Class: MiGA::Cli::Action::IndexWf

Inherits:
MiGA::Cli::Action show all
Includes:
Wf
Defined in:
lib/miga/cli/action/index_wf.rb

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Attributes included from MiGA::Common::Net

#remote_connection_uri

Instance Method Summary collapse

Methods included from Wf

#call_cli, #cleanup, #create_project, #default_opts_for_wf, #download_datasets, #import_datasets, #initialize_empty_project, #opts_for_wf, #opts_for_wf_distances, #run_daemon, #summarize, #transfer_metadata

Methods inherited from MiGA::Cli::Action

#complete, #empty_action, #initialize, #launch, load, #name

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from MiGA::Common::Net

#download_file_ftp, #http_request, #known_hosts, #main_server, #net_method, #normalize_encoding, #remote_connection

Methods included from MiGA::Common::SystemCall

#run_cmd, #run_cmd_opts

Constructor Details

This class inherits a constructor from MiGA::Cli::Action

Instance Method Details

#parse_cli ⇒ Object 



10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
 
# File 'lib/miga/cli/action/index_wf.rb', line 10

def parse_cli
  default_opts_for_wf
  cli.defaults = { mytaxa: false }
  cli.parse do |opt|
    opt.on(
      '-m', '--mytaxa-scan',
      'Perform MyTaxa scan analysis'
    ) { |v| cli[:mytaxa] = v }
    opts_for_wf_distances(opt)
    opts_for_wf(
      opt, 'Input genome assemblies (nucleotides, FastA)',
      cleanup: false, project_type: true
    )
  end
end

#perform ⇒ Object 



26
27
28
29
30
31
32
33
 
# File 'lib/miga/cli/action/index_wf.rb', line 26

def perform
  # Input data
  p = create_project(:assembly, {}, run_mytaxa_scan: cli[:mytaxa])

  # Run
  run_daemon
  summarize
end