<tool id="seedGff" name="seedGff">
  <description>Creates the seed from -15 to -25 bp before ATG</description>
  <command interpreter="perl"> seedGff.pl -i $inputFile -p $startPosFromAtg -e $endPosSeed
    #if $optionSeedSize.seedSize == "Yes":
        -l $optionSeedSize.seedLength
    #end if
    -o $outputFile
  </command>
  <inputs>
    <param name="inputFile" type="data" label="Input File" format="gff"/>
    <param name="startPosFromAtg" type="integer" value="25" help="greather positive number for the start position of the seed from Atg "/>
    <param name="endPosSeed" type="integer" value="15" help="end of the seed (smaller than the sart of the seed, positive number)"/>
    <conditional name="optionSeedSize">
			<param name="seedSize" type="select" label="The length of seed." help="If you have choosed the value of start/end position of seed, you don't need to fill this option.">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="seedLength" type="integer" value="4" label="The length of seed, default: 4nt" />
			</when>
			<when value="No">
			</when>
    </conditional>
    

  </inputs>

  <outputs>
    <data format="gff" name="outputFile" label="[seedGff] Output File"/>
  </outputs>

  <help>
	command example: perl seedGff.pl -i input_annot.gff -p 25 -e 15 -o output_cis_seed.gff
  </help>
</tool>