On Thu, May 24, 2012 at 1:54 PM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
>Julie wrote:
>> 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]

Could multiple <command> entries be flagged as an error in the loader?
That would have helped with Julie's first attempt.

Alternatively, could we have a DTD file for the wrappers to use, and then
an XML editor would be able to spot this kind of mistake?


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