name: "ampir" description: A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs. keywords: - ampir - amp - antimicrobial peptide prediction tools: - "ampir": description: "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale." homepage: "https://github.com/Legana/ampir" documentation: "https://cran.r-project.org/web/packages/ampir/index.html" tool_dev_url: "https://github.com/Legana/ampir" doi: "10.1093/bioinformatics/btaa653" licence: ["GPL v2"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - faa: type: file description: FASTA file containing amino acid sequences pattern: "*.{faa,fasta}" - model: type: value description: Built-in model for AMP prediction pattern: "{precursor,mature}" - min_length: type: value description: Minimum protein length for which predictions will be generated pattern: "[0-9]+" - min_probability: type: value description: Cut-off for AMP prediction pattern: "[0-9][0-9]" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - amps_faa: type: file description: File containing AMP predictions in amino acid FASTA format pattern: "*.{faa}" - amps_tsv: type: file description: File containing AMP predictions in TSV format pattern: "*.tsv" authors: - "@jasmezz"