Thanks this is what I was looking for !!
I succeded to make it work when checking the value on a simple param using the name like this

<inputs>
<param name="qual_file" type="data" format="qual" optional="true" label="Quality reads file (if input is a fasta)" />
</input>
...
<outputs>
<data name="out_qual" format="qual">
     <filter>qual_file != None</filter>
</data>
</outputs>

however when I'm in a conditional tag like this, I tryed :

<inputs>
<conditional name="clean_pairends">
<param name="clean_pairends_select" type="select" label="Clean pairends">
          <option value="y">Yes</option>
          <option selected="true" value="n">No</option>
    </param>
    <when value="y">
<param name="border_limit" type="integer" size="10" value="70" label="Minimal length between the spacer and the read extremity"/> <param name="missmatch" type="integer" size="10" value="10" label="Limit of missmatch"/>
     </when>
     <when value="n">
     </when>
</conditional>
</input>
...
<outputs>
<data name="out_pe_fasta" format="fasta">
      <filter>clean_pairends.clean_pairends_select == "y"</filter>
</data>


but it's not working ... it looks like between filter tag I should provide a python test, am I missing something ?
thx,
Jerome



Peter Cock a écrit :
On Tue, Jun 7, 2011 at 11:38 AM, Mariette <jmari...@toulouse.inra.fr> wrote:
I can only see the usage of the <when> tag into the <outputs>
to change format, is that correct ?


On re-reading the wiki page, yes, I think you are right. I should have
said <filter> with <data>, as in tools/filters/sff_extractor.xml

Peter
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