Planemo lint will fail current galaxyxml generated tools because the order of sections doesn't match the canonical version in lib/galaxy/tool_util/linters/xml_order.py.
Fixing this first one manually and relinting leads to yet more.
WARNING: Best practice violation [stdio] elements should come before [configfiles]
Pity it wasn't alphabetical order like imported modules in python linters but this is what it currently is....
"""This module contains a linting functions for tool XML block order.
For more information on the IUC standard for XML block order see -
https://github.com/galaxy-iuc/standards.
"""
https://github.com/galaxy-iuc/standards
https://github.com/galaxy-iuc/standards/pull/7/files
TAG_ORDER = [
'description',
'macros',
'parallelism',
'requirements',
'code',
'stdio',
'version_command',
'command',
'environment_variables',
'configfiles',
'inputs',
'outputs',
'tests',
'help',
'citations',
]
Planemo lint will fail current galaxyxml generated tools because the order of sections doesn't match the canonical version in lib/galaxy/tool_util/linters/xml_order.py. Fixing this first one manually and relinting leads to yet more.
WARNING: Best practice violation [stdio] elements should come before [configfiles]
Pity it wasn't alphabetical order like imported modules in python linters but this is what it currently is....