Yes it is working too, avoiding an additional wrapper.
Yet, strangely enough, the absolute paths are required in the command line:

<command >python /home/galaxy/galaxy-dist/tools/chrisTools/plotter.py
$input $minsize $maxsize $factor $output |bash
/home/galaxy/galaxy-dist/tools/chrisTools/r_wrapper.sh $Rplotter</command>

The galaxy has still some mysteries ;-)

Chris


2012/11/19 James Taylor <ja...@jamestaylor.org>

> On Sun, Nov 18, 2012 at 1:13 PM, Christophe Antoniewski
> <droso...@gmail.com> wrote:
> > but the second script output is empty. I suspect that the second script
> is
> > launched when the output of the first script is not available yet.
>
> I'm pretty sure we do not currently support multiple "command" tags.
> However whatever is in the command text is always run through a shell
> (sh), so you can use pipes and such directly, just don't specify
> interpreter at all:
>
>         <command>python plotter.py $input $minsize $maxsize $factor
> $output | bash r_wrapper.sh $Rplotter</command>
>
> ...should work.
>



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--

Christophe Antoniewski
Drosophila Genetics and Epigenetics
Laboratoire de Biolologie du Développement

9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

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