name: "vsearch_cluster"
description: Cluster sequences using a single-pass, greedy centroid-based clustering
  algorithm.
keywords:
  - vsearch
  - clustering
  - microbiome
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
      documentation: https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf
      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' ]
    - fasta:
        type: file
        description: Sequences to cluster in FASTA format
        pattern: "*.{fasta,fa,fasta.gz,fa.gz}"
output:
  - aln:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.aln.gz":
          type: file
          description: Results in pairwise alignment format
          pattern: "*.aln.gz"
  - biom:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.biom.gz":
          type: file
          description: Results in an OTU table in the biom version 1.0 file format
          pattern: "*.biom.gz"
  - mothur:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.mothur.tsv.gz":
          type: file
          description: Results in an OTU table in the mothur ’shared’ tab-separated plain
            text file format
          pattern: "*.mothur.tsv.gz"
  - otu:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.otu.tsv.gz":
          type: file
          description: Results in an OTU table in the classic tab-separated plain text
            format
          pattern: "*.otu.tsv.gz"
  - bam:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.bam":
          type: file
          description: Results written in bam format
          pattern: "*.bam"
  - out:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.out.tsv.gz":
          type: file
          description: Results in tab-separated output, columns defined by user
          pattern: "*.out.tsv.gz"
  - blast:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.blast.tsv.gz":
          type: file
          description: Tab delimited results in blast-like tabular format
          pattern: "*.blast.tsv.gz"
  - uc:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.uc.tsv.gz":
          type: file
          description: Tab delimited results in a uclust-like format with 10 columns
          pattern: "*.uc.gz"
  - centroids:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.centroids.fasta.gz":
          type: file
          description: Centroid sequences in FASTA format
          pattern: "*.centroids.fasta.gz"
  - clusters:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.clusters.fasta*.gz":
          type: file
          description: Clustered sequences in FASTA format
          pattern: "*.clusters.fasta*.gz"
  - profile:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.profile.txt.gz":
          type: file
          description: Profile of the clustering results
          pattern: "*.profile.txt.gz"
  - msa:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.msa.fasta.gz":
          type: file
          description: Multiple sequence alignment of the centroids
          pattern: "*.msa.fasta.gz"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@mirpedrol"
maintainers:
  - "@mirpedrol"
