<tool id="srf2fastq" name="SRF to FASTQ">

  <description>conversion</description>

  <command interpreter="sh">srf2fastq.sh $input1 $filter $paired $out_file1 $out_file2

  </command>

  <inputs>

    <param name="input1" type="data" format="srf" label="Select SRF Archive"/>

    <param name="filter" label="Filter out bad reads (QC fail)?" type="boolean" truevalue="Y" falsevalue="N" selected="True"/>

    <param name="paired" label="Is this Paired-end run?" type="boolean" truevalue="Y" falsevalue="N" selected="False"/>

  </inputs>

  <outputs>

      <data format="fastqillumina" name="out_file1"/>

      <data format="fastqillumina" name="out_file2">

         <filter>paired == "Y"</filter>

      </data>

  </outputs>

[…]

</tool>

According to the wiki pages, this syntax should enable the out_file2 if the "paired" checkbox is clicked... Unfortunately I always have the tool running as the checkbox wasn't checked (i.e. out_file2 is None). If I change the filter condition to paired=="N" I always have the tool running with two outputs...

Can anybody help me?

thanks

d