argparse2tool 0.4.9

Running

To generate XML or CWL, run your tool with the appropriate command line flag

$ PYTHONPATH=$(argparse2tool) <tool command> --generate_galaxy_xml <other options> > tool.xml
$ PYTHONPATH=$(argparse2tool) <tool command> --generate_cwl_tool <other options> > tool.cwl

The project includes a sample example.py file which uses as many argparse features as possible. CWL and Galaxy XML support different portions feature sets which will be visible in the generated outputs.

$ PYTHONPATH=$(argparse2tool) python example.py --generate_galaxy_xml
$ PYTHONPATH=$(argparse2tool) python example.py --generate_cwl_tool

$ cnvkit.py batch --generate_cwl_tool -d ~/cnvkit-tools/ --generate_outputs

$ cnvkit.py --generate_cwl_tool

How it works

Internally, argparse2tool, 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, argparse2tool captures the details of those calls and when Tool XML or CWL is requested, it builds up the tool definition and prints it out to standard output.

Examples

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.

It doesn’t work!!

If you are not able to use the --generate_galaxy_xml/--generate_cwl_tool flags after installing, it is probably because of module load order. argparse2tool must precede argparse in the path.

To easily correct this, run the tool argparse2tool which is installed as part of this package. Correctly functioning paths will produce the following:

$ argparse2tool
PATH_TO_THE_DROPINS

while incorrectly ordered paths will produce a helpful error message:

$ argparse2tool
no dropins dir...

This is intended to be used inline:

user@host:$ PYTHONPATH=$(argparse2tool) python my_script.py --generate_galaxy_xml

Limitations

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)

• argparse2tool Galaxy XML Output

  • support declaring output files in an argparse-esque manner

• argparse2tool CWL Output

  • Some of argparse features can not be ported to CWL.

    1. nargs=N. Number of arguments can not be specified in CWL (yet).

    2. const argument of add_argument(). All constants must be specified in job files.

    3. Custom types and custom actions are not supported.

    4. Argument groups don’t work in CWL as arguments are sorted with a special algorithm

    5. Mutual exclusion is not supported.

License

Apache License, v2