ms-xcalibur 0.2.0 → 0.3.0

data/History

@@ -1,3 +1,7 @@
+== 0.3.0 / 2009-05-25
+
+* updates to use tap-0.17.0
+
 == 0.2.0 / 2009-03-31
 
 Updated release to use latest tap.  Removed

data/lib/ms/xcalibur/convert/dta_to_mgf.rb

@@ -1,10 +1,11 @@
+require 'tap/tasks/file_task'
 require 'constants'
 
 module Ms
   module Xcalibur
     module Convert
       
-      # :startdoc::manifest convert dta files to mgf format
+      # :startdoc::task convert dta files to mgf format
       #
       # Converts a set of dta files (Sequest format) into an mgf (Mascot format) 
       # file.  By default the mgf file is printed to $stdout, so redirection is
@@ -42,12 +43,12 @@ module Ms
       # calculated from the {constants}[bioactive.rubyforge.org/constants] gem to be 
       # ~ 1.007276 Da
       #
-      class DtaToMgf < Tap::FileTask
+      class DtaToMgf < Tap::Tasks::FileTask
         include Constants::Libraries
 
         # Returns the unrounded mass of a proton (H - e) as calculated
         # from the {constants}[bioactive.rubyforge.org/constants] gem.
-        config :proton_mass, Element['H'].mass - Particle['Electron'].mass, &c.num_or_nil # Specify the proton mass
+        config :proton_mass, Element['H'].mass - Particle['Electron'].mass, &c.numeric_or_nil # Specify the proton mass
         config :output, $stdout, &c.io(:<<, :binmode) # The output file
         
         def process(*dta_files)
@@ -57,7 +58,7 @@ module Ms
             
             log :convert, "#{dta_files.length} dta files"
             dta_files.each do |file|
-              check_terminate
+              app.check_terminate
               lines = File.read(file).split(/\r?\n/)
 
               # get the mh and z
@@ -79,6 +80,7 @@ END IONS
 }
             end
           end
+          output
         end
       end
     end

data/lib/ms/xcalibur/convert/raw_to_dta.rb

@@ -1,8 +1,10 @@
+require 'tap/tasks/file_task'
+
 module Ms
   module Xcalibur
     module Convert
       
-      # :startdoc::manifest convert RAW files to dta format
+      # :startdoc::task convert RAW files to dta format
       #
       # Converts a RAW file to dta files using extract_msn.exe.  Returns an
       # array of the output dta files.  By default extracted files are put
@@ -27,13 +29,13 @@ module Ms
       #
       #   % tap run -- raw_to_dta  --extract_msn_help
       #
-      class RawToDta < Tap::FileTask
+      class RawToDta < Tap::Tasks::FileTask
         config :extract_msn, 'C:\Xcalibur\System\Programs\extract_msn.exe' # The full path to the extract_msn executable
         config :first_scan, nil, :short => :F, &c.integer_or_nil
         config :last_scan, nil, :short => :L, &c.integer_or_nil
-        config :lower_MW, nil, :short => :B, &c.num_or_nil
-        config :upper_MW, nil, :short => :T, &c.num_or_nil
-        config :precursor_mass_tol, 1.4, :short => :M, &c.num
+        config :lower_MW, nil, :short => :B, &c.numeric_or_nil
+        config :upper_MW, nil, :short => :T, &c.numeric_or_nil
+        config :precursor_mass_tol, 1.4, :short => :M, &c.numeric
         config :num_allowed_intermediate_scans_for_grouping, 1, :short => :S, &c.integer
         config :charge_state, nil, :short => :C, &c.integer_or_nil
         config :num_required_group_scans, 1, :short => :G, &c.integer_or_nil
@@ -45,7 +47,7 @@ module Ms
         config :perform_charge_calculations, nil, :short => :K, &c.flag
         config :template_file, nil, :short => :O
         config :options_string, nil, :short => :A
-        config :minimum_signal_to_noise, 3, :short => :R, &c.num
+        config :minimum_signal_to_noise, 3, :short => :R, &c.numeric
         config :minimum_number_of_peaks, 5, :short => :r, &c.integer
         
         config :output_dir, nil, &c.string_or_nil # The output directory

data/lib/ms/xcalibur/peakify.rb

@@ -1,8 +1,9 @@
+require 'tap/tasks/file_task'
 require 'ms/xcalibur/peak_file'
 
 module Ms
   module Xcalibur
-    # :startdoc::manifest adds graph data to an exported peak file
+    # :startdoc::task adds graph data to an exported peak file
     #
     # Peakify adds points to signify the relative intensity (ie the rounded
     # intensity/max_intensity) of peaks to a peak list extracted from Xcalibur
@@ -24,18 +25,18 @@ module Ms
     # Options can be specified to filter out points within a range of relative
     # intensities.
     #
-    class Peakify < Tap::FileTask
+    class Peakify < Tap::Tasks::FileTask
 
       config :point_char, '.'                          # A character used for each intensity point
-      config :min, 0, &c.num                           # Min relative intenisty
-      config :max, 100, &c.num                         # Max relative intenisty
+      config :min, 0, &c.numeric                       # Min relative intenisty
+      config :max, 100, &c.numeric                     # Max relative intenisty
       config :sort, false, &c.flag                     # Sort by intensity
       config :output, $stdout, &c.io(:<<, :binmode)    # The output file
 
       def process(source)
         prepare(output) if output.kind_of?(String)
-        open_io(output, 'w') do |target|
-          target.binmode
+        open_io(output, 'w') do |target|
+          target.binmode
           
           # now perform the task...
           peak_file = PeakFile.parse File.read(source)
@@ -59,6 +60,7 @@ module Ms
 
           target << peak_file.to_s
         end
+        output
       end
     end
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ms-xcalibur
 version: !ruby/object:Gem::Version 
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,28 +9,28 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-03-31 00:00:00 -06:00
+date: 2009-05-25 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: configurable
+  name: tap
   type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.4.2
+        version: 0.17.0
     version: 
 - !ruby/object:Gem::Dependency 
-  name: tap
+  name: tap-tasks
   type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.12.4
+        version: 0.2.0
     version: 
 - !ruby/object:Gem::Dependency 
   name: constants
@@ -42,6 +42,16 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0.1"
     version: 
+- !ruby/object:Gem::Dependency 
+  name: tap-test
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.1.0
+    version: 
 description: 
 email: simon.a.chiang@gmail.com
 executables: []