Argparse Wrapper for Galaxy
Project description
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.
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