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.

I think, I will use your first proposition with symbolic links.
Thank you.

2012/5/24 Jeremy Goecks <>

> Is it possible to change this with a simple change in a configuration file
> or in a script file ?
> No, they must be named as is for Galaxy to find them. You could, however,
> create symbolic links to files and use an extension of your choice.
> Or, must I write my owner script, and if yes, how can I configure Galaxy
> so that it launches it automatically  after one application like MACS for
> exemple which have a file configuration : macs.xml in the tools directory?
> Because I've tried to add a line like this in this file :
> <command interpreter ="perl"> mon</command>
> I've placed it after the line <command...> which launches the MACS script,
> but my script seems not work.
> It's not possible to launch Galaxy automatically on local files. You'll
> need to upload the file to Galaxy and run the tool using the uploaded file
> as input.
> Hopefully I answered your question; if not, can be more specific about
> what you're trying to do?
> Best,
> J.
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