lib/miga/cli/action/gtdb_get.rb
# frozen_string_literal: true
require 'miga/cli/action'
class MiGA::Cli::Action::GtdbGet < MiGA::Cli::Action
require 'miga/cli/action/download/gtdb'
include MiGA::Cli::Action::Download::Gtdb
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
end