class MiGA::Cli::Action::GtdbGet

def parse_cli
  cli.defaults = {
    query: false, unlink: false,
    reference: false, add_version: true, dry: false,
    get_md: false, only_md: false, save_every: 1
  }
  cli.parse do |opt|
    cli.opt_object(opt, [:project])
    opt.on(
      '-T', '--taxon STRING',
      '(Mandatory) Taxon name in GTDB format (e.g., g__Escherichia)'
    ) { |v| cli[:taxon] = v }
    cli_base_flags(opt)
    opt.on(
      '--ncbi-taxonomy',
      'Retrieve NCBI taxonomy instead of GTDB taxonomy'
    ) { |v| cli[:get_ncbi_taxonomy] = v }
    cli_task_flags(opt)
    cli_name_modifiers(opt)
    cli_filters(opt)
    cli_save_actions(opt)
    opt.on(
      '--ncbi-api-key STRING',
      'NCBI API key'
    ) { |v| ENV['NCBI_API_KEY'] = v }
  end
end

def perform
  generic_perform
end