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 > >>> > >>___________________________________________________________ > >>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.be...@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() ___________________________________________________________ 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/
