Hi Helena,
Thanks for your efforts.
Seems to work (somehow it worked only after resetting my venv).
I also tested it for the tool I want to wrap :)
Just an idea: making
`python examples/example-sub.py foo --generate_galaxy_xml` `python examples/example-sub.py bar --generate_galaxy_xml` ...
work, could be handy to create xml files for each subparser.
Anyway, thanks a lot.
Best, Matthias
On 28.05.2018 18:23, H. Rasche wrote:
I've published version 0.4.4 which should fix that. Please upgrade and let me know.
For now all of the output will be in a single (invalid, no single root element) XML file that will have multiple tools concatenated together.
Cheers, Helena
On 2018-05-28, Matthias Bernt wrote:
Hi Helena,
got it running, but I struggling with subparsers (the tools that I try to wrap basically only uses subparsers .. a lot of them). I adapted the example.py in your repo to include a subparser which seems to be excluded from the xml.
I call `python example.py --generate_galaxy_xml`
since `python example.py sub --generate_galaxy_xml` seems not to work.
Any suggestions?
Best, Matthias
On 28.05.2018 10:02, H. Rasche wrote:
Hey Matthias,
And let me know if you have any questions or bugs!
There are a couple of things it won't do, but if you're looking to get 90% of the way from python script to tool interface, it will do that. It won't get you the last 10% of nice repeat blocks and sections and all of the things that help make galaxy tools more user-friendly. But this can still be a huge time savings
Cheers, Helena (@erasche)
On 2018-05-28, Björn Grüning wrote:
Hi Matthias,
check this one out: https://github.com/erasche/argparse2tool
Cheers, Bjoern
Am 28.05.2018 um 09:43 schrieb Matthias Bernt:
Dear list,
just a question for advice: I plan to wrap a python script (with lots of options) which uses the argparse library. I was wondering if somebody has an idea to generate the tool xml (semi-)automatically? For instance, by subclassing the formatter, parsing the python code, or parsing the command line...
Cheers, Matthias
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Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
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# /usr/bin/python3 import argparse
parser = argparse.ArgumentParser(description='Process some integers.', prefix_chars='-+', epilog="here's some epilog text", formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('keyword', metavar='Q', type=str, nargs=1, help='action keyword')
parser.add_argument('integers', metavar='N', type=int, nargs='+', help='an integer for the accumulator')
parser.add_argument('--sum', '-s', dest='accumulate', action='store_const', const=sum, default=max, help='sum the integers (default: find the max)')
parser.add_argument('--foo', nargs='?', help='foo help') parser.add_argument('--bar', nargs='*', default=[1, 2, 3], help='BAR!') parser.add_argument('--true', action='store_true', help='Store a true') parser.add_argument('--false', action='store_false', help='Store a false') parser.add_argument('--append', action='append', help='Append a value')
parser.add_argument('--nargs2', nargs=2, help='nargs2')
parser.add_argument('--mode', choices=['rock', 'paper', 'scissors'], default='scissors')
parser.add_argument('--version', action='version', version='2.0')
subparsers = parser.add_subparsers() subparser = subparsers.add_parser('sub', help='test subparser') subparser.add_argument('keyword', type=str) subparser.add_argument('--subtrue', action='store_true', help='Store a true')
args = parser.parse_args()