> 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]

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