fubar2 / galaxyxml

XML Generation libraries for Galaxy Tool/ToolDeps XML

Galaxy XML Generation Libraries

These libraries will support building of Tool XML and Tool Dependencies XML. We'd be happy to support any other XML that Galaxy supports, just make an issue or PR if you're feeling motivated.

Known Bugs

• no validation of unique names
• repeats aren't named properly
• conditional/whens aren't named properly
• conditionals not handled in CLI

License

• Apache License, v2

Changelog

• 0.5.2
  • Debugging Build
• 0.5.1
  • Debugging Build
• 0.5.0
  • Added support for toolprofile (@fubar2)
  • Removed default stdio addition (@fubar2)
  • Github Actions (@bernt-matthias)
• 0.4.14
  • Fix for TestRepeats (@fubar2)
• 0.4.13
  • Add TestOutputCollection, TestRepeat and tests (thanks @fubar2)
• 0.4.12
  • Correct the ordering of elements for planemo (thanks @fubar2)
  • Properly read stdio on loading tools (thanks @fubar2)
• 0.4.11
  • Update to command line override (thanks @fubar2)
• 0.4.10
  • Allow overriding of command line in support of positional args (thanks @fubar2)
• 0.4.9
  • Fix quoting of text params (thanks @fubar2!)
• 0.4.8
  • Fix travis deploy process
  • Fix testing
  • py36 only
• 0.4.6
  • Deprecate py2
  • Wrap version command in CDATA
• 0.4.5
  • Bug fixes:
    • Write catched error to logger instead of STDOUT
    • Fix Travis: install xmllint
    • Fix Travis: Deal with new flake8 restrictions for exceptions
• 0.4.3
  • Bug fixes:
    • Allow <discover_dataset> within <data> in <outputs>
    • Allow import of existing XML with no description
• 0.4.2
  • Add methods to check presence of EDAM and citations (thanks @khillion)
• 0.4.0
  • Add feature to import existing Galaxy xml
• 0.3.3
  • @khillion implemented the following:
    • <options> with <filter> and <column>
    • <container> for <requirements>
    • Started to add <tests> section
    • <section> in <inputs>
    • <collection> with <discover_datasets> in <outputs>
  • Please note that tool.parameters.OutputParam() has been changed to tool.parameters.OutputData()
• 0.3.2
  • configfiles (#8)
• 0.3.0
  • Travis auto-deploys on new tags
  • Testing
  • p3k
• 0.2.3
  • First widely used/stable version