lib/mspire/imzml/writer/commandline.rb in mspire-0.7.18 vs lib/mspire/imzml/writer/commandline.rb in mspire-0.8.0

@@ -11,24 +11,26 @@
   end
 end
 
 module Mspire::Imzml::Writer::Commandline
 
-  def self.run(argv, progname=$0)
+  # generates the Trollop parser
+  def self.parser
+    return @parser if @parser
 
     default_config = "config.yaml"
     scan_patterns = %w(flyback meandering random)
     scan_types = %w(horizontal vertical)
     scan_direction = %w(left-right right-left bottom-up top-down none)
     scan_sequence = %w(top-down bottom-up left-right right-left)
     default_dims = '800x600'
     default_pixel_size = '1x1'
     matrix_application_types = %w(sprayed precoated printed drieddroplet)
 
-    parser = Trollop::Parser.new do
+    @parser = Trollop::Parser.new do
       banner <<-EOS
-usage: #{File.basename(progname)} [OPTIONS] <file>.mzML ..."
+usage: mspire to_imzml [OPTIONS] <file>.mzML ..."
 output: <file>.imzML and <file>.ibd
 
 * imzML docs: 
     http://www.maldi-msi.org/index.php?option=com_content&view=article&id=187&Itemid=67
 * explanation of vocabulary (followed here): 
@@ -41,10 +43,13 @@
       opt :print_config, "print current options to #{default_config} and exit"
       opt :omit_zeros, "remove zero values"
       opt :combine, "combine all files and set the base name of resulting imzML and ibd files", :type => String
       opt :outfile, "use a specific basename for the resulting file. Acts like --combine for multiple files", :type => String
 
+      text "\nediting:"
+      opt :trim_files, "determines the least number of spectra in a file and shortens all spectra to be the same length"
+
       text "\nimaging:"
       opt :continuous, "assumes m/z values are the same for every scan. The 'processed' storage format is used unless this flag is given."
       opt :scan_pattern, scan_patterns.join('|'), :default => scan_patterns.first
       opt :scan_type, scan_types.join('|'), :default => scan_types.first
       opt :linescan_direction, scan_direction.join('|'), :default => scan_direction.first
@@ -74,12 +79,19 @@
 
       # things to add: data types for m/z and intensity
       # filters (cutoff / max # peaks, etc.)
       # ms_level, etc.
     end
+  end
 
-    opts = parser.parse(argv)
+  def self.run(argv, globalopts)
+    begin
+      opts = parser.parse(argv)
+    rescue Trollop::HelpNeeded
+      return parser.educate
+    end
+
     opts = Hash[YAML.load_file(opts[:config]).map {|k,v| [k.to_sym, v]}].merge(opts) if opts[:config]
 
     opts[:combine] ||= opts.delete(:outfile)
 
     if opts.delete(:print_config)
@@ -102,8 +114,5 @@
     writer = Mspire::Imzml::Writer.new
     writer.write(argv, opts)
 
   end
 end
-
-
-