name: "tiara_tiara"
description: Domain-level classification of contigs to bacterial, archaeal, eukaryotic, or organelle
keywords:
  - contigs
  - metagenomics
  - classify
tools:
  - "tiara":
      description: "Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch."
      homepage: "https://ibe-uw.github.io/tiara/"
      documentation: https://ibe-uw.github.io/tiara/"
      tool_dev_url: "https://github.com/ibe-uw/tiara"
      doi: "10.1093/bioinformatics/btab672"
      licence: "MIT"

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

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - classifications:
      type: file
      description: TSV file containing per-contig classification probabilities and overall classifications. Gzipped if flag --gz is set.
      pattern: "*.{txt,txt.gz}"
  - log:
      type: file
      description: Log file containing tiara model parameters. Gzipped if flag --gz is set.
      pattern: "log_*.{txt,txt.gz}"
  - fasta:
      type: file
      description: |
        (optional) - fasta files for each domain category specified in command flag `-tf`, containing classified contigs
      pattern: "*.{fasta,fasta.gz}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@prototaxites"
