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.
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
File details
Details for the file galaxygetopt-0.9.5.tar.gz.
File metadata
- Download URL: galaxygetopt-0.9.5.tar.gz
- Upload date:
- Size: 16.1 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 24754eb929c0c4161687b904e3c570ff6c8ee01b07e3151b540144c442df8347 |
|
| MD5 | 3bf393e3cf7daeb9b90d795b72b03bb7 |
|
| BLAKE2b-256 | 623b6a2e34ceb22b8e69bbad03a6fb4abeae5c4b07a5b4743108ff2ebc1f06f2 |
File details
Details for the file galaxygetopt-0.9.5.linux-x86_64.tar.gz.
File metadata
- Download URL: galaxygetopt-0.9.5.linux-x86_64.tar.gz
- Upload date:
- Size: 37.6 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | b106fe37dee72527091e9eba7b8f28705eeb0108512bd39388ab147c9eecd0c8 |
|
| MD5 | 03860062977f8cbae8e5809b09b82ad8 |
|
| BLAKE2b-256 | b012ae510a8c4091ac0e2ca1d0e7cf9a9dea6abcd62a6f4a388ab4364c8ef50d |
File details
Details for the file galaxygetopt-0.9.5-py2.7.egg.
File metadata
- Download URL: galaxygetopt-0.9.5-py2.7.egg
- Upload date:
- Size: 59.9 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | b700942853e00d03aff4e4812ef50c891740b2546c11321d7c1cc01eba1c99d9 |
|
| MD5 | 7402bcf10b1a8a9cdcac37c62494037d |
|
| BLAKE2b-256 | 759870cd8e019087ead96202aabf826f5658ef4c92eff8a1a6dacd1fabcb033e |
