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.goecks@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.