casts = []
casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'scaffold', :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'metagenome', :short=>'m', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>false, :default=>25, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>false, :default=>50, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'count_min', :short=>'c', :type=>'uint', :mandatory=>false, :default=>2, :allowed=>nil, :disallowed=>nil}
commands = []
commands << "nice -n 19"
- commands << "idba"
+
+ if options[:metagenome]
+ commands << "metaidba"
+ else
+ commands << "idba"
+ end
+
commands << "--read #{file_fasta}"
commands << "--output #{prefix}"
commands << "--scaffold" if options[:scaffold]