name: "taxpasta_standardise"
description: "Standardise the output of a wide range of taxonomic profilers"
keywords:
  - taxonomic profile
  - standardise
  - standardisation
  - metagenomics
  - taxonomic profiling
  - otu tables
  - taxon tables
tools:
  - "taxpasta":
      description: "TAXonomic Profile Aggregation and STAndardisation"
      homepage: "https://taxpasta.readthedocs.io/"
      documentation: "https://taxpasta.readthedocs.io/"
      tool_dev_url: "https://github.com/taxprofiler/taxpasta"

      licence: "['Apache-2.0']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - profile:
      type: file
      description: profiler output file (mandatory)
      pattern: "*"
  - taxonomy:
      type: directory
      description: Directory containing at a minimum nodes.dmp and names.dmp files (optional)
      pattern: "*/"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - standardised_profile:
      type: file
      description: Standardised taxonomic profile
      pattern: "*.{tsv,csv,arrow,parquet,biom}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@Midnighter"
