CMD_example

python3 amplicon_pipeline.py --featureTable test_data/feature_table.tsv --phylogenyTree test_data/rooted_amplicons.tree.txt --amplicons test_data/amplicons.faa --MiBIGAmplicons databases/parsed_AMP_MIBIG.faa --antismashDBAmplicons databases/parsed_AMP_antismashdb2.faa --metagenomeAmplicons databases/parsed_AMP_metagenome.faa --parsedAsdbGenbank --parsedAsdbGenbank databases/asdb_parsed_product_list.txt --MiBIGOutputDir out/mibig/ --antismashOutputDir out/asdb/ --metagenomeOutputDir out/metagenome/ --outputDir out/test/ --parsedTaxonomy databases/antismashdb2_taxa_dict.txt --sampleNames S01,S02,S03 --replicateList S01_1,S01_2,S01_3,S02_1,S02_2,S02_3,S03_1,S03_2,S03_3