Hi all,
Apparently I cannot have the <filter> tag working for outputs in the small tool I'm wrinting:

<tool id="srf2fastq" name="SRF to FASTQ">
  <command interpreter="sh">srf2fastq.sh $input1 $filter $paired $out_file1 $out_file2
    <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"/>
      <data format="fastqillumina" name="out_file1"/>
      <data format="fastqillumina" name="out_file2">
         <filter>paired == "Y"</filter>

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?



Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano

tel.: +39(02)574303007
e-mail: davide.cittaro@ifom-ieo-campus.it