name: fargene
description: tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.
keywords:
  - antibiotic resistance genes
  - ARGs
  - identifier
  - metagenomic
  - contigs
tools:
  - fargene:
      description: Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output
      homepage: https://github.com/fannyhb/fargene
      documentation: https://github.com/fannyhb/fargene
      tool_dev_url: https://github.com/fannyhb/fargene
      doi: ""
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)
      pattern: "*.{fasta}"
  - hmm_model:
      type: string
      description: name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]

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"
  - log:
      type: file
      description: log file
      pattern: "*.{log}"
  - txt:
      type: file
      description: analysis summary text file
      pattern: "*.{txt}"
  - hmm:
      type: file
      description: output from hmmsearch
      pattern: "*.{out}"
  - orfs:
      type: file
      description: open reading frames (ORFs)
      pattern: "*.{fasta}"
  - orfs_amino:
      type: file
      description: protein translation of open reading frames (ORFs)
      pattern: "*.{fasta}"
  - contigs:
      type: file
      description: (complete) contigs that passed the final full-length classification
      pattern: "*.{fasta}"
  - contigs_pept:
      type: file
      description: parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences
      pattern: "*.{fasta}"
  - filtered:
      type: file
      description: sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene
      pattern: "*.{fasta}"
  - filtered_pept:
      type: file
      description: sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located
      pattern: "*.{fasta}"
  - fragments:
      type: file
      description: All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files
      pattern: "*.{fastq}"
  - trimmed:
      type: file
      description: The quality controlled retrieved fragments from each input file.
      pattern: "*.{fasta}"
  - spades:
      type: directory
      description: The output from the SPAdes assembly
      pattern: "spades_assembly"
  - metagenome:
      type: file
      description: The FASTQ to FASTA converted input files from metagenomic reads.
      pattern: "*.{fasta}"
  - tmp:
      type: file
      description: The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used.
      pattern: "*.{fasta}"

authors:
  - "@louperelo"