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 <[email protected]> > On Sun, Nov 18, 2012 at 1:13 PM, Christophe Antoniewski > <[email protected]> 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. > -- ¡ Note that my email address has changed ! ¡ Please update your records with ! ¡ *[email protected]*<[email protected]>! -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org
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