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 >

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/

Hi Matthias, 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. Yeah, I never implemented support for subparsers. What sort of XML would you expect that to output? I think, to me, it feels like it should output multiple tool XMLs, one for each subparser. > 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()

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.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()