<tool id="modifySequenceList" name="modify sequence list">
  <description>Extend or shring a list of sequences. </description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
  <command interpreter="python"> ../Java/Python/modifySequenceList.py -i $inputFile -f fasta
	#if $OptionStart.Start == "Yes":
		-s $OptionStart.StartVal
	#end if		
	#if $OptionEnd.End == "Yes":
		-e $OptionEnd.EndVal
	#end if	
  	-o $outputFile  
  </command>
  
  
  <inputs>
	<param name="inputFile" type="data" format="fasta" label="input file"/>

	<conditional name="OptionStart">
		<param name="Start" type="select" label="keep first nucleotides">
			<option value="Yes">Yes</option>
			<option value="No" selected="true">No</option>
		</param>
		<when value="Yes">
			<param name="StartVal" type="integer" value="0" />
		</when>
		<when value="No">
		</when>
	</conditional>
		
	<conditional name="OptionEnd">
		<param name="End" type="select" label="keep last nucleotides">
			<option value="Yes">Yes</option>
			<option value="No" selected="true">No</option>
		</param>
		<when value="Yes">
			<param name="EndVal" type="integer" value="0"/>
		</when>
		<when value="No">
		</when>
	</conditional>	
  </inputs>

  <outputs>
    	<data format="fasta" name="outputFile" label="[modify sequence list] output file"/>
  </outputs>

  <help>
  This tool reads a list of sequences (in multi-FASTA/Q format) that you provide and shrinks each sequence to the *n* first nucleotides or the *n* last nucleotides.
  </help>
</tool>