name: "entrezdirect_xtract"
description: Queries an NCBI database using an UID
keywords:
  - public datasets
  - entrez
  - search
  - ncbi
  - database
tools:
  - entrezdirect:
      description: |
        Entrez Direct (EDirect) is a method for accessing the NCBI's set of
        interconnected databases (publication, sequence, structure, gene,
        variation, expression, etc.) from a UNIX terminal window. Functions
        take search terms from command line arguments. Individual operations
        are combined to build multi-step queries. Record retrieval and
        formatting normally complete the process.
      homepage: https://www.ncbi.nlm.nih.gov/books/NBK179288/
      documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/
      tool_dev_url: https://www.ncbi.nlm.nih.gov/books/NBK25498/
      doi: 10.1016/S0076-6879(96)66012-1
      licence: ["PUBLIC DOMAIN"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - xml_input:
      type: file
      description: XML text file containing query results from database.
  - pattern:
      type: value
      description: String in xml_input that encloses element to search.
  - element:
      type: value
      description: Space-delimited strings that will be converted to columns.
  - sep:
      type: value
      description: Separator/delimiter between columns (for instance "," or "\t").

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"
  - xtract_table:
      type: file
      description: TXT file containing columns searched from element.
      pattern: "*.txt"

authors:
  - "@alxndrdiaz"