<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>