skip to navigation
skip to content

Not Logged In

galaxygetopt 0.9.8

Argparse Wrapper for Galaxy

Package Documentation

You write stuff that looks like this, containing all of the information you would ever need about a tool; options, test cases, metadata

from galaxygetopt.ggo import GalaxyGetOpt as GGO
c = GGO(
    options=[
        ['int', 'An integer parameter', {'required': True, 'validate':
                                         'Int', 'default': 10}],
        ['float', 'A float', {'required': True, 'validate': 'Float',
                              'default': 1e-4}],
        ['string', 'A string value', {'required': True, 'multiple': True,
                                      'default': ['Hello', 'World'],
                                      'validate': 'String'}],

And you get data back in a nice dict

{'int': 40, 'float': '1e-4', 'string': ['Hello', 'World'] }

Known Bugs

Currently there is a known bug in the galaxy XML, under highly specific circumstances. If you define a parameter that is

  • required
  • hidden
  • validate String (probably not a hard req)
  • _galaxy_specific

and expect it to properly generate the value, it will not. See lines 206/207 of galaxygetopt/ggo.py for the current hack I use to get around this.

Other

This library features a number of subclasses of galaxygetopt.parameter.parameter, all of which have myriad numbers of options. In order to brutally test these, I have added a class galaxygetopt/tests/parameter_generator.py which can generate every single possible combination of functional calls, given rules you specify. You can then generate hundreds of objects with different sets of options, which you can filter a subset out and test at will. See that classes’s documentation for more information.

 
File Type Py Version Uploaded on Size
galaxygetopt-0.9.8-py2.7.egg (md5, pgp) Python Egg 2.7 2014-10-09 59KB
galaxygetopt-0.9.8.linux-x86_64.tar.gz (md5, pgp)
built for Linux-3.11.0-23-generic-x86_64-with-glibc2.4
"dumb" binary any 2014-10-09 37KB
galaxygetopt-0.9.8.tar.gz (md5, pgp) Source 2014-10-09 15KB
  • Downloads (All Versions):
  • 66 downloads in the last day
  • 322 downloads in the last week
  • 1206 downloads in the last month