# File lib/miga/cli/action/preproc_wf.rb, line 11 def parse_cli default_opts_for_wf cli.defaults = { mytaxa: false } cli.parse do |opt| opt.on( '-i', '--input-type STRING', '(Mandatory) Type of input data, one of the following:', *MiGA::Cli::Action::Add.INPUT_TYPES.map { |k, v| "~ #{k}: #{v[0]}" } ) { |v| cli[:input_type] = v.downcase.to_sym } opt.on( '-m', '--mytaxa_scan', 'Perform MyTaxa scan analysis' ) { |v| cli[:mytaxa] = v } opts_for_wf(opt, 'Input files as defined by --input-type', multi: true, cleanup: false, ncbi: false) end end
# File lib/miga/cli/action/preproc_wf.rb, line 29 def perform # Input data cli.ensure_par(input_type: '-i') p_metadata = Hash[ %w[project_stats haai_distances aai_distances ani_distances clade_finding] .map { |i| ["run_#{i}", false] } ] d_metadata = { run_distances: false } unless cli[:mytaxa] d_metadata[:run_mytaxa_scan] = false d_metadata[:run_mytaxa] = false end p = create_project(cli[:input_type], p_metadata, d_metadata) # Run run_daemon summarize end