<commit_before>Feature: A CLI to run biobox-compatible Docker containers

  Scenario Outline: Getting help documentation
    When I run the command:
      """
      biobox <cmd>
      """
    Then the stderr should be empty
    And the exit code should be 0
    And the stdout should contain
      """
      Usage
      """

    Examples:
      | cmd    |
      | --help |
      | -h     |

  Scenario: Getting help documentation for a biobox type
    When I run the command:
      """
      biobox short_read_assembler --help
      """
    Then the stderr should be empty
    And the exit code should be 0
    And the stdout should contain
      """
      biobox short_read_assembler <container> [options]
      """

  Scenario Outline: Trying to run an unknown container type
    When I run the command:
      """<commit_msg>Fix feature test for updated output<commit_after>Feature: A CLI to run biobox-compatible Docker containers

  Scenario Outline: Getting help documentation
    When I run the command:
      """
      biobox <cmd>
      """
    Then the stderr should be empty
    And the exit code should be 0
    And the stdout should contain
      """
      Usage
      """

    Examples:
      | cmd    |
      | --help |
      | -h     |

  Scenario: Getting help documentation for a biobox type
    When I run the command:
      """
      biobox short_read_assembler --help
      """
    Then the stderr should be empty
    And the exit code should be 0
    And the stdout should contain
      """
      biobox short_read_assembler <image> [options]
      """

  Scenario Outline: Trying to run an unknown container type
    When I run the command:
      """
{'fraction_non_alphanumeric': 0.06698564593301436, 'fraction_numerical': 0.0023923444976076554, 'mean_word_length': 2.0867158671586714, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2063285', 'n_tokens_mistral': 478, 'n_tokens_neox': 451, 'n_words': 195}