<tool id="modifyFasta" name="modify fasta">
  <description>Extend or shring a list of sequences.</description>
  <command interpreter="python"> ../Java/Python/modifyFasta.py -i $inputFile 
  	#if $OptionStart.start == "Yes":
			-s $OptionStart.startValue
  	#end if
  	
  	#if $OptionEnd.end == "Yes":
			-e $OptionEnd.endValue
  	#end if
  	-o $outputFile  
  
  </command>
  
  
  <inputs>
    <param name="inputFile" type="data" label="Input fasta File" format="fasta"/>
	<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="startValue" 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="endValue" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
	</conditional>   
  </inputs>

  <outputs>
    <data format="fasta" name="outputFile" label="[modifyFasta] Output File"/>
  </outputs>

  <help>
  </help>
</tool>