On Tue, Jun 7, 2011 at 10:56 AM, Mariette <jmari...@toulouse.inra.fr> wrote:
>
> Thanks for the answer,
> Still considering the number of outputed files problem. In my script I know
> that if
> a cleaning option is set 2 other files will be created, so I check if the
> option is asked by the
> user and try this :
>
>  <outputs>
>   <data name="log" format="txt" />
>   #if $clean_pairends.clean_pairends_select=="y":
>       <data name="output" format="input"/>
>   #end if
>  </outputs>
>
> but this is not working ... there is a way to do what I want ?
> thx
> Jerome

The #if stuff is Cheetah syntax, and only applies within the <command>
tag - not to the XML file in general.

You probably want a conditional output using <when>, see:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax

Peter

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