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? Regards, Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
