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.