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 <james@jamestaylor.org>
On Sun, Nov 18, 2012 at 1:13 PM, Christophe Antoniewski
<drosofff@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
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