name: macrel_contigs
description: A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.
keywords:
  - AMP
  - antimicrobial peptides
  - genome mining
  - metagenomes
  - peptide prediction
tools:
  - macrel:
      description: A pipeline for AMP (antimicrobial peptide) prediction
      homepage: https://macrel.readthedocs.io/en/latest/
      documentation: https://macrel.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/BigDataBiology/macrel
      doi: "10.7717/peerj.10555"
      licence: ['MIT']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: A fasta file with nucleotide sequences.
      pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}"

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"
  - amp_prediction:
      type: file
      description: A zipped file, with all predicted amps in a table format.
      pattern: "*.prediction.gz"
  - smorfs:
      type: file
      description: A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.
      pattern: "*.smorfs.faa.gz"
  - all_orfs:
      type: file
      description: A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.
      pattern: "*.all_orfs.faa.gz"
  - readme_file:
      type: file
      description: A readme file containing tool specific information (e.g. citations, details about the output, etc.).
      pattern: "*.md"
  - log_file:
      type: file
      description: A log file containing the information pertaining to the run.
      pattern: "*_log.txt"

authors:
  - "@darcy220606"