ENH: Adds transformer for AMRFinderPlusAnnotationsDirFmt to qiime2.Metadata

[VinzentRisch]

solves #99

• Adds new transformer from AMRFinderPlusAnnotationsDirFmt to qiime2.Metadata.
• Now all output files by amrfinderplus actions can be used with metadata tabulate

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/102/head:pr-102
git checkout pr-102
pip install -e .

2. Download test files
   PR-102.zip

3. Test it out!

qiime metadata tabulate --m-input-file amr_all_mutations_contigs.qza --o-visualization amr_all_mutations_contigs.qzv
qiime metadata tabulate --m-input-file amr_all_mutations_feature.qza --o-visualization amr_all_mutations_feature.qzv
qiime metadata tabulate --m-input-file amr_all_mutations_sample_mags.qza --o-visualization amr_all_mutations_sample_mags.qzv
qiime metadata tabulate --m-input-file amr_annotations_contigs.qza --o-visualization amr_annotations_contigs.qzv
qiime metadata tabulate --m-input-file amr_annotations_feature.qza --o-visualization amr_annotations_feature.qzv
qiime metadata tabulate --m-input-file amr_annotations_sample_mags.qza --o-visualization amr_annotations_sample_mags.qzv

4. open them with

qiime tools view amr_annotations_sample_mags.qzv