name: deeparg_predict
description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
keywords:
  - deeparg
  - antimicrobial resistance
  - antimicrobial resistance genes
  - arg
  - deep learning
  - prediction
  - contigs
  - metagenomes
tools:
  - deeparg:
      description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
      homepage: https://bench.cs.vt.edu/deeparg
      documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
      tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
      doi: "10.1186/s40168-018-0401-z"
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: FASTA file containing gene-like sequences
      pattern: "*.{fasta,fa,fna}"
  - model:
      type: string
      description: Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively
      pattern: "LS|LS"
  - db:
      type: directory
      description: Path to a directory containing the deepARG pre-built models
      pattern: "*/"

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"
  - daa:
      type: file
      description: Sequences of ARG-like sequences from DIAMOND alignment
      pattern: "*.align.daa"
  - daa_tsv:
      type: file
      description: Alignments scores against ARG-like sequences from DIAMOND alignment
      pattern: "*.align.daa.tsv"
  - arg:
      type: file
      description: Table containing sequences with an ARG-like probability of more than specified thresholds
      pattern: "*.mapping.ARG"
  - potential_arg:
      type: file
      description: Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection
      pattern: "*.mapping.potential.ARG"

authors:
  - "@jfy133"