<tool id="PileupVariant" name="PileupVariant" version="1.10">
<description>Keep only mpileup line with variant</description>
<command interpreter="perl">
  #if $exclude.do=="YES"
	PileupVariant.pl -input_pileup_file $input_pileup_file -input_exclusion_file $input_exclusion_file -log_file $log_file > $output_pileup_file 
  #else
        PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file 
  #end if
  
</command>
<inputs>
	<param name="input_pileup_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
	<conditional name="exclude">
	  <param name="do" type="select" label="Exclude some position">
	    <option value="NO">NO</option>
	    <option value="YES">YES</option>
	  </param>
	  <when value="YES">
		<param name="input_exclusion_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
	  </when>
	  <when value="NO">
	    
	  </when>
	</conditional> 
</inputs>
<outputs>
	<data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/>
	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>	
</outputs>

<help>



</help>
</tool>