This is the galaxy wrapper I am trying to write a unit test for: https://github.com/elmbeech/physicelldataloader/blob/galaxy/pcdl/pcdl_get_version.xml
Using planemo test pcdl_get_version.xml --update_test_data, the unit test passes flawless.
Using planemo lint pcdl_get_version.xml I get a warning and the linting fails.
(pcdlenv) bb8@milleniumfalcon:~/physicelldataloader/pcdl$ planemo lint pcdl_get_version.xml
Linting tool /home/bb8/physicelldataloader/pcdl/pcdl_get_version.xml
.. WARNING (TestsCaseValidation): Test 1: failed to validate test parameters against inputs - tests won't run on a modern Galaxy tool profile version. Validation errors are [1 validation error for PydanticModelFor[pcdl_get_version]
positional_arguments.path
Field required [type=missing, input_value={}, input_type=dict]]
.. CHECK (TestsNoValid): 1 test(s) found.
.. INFO (OutputsNumber): 1 outputs found.
.. INFO (InputsNum): Found 2 input parameters.
.. CHECK (HelpPresent): Tool contains help section.
.. CHECK (HelpValidRST): Help contains valid reStructuredText.
.. CHECK (ToolIDValid): Tool defines an id [pcdl_get_version].
.. CHECK (ToolNameValid): Tool defines a name [pcdl_get_version].
.. CHECK (ToolProfileValid): Tool specifies profile version [21.05].
.. CHECK (ToolVersionValid): Tool defines a version [3.0.0+galaxy0].
.. INFO (CommandInfo): Tool contains a command.
.. CHECK (CitationsFound): Found 1 citations.
Failed linting
I tried to add the missing fields, searched all the documents, greped, and googled for hours to figure out what I have to change to get rid of this warning and pass the liniting too. Without success. I am sure this is a piece of cake for a seasoned galaxy developer.
Could you please point me in the right direction?
Thank you, Elmar
Hi @bb-8,
the error is rather cryptic indeed
Maybe try to specify the galaxy datatypes for all your test collection elements with ftype="txt" for example inside each element tag.
Just a guess though.
That test is not valid, collection is not valid inside a param tag, so as far as the galaxy test framework is concerned you haven’t provided anything to section.path. Galaxy Tool XML File — Galaxy Project 25.1.dev0 documentation is how you specify an output collection test.
