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::'
) { |v| ENV['NCBI_API_KEY'] = v }
opt.on(
'--ncbi-table-file STRING',
'::HIDE::'
) { |v| cli[:ncbi_table_file] = v }
opt.on(
'--ncbi-api-key STRING',
'NCBI API key'
) { |v| ENV['NCBI_API_KEY'] = v }
end
end