<tool id="trimAdaptor" name="trim adaptors">
  <description>Remove the 3' adaptor of a list of reads.</description>
  <command interpreter="python"> ../Java/Python/trimAdaptor.py -i $inputFile -f fastq
  	-a $adaptor
  	#if $OptionError.Error == "Yes":
		-e $OptionError.ErrorVal
	#end if	
  	$noAdaptor $noAdaptorFile
  	-o $outputFile  
  </command>
  
  
  <inputs>
    <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
	<param name="adaptor" type="text" value="None" label="adaptor [compulsory option]"/> 
	<conditional name="OptionError">
		<param name="Error" type="select" label="number of errors in percent">
			<option value="Yes">Yes</option>
			<option value="No" selected="true">No</option>
		</param>
		<when value="Yes">
			<param name="ErrorVal" type="integer" value="0" />
		</when>
		<when value="No">
		</when>
	</conditional>	
	<param name="noAdaptor" type="boolean" truevalue="-n" falsevalue="" checked="false" label="log option" help="file name where to print sequences with no adaptor"/>
  </inputs>

  <outputs>
    <data format="fastq" name="outputFile" label="[trimAdaptor] Output File"/>
	<data name="noAdaptorFile" format="fastq" label="[trimAdaptor] Log File">
		<filter>noAdaptor</filter>
	</data>
  </outputs>
  <tests>
    <test>
      <param name="inputFile" value="short_fastq.fastq" />
      <param name="adaptor" value="AAAA" />
      <param name ="Error" value="No"/>
      <param name ="noAdaptor" value="False"/>
      <output name="outputFile" file="exp_trimadaptator_short_fastq.fastq" />     
    </test>
  </tests>
  <help>
  </help>
</tool>