I feel this must be simple, but I cannot find it.

I'm making a wrapper for a tool that requires the output directory to be specified on the command line of a python script (otherwise it uses the path of the input file for the multiple output files). How can I pass the working directory to the tool from the xml file?

<command interpreter="python"> -o $DIRECTORY_WHERE_GALAXY_RUNS_THE_TOOL

This is similar to from_work_dir in the outputs -- but I need the path of the directory that does not include any file names.


Todd Oakley, UCSB
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