ENH: Action to annotate MAGs and contigs with AMRFinderPlus

[VinzentRisch]

solves #87

Adds new action that can annotate MAGs and contigs.

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/87/head:pr-87
git checkout pr-87
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" --p-report-all-equal --p-coverage-min 0.4 --p-translation-table "11"
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" --p-report-all-equal --p-coverage-min 0.4 --p-translation-table "11"

[ChristosMatzoros]

@VinzentRisch it works as expected! Have a look at my comments for some minor changes.

[ChristosMatzoros]

@VinzentRisch , seems good to me!