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[WIP]: changes that accumulate during working on checkm parsers #65

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[WIP]: changes that accumulate during working on checkm parsers #65

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Commits on Jul 29, 2020

  1. subparsers that are parents become macros 

    - implement output to dir (--directory) to output separate tool
  per subparser
- prepare to include global macro file (for including
  requirements, citations, help, ...)
    @bernt-matthias
    bernt-matthias committed Jul 29, 2020
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  2. install galaxyxml from branch 

    corresponding to hexylena/galaxyxml#18
    @bernt-matthias
    bernt-matthias committed Jul 29, 2020
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  3. adapt travis test for submodules 

    - output to dir, diff dirs, planemo dir
    @bernt-matthias
    bernt-matthias committed Jul 29, 2020
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  4. switch to py3.7 for testing 

    since dicts (and hopefully also attributes) are ordered
    @bernt-matthias
    bernt-matthias committed Jul 29, 2020
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  5. update example.py

    @bernt-matthias
    bernt-matthias committed Jul 29, 2020
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  6. extend example-sub for parent parsers

    @bernt-matthias
    bernt-matthias committed Jul 29, 2020
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  7. beautify tool name and id 

    - remove '.py' extension if existent
- replace '-' by '_'
- for id: replace ' ' by '_'

also overwrite tool xml files (wo warning)
    @bernt-matthias
    bernt-matthias committed Jul 29, 2020
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  8. fix prog/tool naming issues

    @bernt-matthias
    bernt-matthias committed Jul 29, 2020
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Commits on Dec 22, 2020

  1. create sections from Groups create elements from _actions

    @bernt-matthias
    bernt-matthias committed Dec 22, 2020
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  2. Merge branch 'master' into topic/improvements_for_checkm

    @bernt-matthias
    bernt-matthias authored Dec 22, 2020
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Commits on Dec 23, 2020

  1. update travis

    @bernt-matthias
    bernt-matthias committed Dec 23, 2020
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  2. Merge branch 'topic/improvements_for_checkm' of https://github.com/be… 

    …rnt-matthias/argparse2tool into topic/improvements_for_checkm
    @bernt-matthias
    bernt-matthias committed Dec 23, 2020
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  3. update travis flake exceptions

    @bernt-matthias
    bernt-matthias committed Dec 23, 2020
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  4. fix whitespace on empty line

    @bernt-matthias
    bernt-matthias committed Dec 23, 2020
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  5. adapt tests for macros

    @bernt-matthias
    bernt-matthias committed Dec 23, 2020
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  6. allow to use multiple global macro files 

    and test cleanup
    @bernt-matthias
    bernt-matthias committed Dec 23, 2020
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  7. fixes to make output parameters work

    @bernt-matthias
    bernt-matthias committed Dec 23, 2020
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Commits on Jan 4, 2021

  1. fix typo in argument help

    @bernt-matthias
    bernt-matthias committed Jan 4, 2021
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  2. copy macros to destination

    @bernt-matthias
    bernt-matthias committed Jan 4, 2021
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Commits on Jan 5, 2021

  1. remove debug statements

    @bernt-matthias
    bernt-matthias committed Jan 5, 2021
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  2. travis fixes

    @bernt-matthias
    bernt-matthias committed Jan 5, 2021
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  3. use basename of macros in xml import 

    if directory is specified.
    @bernt-matthias
    bernt-matthias committed Jan 5, 2021
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  4. add missing actions 

    - print error message if parameter can not be translated
- cwl: implement StoreConst, Help, and Version actions
- xml: implement HelpAction
    @bernt-matthias
    bernt-matthias committed Jan 5, 2021
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Commits on Feb 8, 2021

  1. just my latest changes

    @bernt-matthias
    bernt-matthias committed Feb 8, 2021
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  2. differentiate parents handling for galaxy xml

    @bernt-matthias
    bernt-matthias committed Feb 8, 2021
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