It works !!!
I've changed the extension of output file of an application.
But in Galaxy, it's referenced over the old file with .dat in history, so if we want to re-use this file with other tool it's not the best way to change this extension after the run of tool.
If I could change the extension before the chargement in history, that would be perfect.
But I suppose it's not possible.
I'm already satisfied of the possibility I've discover with the modification of xml files.

Thank you for your help
Julie

2012/5/24 Peter Cock <p.j.a.cock@googlemail.com>
On Thu, May 24, 2012 at 3:27 PM, julie dubois <dubjulie@gmail.com> wrote:
> 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

Well, yes, if you do this at the command line:

cmdA; cmdB

then cmdA is executed before cmdB.

Try it yourself at the Unix/Linux prompt, e.g.

date; ls

compared to:

ls; date

If you want to run it first, try putting your script BEFORE the existing
entry in the tool XML's <command> tag.

Peter