name: anndata_barcodes
description: Module to subset AnnData object to cells with matching barcodes
  from the csv file
keywords:
  - single-cell
  - barcodes
  - anndata
  - subsetting
  - transcriptomics
tools:
  - "anndata":
      description: "An annotated data matrix."
      homepage: "https://anndata.readthedocs.io"
      documentation: "https://anndata.readthedocs.io"
      tool_dev_url: "https://github.com/theislab/anndata"
      doi: "10.21105/joss.04371"
      licence:
        - "BSD-3-clause"
      identifier: biotools:anndata
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - h5ad:
        type: file
        description: Anndata object as H5AD file
        pattern: "*.h5ad"
        ontologies:
          - edam: "http://edamontology.org/format_3590" # HDF5
    - barcodes:
        type: file
        description: |
          CSV file containing barcodes. Barcodes are written in plain text. One column, no header
        pattern: "*.csv"
        ontologies:
          - edam: "http://edamontology.org/format_3752" # CSV
output:
  h5ad:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
          pattern: "*.h5ad"
      - "*.h5ad":
          type: file
          description: |
            AnnData file containing all cells with barcodes that match those in the input barcodes csv file
          pattern: "*.h5ad"
          ontologies:
            - edam: "http://edamontology.org/format_3590" # HDF5
  versions_anndata:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: "http://edamontology.org/format_3750" # YAML
topics:
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: "http://edamontology.org/format_3750"
authors:
  - "@nictru"
  - "@chaochaowong"
  - "@LeonHafner"
maintainers:
  - "@nictru"
  - "@LeonHafner"
