name: "vsearch_usearchglobal"
description: Compare target sequences to fasta-formatted query sequences using global
  pairwise alignment.
keywords:
  - vsearch
  - usearch
  - alignment
  - fasta
tools:
  - "vsearch":
      description: "VSEARCH is a versatile open-source tool for microbiome analysis,
        including chimera detection, clustering, dereplication and rereplication, extraction,
        FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction
        site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification
        of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH
        alternative)"
      homepage: "https://github.com/torognes/vsearch"
      tool_dev_url: "https://github.com/torognes/vsearch"
      doi: "10.7717/peerj.2584"
      licence: ["GPL v3-or-later OR BSD-2-clause"]
      identifier: biotools:vsearch
input:
  - - meta:
        type: map
        description: Groovy Map containing sample information e.g. [ id:'test' ]
    - queryfasta:
        type: file
        description: Query sequences in FASTA format
        pattern: "*.{fasta,fa,fna,faa}"
  - - db:
        type: file
        description: Reference database file in FASTA or UDB format
        pattern: "*"
  - - idcutoff:
        type: float
        description: Reject the sequence match if the pairwise identity is lower than
          the given id cutoff value (value ranging from 0.0 to 1.0 included)
  - - outoption:
        type: string
        description: Specify the type of output file to be generated by selecting one
          of the vsearch output file options
        pattern: "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout"
  - - user_columns:
        type: string
        description: If using the `userout` option, specify which columns to include
          in output, with fields separated with `+` (e.g. query+target+id). See USEARCH
          manual for valid options. For other output options, use an empty string.
output:
  - aln:
      - meta:
          type: file
          description: Results in pairwise alignment format
          pattern: "*.{aln}"
      - "*.aln":
          type: file
          description: Results in pairwise alignment format
          pattern: "*.{aln}"
  - biom:
      - meta:
          type: file
          description: Results in an OTU table in the biom version 1.0 file format
          pattern: "*.{biom}"
      - "*.biom":
          type: file
          description: Results in an OTU table in the biom version 1.0 file format
          pattern: "*.{biom}"
  - lca:
      - meta:
          type: file
          description: Last common ancestor (LCA) information about the hits of each query
            in tab-separated format
          pattern: "*.{lca}"
      - "*.lca":
          type: file
          description: Last common ancestor (LCA) information about the hits of each query
            in tab-separated format
          pattern: "*.{lca}"
  - mothur:
      - meta:
          type: file
          description: Results in an OTU table in the mothur ’shared’ tab-separated plain
            text file format
          pattern: "*.{mothur}"
      - "*.mothur":
          type: file
          description: Results in an OTU table in the mothur ’shared’ tab-separated plain
            text file format
          pattern: "*.{mothur}"
  - otu:
      - meta:
          type: file
          description: Results in an OTU table in the classic tab-separated plain text
            format
          pattern: "*.{otu}"
      - "*.otu":
          type: file
          description: Results in an OTU table in the classic tab-separated plain text
            format
          pattern: "*.{otu}"
  - sam:
      - meta:
          type: file
          description: Results written in sam format
          pattern: "*.{sam}"
      - "*.sam":
          type: file
          description: Results written in sam format
          pattern: "*.{sam}"
  - tsv:
      - meta:
          type: file
          description: Results in tab-separated output, columns defined by user
          pattern: "*.{tsv}"
      - "*.tsv":
          type: file
          description: Results in tab-separated output, columns defined by user
          pattern: "*.{tsv}"
  - txt:
      - meta:
          type: file
          description: Tab delimited results in blast-like tabular format
          pattern: "*.{txt}"
      - "*.txt":
          type: file
          description: Tab delimited results in blast-like tabular format
          pattern: "*.{txt}"
  - uc:
      - meta:
          type: file
          description: Tab delimited results in a uclust-like format with 10 columns
          pattern: "*.{uc}"
      - "*.uc":
          type: file
          description: Tab delimited results in a uclust-like format with 10 columns
          pattern: "*.{uc}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@jtangrot"
maintainers:
  - "@jtangrot"
