INPUT_FILTER and FILTER_PATTERNS have differing functionality.  I can give INPUT_FILTER a string containing a command and its arguments, but when I try to set FILTER_PATTERN to do the same, doxygen is unable to run the command.

For example, I can have:

INPUT_FILTER = "doxypy.py --autobrief"

and the filter if found and run.

But since doxypy.py only filters Python files, I'd like to have

FILTER_PATTERNS = *.py="doxypy.py --autobrief"

But Doxygen can't parse that properly.  Instead, I get the error message:

sh: doxypy.py --autobrief: command not found

If I remove the command-line argument ("--autobrief"), the filter is found and run without errors.