name: "taxpasta_merge"
description: Standardise and merge two or more taxonomic profiles into a single table
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 ]
  - profiles:
      type: file
      description: A list of taxonomic profiler output files (typically in text format, mandatory)
      pattern: "*.{tsv,csv,arrow,parquet,biom}"
  - samplesheet:
      type: file
      description:
        A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative
        from the work environment. The profiles must be provided even if you give a samplesheet as argument (optional)
      pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}"
  - 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 ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - merged_profiles:
      type: file
      description: Output file with standardised multiple profiles in one go and have all profiles combined into a single table.
      pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}"

authors:
  - "@sofstam"
  - "@jfy133"
