<tool id="trimSequences" name="trim sequences">
  <description>Remove the 5' and/or 3' adapters 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	
	-e $errors
	$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' adapter">
			<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' adapter">
			<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>
	
	<param name="errors" type="integer" label="number of errors in percent" value="0" />
	<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' adapter "/>
	<param name="noAdaptor3p" type="boolean" truevalue="-m" falsevalue="" checked="false" label="noAdaptor 3' option" help="file name where to print sequences with no 3' adapter "/>
	
  </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>

  <help>
This function removes the adaptor from the 5' or 3' end of your reads. It can even recognize the adaptators which are partially present. You can specify whether you are ready to accept indels or not.
  </help>
</tool>