<tool id="trimSequences" name="trim sequences">
  <description>Remove the 5' and/or 3' adaptors of a list of reads.</description>
  <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
  	#if $OptionFPADP.FPADP == "Yes":
		-5 $OptionFPADP.fivePAdaptor
	#end if	  
	 #if $OptionTPADP.TPADP == "Yes":
		-3 $OptionTPADP.threePAdaptor
	#end if	
  	#if $OptionError.Error == "Yes":
		-e $OptionError.ErrorVal
	#end if	

	$indels
  	$noAdaptor5p $noAdaptorFile5p
  	$noAdaptor3p $noAdaptorFile3p
  	-o $outputFile  
  
  </command>
  
  
  <inputs>
    <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
	
	<conditional name="OptionFPADP">
		<param name="FPADP" type="select" label="5'adaptor">
			<option value="Yes">Yes</option>
			<option value="No" selected="true">No</option>
		</param>
		<when value="Yes">
			<param name="fivePAdaptor" type="text" value="None" />
		</when>
		<when value="No">
		</when>
	</conditional>	
	
	<conditional name="OptionTPADP">
		<param name="TPADP" type="select" label="3'adaptor">
			<option value="Yes">Yes</option>
			<option value="No" selected="true">No</option>
		</param>
		<when value="Yes">
			<param name="threePAdaptor" type="text" value="None" />
		</when>
		<when value="No">
		</when>
	</conditional>
	
	<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="indels" type="boolean" truevalue="-d" falsevalue="" checked="false" label="indels option" help="also accept indels"/>
	<param name="noAdaptor5p" type="boolean" truevalue="-n" falsevalue="" checked="false" label="noAdaptor 5' option" help="file name where to print sequences with no 5' adaptor "/>
	<param name="noAdaptor3p" type="boolean" truevalue="-m" falsevalue="" checked="false" label="noAdaptor 3' option" help="file name where to print sequences with no 3' adaptor "/>
	
	
	
  </inputs>

  <outputs>
    <data format="fastq" name="outputFile" label="[trimSequences] Output File"/>
	<data name="noAdaptorFile5p" format="fastq" label="[trimSequences] noAdaptor5p File">
		<filter>noAdaptor5p</filter>
	</data>
	<data name="noAdaptorFile3p" format="fastq" label="[trimSequences] noAdaptor3p File">
		<filter>noAdaptor3p</filter>
	</data>
  </outputs>

  <help>
  </help>
  <tests>
	<test>
 		<param name="inputFile" value="short_fastq.fastq" />
 		<param name="FPADP" value="Yes"/>
      		<param name="fivePAdaptor" value="AAAA" />
		<param name="TPADP" value="No"/>
      		<param name ="Error" value="No"/>
		<param name="indels" value="False"/>
      		<param name ="noAdaptor5p" value="False"/>
		<param name= "noAdaptor3p" value="False"/>
      		<output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
	</test>
  </tests>
</tool>