name: "amplify_predict"
description: AMPlify is an attentive deep learning model for antimicrobial peptide prediction.
keywords:
  - antimicrobial peptides
  - AMPs
  - prediction
  - model
tools:
  - "amplify":
      description: "Attentive deep learning model for antimicrobial peptide prediction"
      homepage: "https://github.com/bcgsc/AMPlify"
      documentation: "https://github.com/bcgsc/AMPlify"
      tool_dev_url: "https://github.com/bcgsc/AMPlify"
      doi: "https://doi.org/10.1186/s12864-022-08310-4"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - faa:
      type: file
      description: amino acid sequences fasta
      pattern: "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}"
  - model_dir:
      type: directory
      description: Directory of where models are stored (optional)

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"
  - tsv:
      type: file
      description: amino acid sequences with prediction (AMP, non-AMP) and probability scores
      pattern: "*.{tsv}"

authors:
  - "@louperelo"
