name: "kmcp_profile"
description: Generate taxonomic profile from search results
keywords:
  - metagenomics
  - classify
  - taxonomic profiling
  - fastq
  - sequences
  - kmers
  - index
tools:
  - "kmcp":
      description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping"
      homepage: "https://github.com/shenwei356/kmcp"
      documentation: "https://bioinf.shenwei.me/kmcp/usage/#profile"
      tool_dev_url: "https://github.com/shenwei356/kmcp"
      doi: "10.1093/bioinformatics/btac845"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - db:
      type: directory
      description: Database directory containing taxdump files and taxid file
  - search_results:
      type: file
      description: Gzipped file output from kmcp search module
      pattern: "*.gz"
  - mode:
      type: integer
      description: Profiling mode.
        0-pathogen detection
        1-higher recall
        2-high recall
        3-default
        4-high precision
        5-higher precision
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"
  - profile:
      type: file
      description: Tab-delimited format file with 17 columns.
      pattern: "*.profile"

authors:
  - "@sofstam"
