment score by this factor</label> | |
| 45 </param> | |
| 46 <param name="wiggle" size="4" type="text" value="5"> | |
| 47 <label>gap "wiggle"</label> | |
| 48 </param> | |
| 49 <param name="numReads" size="4" type="text" value="-1"> | |
| 50 <label>number of raw input paired-end reads (otherwise, inferred from all SAM records present)</label> | |
| 51 </param> | |
| 52 <param name="minMapq" size="4" type="text" value="0"> | |
| 53 <label>consider only alignments with this mapping quality or greater</label> | |
| 54 </param> | |
| 55 <param name="singleEnd" type="boolean" truevalue="-z" falsevalue="" checked="False" label="input contains only single end reads"/> | |
| 56 <param name="printIncorrect" type="boolean" truevalue="-p" falsevalue="" checked="False" label="print incorrect alignments"/> | |
| 57 <param name="numSnps" size="4" type="text" value="-1"> | |
| 58 <label>consider only alignments with the number of specified SNPs</label> | |
| 59 </param> | |
| 60 <param name="numErrors" size="4" type="text" value="-1"> | |
| 61 <label>consider only alignments with the number of specified errors</label> | |
| 62 </param> | |
| 63 <param name="indels" type="boolean" truevalue="-i" falsevalue="" checked="False" label="consider only alignments with indels"/> | |
| 64 </inputs> | |
| 65 <outputs> | |
| 66 <data format="text" name="output"/> | |
| 67 </outputs> | |
| 68 | |
| 69 <help> | |
| 70 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 | |
| 71 </help> | |
| 72 | |
| 73 </tool> |