class MiGA::Cli::Action::NcbiGet

# File lib/miga/cli/action/ncbi_get.rb, line 9
def parse_cli
  cli.defaults = {
    query: false, unlink: false,
    reference: false, legacy_name: false,
    complete: false, chromosome: false,
    scaffold: false, contig: 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 (e.g., a species binomial)'
    ) { |v| cli[:taxon] = v }
    cli_base_flags(opt)
    cli_task_flags(opt)
    cli_name_modifiers(opt)
    cli_filters(opt)
    cli_save_actions(opt)
    opt.on(
      '--api-key STRING',
      '::HIDE::' # For backwards compatibility
    ) { |v| ENV['NCBI_API_KEY'] = v }
    opt.on(
      '--ncbi-table-file STRING',
      '::HIDE::' # Only meant for debugging
      # It can take the table returned by NCBI and parse it from a file
      # instead of downloading it directly
    ) { |v| cli[:ncbi_table_file] = v }
    opt.on(
      '--ncbi-api-key STRING',
      'NCBI API key'
    ) { |v| ENV['NCBI_API_KEY'] = v }
  end
end

# File lib/miga/cli/action/ncbi_get.rb, line 45
def perform
  generic_perform
end