Re: [galaxy-dev] argparse -> tool xml advice

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 >>> >>___________________________________________________________ >>Please keep all replies on the list by using "reply all" >>in your mail client. To manage your subscriptions to this >>and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >>To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ -- ------------------------------------------- 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(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

# /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()