drop in replacement for argparse with Galaxy XML generation on the side
Python
Latest commit f57b4a8 Feb 7, 2017 @erasche committed on GitHub Merge pull request #42 from hmenager/patch-3
correct foo parameter type

README.rst

argparse2tool

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This project aims to be a drop-in replacement for argparse which allows generating Galaxy XML and CWL Tools.

It is quite literally a drop-in replacement. You (or the upstream tool author) can use argparse completely as normal

import argparse

When this package is installed, with its argparse module ahead of the system argparse, argparse2tool will capture all argparse function calls, and process them specially.

This information captured in this process is used to produce Galaxy Tool XML when it's requested with the --generate_galaxy_xml flag, or CWL Tools when requested with the --generate_cwl_tool flag.

For our example python script you can see the generated Galaxy XML and CWL Tools.

Running

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

$ <tool command> --generate_galaxy_xml <other options> > tool.xml
$ <tool command> --generate_cwl_tool <other options> > tool.cwl

The project inclues 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.

$ python example.py --generate_galaxy_xml
$ python example.py --generate_cwl_tool

CWL Specific Functionality

Example for CNVkit toolkit

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

If there are subcommands in the provided command, all possible tools will be generated, for instance, for CNVkit

$ cnvkit.py --generate_cwl_tool

will produce CWL tool descriptions for cnvkit.py batch, cnvkit.py access, cnvkit.py export bed, cnvkit.py export cdt and all other subcommands.

Other options (which work only with --generate_cwl_tool provided, except for help message) are:

  • -o FILENAME, --output_section FILENAME: File with manually filled output section which is put to a formed CWL tool. argparse2tool is not very good at generating outputs, it recognizes output files only if they have type argparse.FileType('w'), so output section is often blank and should be filled manually.

  • -go, --generate_outputs: flag for generating outputs not only from arguments that are instances of argparse.FileType('w'), but also from every argument which contains output keyword in its name. For instance, argument --output-file with no type will also be placed to output section. However, '--output-directory' argument will also be treated like File, so generated tools must be checked carefully if when this option is selected.

  • -b, basecommand: command which appears in basecommand field in a resulting tool. It is handy to use this option when you run tool with shebang, but want python to be in basecommand field and the file amidst arguments. Example:

    $ .search.py --generate_cwl_tool -b python.

Basecommand of the formed tool will be ['python'], and search will be a positional argument on position 0.

  • -d, --directory: directory for storing tool descriptions.
  • --help_arg2cwl: prints this help message.

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.

NB: Please do not install this system-wide. It may have bugs which could break your python installation. Please only install this in a virtualenv.

To easily correct this, run the tool argparse2tool_check_path which is installed as part of this package. Correctly functioning paths will produce the following:

$ argparse2tool_check_path
Ready to go!

while incorrectly ordered paths will produce a helpful error message:

$ argparse2tool_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=$(argparse2tool_check_path -q) 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