Updated autoBIGS tool

[RealYHD]

Simply lowers the minimum Galaxy version that should be required to run this tool.

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[SaimMomin12]

Failed linting
.. 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[autobigs-cli]
mode.absent.fasta
Field required [type=missing, input_value={}, input_type=dict]]
.. WARNING (TestsCaseValidation): Test 2: 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[autobigs-cli]
mode.absent.fasta
Field required [type=missing, input_value={}, input_type=dict]]
.. WARNING (TestsCaseValidation): Test 3: 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[autobigs-cli]
mode.absent.fasta
Field required [type=missing, input_value={}, input_type=dict]]
.. WARNING (TestsCaseValidation): Test 4: 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[autobigs-cli]
mode.absent.fasta
Field required [type=missing, input_value={}, input_type=dict]]
.. WARNING (TestsCaseValidation): Test 5: 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[autobigs-cli]
mode.absent.fasta

[SaimMomin12]

@RealYHD Please add .lint_skip file with TestsCaseValidation as its contents (For Eg. https://github.com/galaxyproject/tools-iuc/blob/4fde0bb4e8badcb215d1e8ee0bc787c3b98b6958/tools/mcl/.lint_skip)

[bernt-matthias]

The from_url feature has been introduced only in 24.0 galaxyproject/galaxy#17087

So I think this should be the minimal version, or is the tool still usable in older galaxy versions?

[nilchia]

@RealYHD in the test specify the conditional

            <param name="operation" value="st" />
            <param name="fasta" value="tohama_I_bpertussis_minimized_features.fasta" />
            <param name="scheme" value="MLST"

to

            <conditional name="mode">
                <param name="operation" value="st" />
                <param name="fasta" value="tohama_I_bpertussis_minimized_features.fasta" />
                <param name="scheme" value="MLST" />
            </conditional>

[RealYHD]

The from_url feature has been introduced only in 24.0 galaxyproject/galaxy#17087

So I think this should be the minimal version, or is the tool still usable in older galaxy versions?

Hi @bernt-matthias, thanks for that catch. Unfortunately, no, it would no longer be usable. I will need to change a few of the inputs. I did not see this listed on the tool XML changelogs, hence my lapse in judgement. I should have, and will be more careful going forward. As a side note, this may be a good addition to the list of behaviour changes? 😛

Thank you everyone for your very helpful input. I've converted this PR into a draft as this turned out to be a much more complicated change than I initially thought. I will work on these items and mark it as ready for review after more thorough testing.

[bernt-matthias]

I will need to change a few of the inputs.

How? What would be your idea?

As a side note, this may be a good addition to the list of behaviour changes?

If we would include every new feature in this list, it would cover most of the Galaxy's changelog. This list is about changed behavior only (so called profile versions where we change Galaxy's behavior depending on tool version).