ENH: Add three new parameters to run_amrfinderplus_n

[VinzentRisch]

solves #96

Adds three new parameters to run_amrfinderplus_n. Two of those can be used with the action annotate_sample_data_amrfinderplus.

Set up an environment

https://github.com/bokulich-lab/q2-amr?tab=readme-ov-file#installation

Run it locally

1. First, clone the repo and checkout the PR branch:

git clone https://github.com/bokulich-lab/q2-amr.git
cd q2-amr
git fetch origin pull/97/head:pr-97
git checkout pr-97
pip install -e .

2. Download test files
   PR-88.zip

3. Test it out!

qiime amr fetch-amrfinderplus-db --o-amrfinderplus-db amrfinderplus_db.qza 
qiime amr annotate-sample-data-amrfinderplus --i-sequences test_mags.qza --output-dir output_mags --i-amrfinderplus-db amrfinderplus_db.qza --p-plus --p-curated-ident --p-organism "Escherichia_coli_Shigella" --p-report-all-equal --p-coverage-min 0.4 --p-translation-table "11" --p-gpipe-org True --p-report-common
qiime amr annotate-sample-data-amrfinderplus --i-sequences test_contigs.qza --output-dir output_contigs --i-amrfinderplus-db amrfinderplus_db.qza --p-plus --p-curated-ident --p-organism "Escherichia_coli_Shigella" --p-report-all-equal --p-coverage-min 0.4 --p-translation-table "11" --p-gpipe-org True --p-report-common

[VinzentRisch]

@misialq could you have a look at the added typemap in this PR.
so i want to have different choices for one parameter depending if one parameter is true or false
And i have this. I saw that placeholder type with _ and Int in moshpit, but there it also says it is using Int because visualizations dont have types so Im not sure if i should be doing it like this.

P_gpipe_org, P_organism, _ = TypeMap(
    {
        (Bool % Choices(True), Str % Choices(organisms_gpipe)): Int,
        (Bool % Choices(False), Str % Choices(organisms)): Int,
    }
)

Also this leads to the parameter gpipe_org not behaving like a bool parameter anymore. So it is not possible to just put --p-gpipe-org but you have to give it a value of eighter True or False. Is this the normal behaviour because I use Bool % Choices(True)? Or is there a better solution?

[misialq]

Hey @VinzentRisch, I think it's fine for the Int as a placeholder - you are not using it after all. For the boolean, though, I'm not sure if there is a better way - we have it like this somewhere in MOSHPIT and Santiago spent some time exploring this (ending up with a solution like yours) but maybe we could ask tomorrow just to be sure?

[ChristosMatzoros]

Hi @VinzentRisch,

Runs as expected with no errors and code looks good. See a minor change to make and after that we are set to merge.

[VinzentRisch]

Thanks for the review, added the full stop :)