Galaxy argparse aims to be a drop-in replacement for argparse, quite literally. You can write use your normal import

import argparse

and continue writing code. All functions are passed straight through to argparse, but gxargparse captures them and copies some information along the way. This information captured is used to produce Galaxy Tool XML when it's requested with the --generate_galaxy_xml flag.

Internally, gxargparse, masquerading as argparse attempts to find and import the real argparse. It then stores a reference to the code module for the system argparse, and presents the user with all of the functions that stdlib's argparse provides. Every function call is passed through the system argparse. However, gxargparse captures the details of those calls and when Tool XML is requested, it builds up the tool definition according to IUC tool standards.

You can see the example.py file for an example with numerous types of arguments and options that you might see in real tools. Accordingly there is an example.xml file with the output.

If you are not able to use the --generate_galaxy_xml flag after installing, it is probably because of module load order. gxargparse must precede argparse in the path. Certain cases seem to work correctly (python setup.py install in a virtualenv) while other cases do not (pip install gxargparse).

To easily correct this, run the tool gxargparse_check_path which is installed as part of this package. Correctly functioning paths will produce the following:

$ gxargparse_check_path
Ready to go!

while incorrectly ordered paths will produce a helpful error message:

$ gxargparse_check_path
Incorrect ordering, please set

    PYTHONPATH=/home/users/esr/Projects/test/.venv/local/lib/python2.7/site-packages

This can even be used inline:

user@host:$ PYTHONPATH=$(gxargparse_check_path -q) python my_script.py --generate_galaxy_xml

This code doesn't cover the entirety of the argparse API yet, and there are some bugs to work out on the XML generation side:

• argparse
  • groups not supported (in galaxy, everything should still work in argparse)
  • some features like templating of the version string (please submit bugs)
• galaxyxml
  • bugs in conditionals/whens (probably)
  • bugs, bugs, bugs!
• gxargparse
  • support help text
  • support declaring output files in an argparse-esque manner

• Apache License, v2