<tool id="filler" name="Filler" version="1.0.0">
    <description>Filler Function to deal with paired collection</description>
    <command interpreter="python"><![CDATA[
      filler.py 
        #if str( $data_input.data_selector ) == "paired"       
          -i $data_input.input1.forward.element_identifier      
        #end if
        #if str( $data_input.data_selector ) == "single"       
          -i "$data_input.input2.element_identifier"
        #end if
        
        -o $output
    ]]></command>
    <inputs>
      <conditional name="data_input">
        <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset">
          <option value="paired">Paired</option>
          <option value="single">Single</option>
        </param>
        <when value="paired">
          <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
        </when>
        <when value="single">
          <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
        </when>
      </conditional>
    </inputs>
    <outputs>
        <data name="output" type="data_collection"/>
    </outputs>
    <help>
This tool processes the PRINCE galaxy output such that it is in line with the command line
    </help>
    <citations>
    </citations>
</tool>