Change <filter>paired == "Y"</filter> to <filter>paired is True</filter> Cheers Michael ;-) Am 09.08.2010 16:23, schrieb Davide Cittaro:

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"> <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

/* Davide Cittaro

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

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

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