Ok I've tried to add my script perl in the command line with semi-colon.
It's work
But this script sets in entry the variable $wigoutput of my file xml. But
when I show it, it's not what I want; It's just the value : 1 .
I think it's because the script of the application (macs) is called before
my script, the $wigoutput doesn't contain the good value when it stops.
It is what I think, it's not possible to change the extension.

Thank you for your attention and your answers
Julie

2012/5/24 Jeremy Goecks <jeremy.goe...@emory.edu>

>
> > Thank you Jeremy,
> > you answered partially. I would like insert a command, to launch my
> script, in the script or in the xml files of my tools to force it to change
> the extension of output files.
> > But it seems impossible because my command perl after the command of
> tool's script doesn't work in xml file.
>
> The key thing to know is that Galaxy creates a single command line when
> running a tool, not a script. So, to add your command to a tool, you could
> try adding a semi-colon as a separator and then your command. E.g.
>
> ...; python my_prog.py [inputs]
>
>
> Best,
> J.
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