- name: bactopia-citations_help
  command: bash -c 'bin/bactopia/bactopia-citations.py --help > bactopia-citations.txt'
  tags:
    - bactopia
    - bactopia_help
    - bactopia_citations
  files:
    - path: bactopia-citations.txt
      contains: ['name', 'bactopia', 'citations', 'exit']

- name: bactopia-citation
  command: bash -c 'bin/bactopia/bactopia --citation > bactopia-citation.txt'
  tags:
    - bactopia
    - bactopia_subcommands
    - bactopia_citations
  files:
    - path: bactopia-citation.txt
      contains: ['Petit', 'Read', 'mSystems', 'pipeline']

- name: bactopia-citation2
  command: bash -c 'bin/bactopia/bactopia citation > bactopia-citation.txt'
  tags:
    - bactopia
    - bactopia_subcommands
    - bactopia_citations
  files:
    - path: bactopia-citation.txt
      contains: ['Petit', 'Read', 'mSystems', 'pipeline']

- name: bactopia-citations
  command: bash -c 'bin/bactopia/bactopia-citations.py --bactopia ./ > bactopia-citations.txt'
  tags:
    - bactopia
    - bactopia_subcommands
    - bactopia_citations
  files:
    - path: bactopia-citations.txt
      contains: ['Petit', 'Seemann', 'annotator', 'staphopia-sccmec']

- name: bactopia-citations_single
  command: bash -c 'bin/bactopia/bactopia-citations.py --bactopia ./ --name staphopiasccmec > bactopia-citations.txt'
  tags:
    - bactopia
    - bactopia_subcommands
    - bactopia_citations
  files:
    - path: bactopia-citations.txt
      contains: ['Petit', 'Read', 'Staphylococcus', 'PeerJ']
