--- a/interprophet_wrapper.rb	Tue Mar 11 20:50:51 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-require 'pathname'
-
-$VERBOSE=nil
-
-# Hard-Coded argument order and number of arguments
-#
-actual_output_path_string=ARGV[0]
-use_nss=ARGV[1]
-use_nrs=ARGV[2]
-use_nse=ARGV[3]
-use_nsi=ARGV[4]
-use_nsm=ARGV[5]
-minprob=ARGV[6]
-minprob_val=ARGV[7]
-
-wd= Dir.pwd
-original_input_files=ARGV.drop(7)
-# End hard coded args #
-
-cmd=""
-
-output_substitution_cmds=""
-
-input_files=original_input_files.collect do |input|
-
-  # We append ".pep.xml" to the input file name because interprophet can't handle anything else
-  # In order for this to work properly we need to create a symbolic link our working directory
-  #
-  original_input_path=Pathname.new("#{input}")
-  actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml"
-
-  cmd << "ln -s #{input} #{actual_input_path_string};"
-  output_substitution_cmds << "ruby -pi -e \"gsub('#{actual_input_path_string}', '#{input}.pep.xml')\" interprophet_output.pep.xml;"
-  actual_input_path_string
-end
-
-cmd << "rvm 1.9.3@protk-1.2.0 do interprophet.rb"
-
-cmd << " --no-nss" unless use_nss=="blank"
-cmd << " --no-nrs" unless use_nrs=="blank"
-cmd << " --no-nse" unless use_nse=="blank"
-cmd << " --no-nsi" unless use_nsi=="blank"
-cmd << " --no-nsm" unless use_nsm=="blank"
-
-
-input_files.each { |input|
-  cmd << " #{input}"
-}
-
-
-cmd << " -o interprophet_output.pep.xml -r"
-
-cmd << ";#{output_substitution_cmds}"
-
-%x[#{cmd}]
-

--- a/peptide_prophet_wrapper.rb	Tue Mar 11 20:50:51 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-require 'pathname'
-
-$VERBOSE=nil
-
-actual_output_path_string=ARGV.shift
-
-# Second argument is the original input file name ... we'll change this below
-original_input_file=ARGV[0]
-
-# Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input 
-# name because peptide prophet can't handle anything else
-
-wd= Dir.pwd
-
-original_input_path=Pathname.new("#{original_input_file}")
-actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml"
-full_tmp_output_path_string="#{wd}/peptide_prophet_output.pep.xml"
-
-cmd = "ln -s #{original_input_file} #{actual_input_path_string};"
-
-cmd << "rvm 1.9.3@protk-1.2.0 do peptide_prophet.rb"
-
-
-ARGV[0]="#{actual_input_path_string}"
-
-ARGV.each { |a|    
-  cmd << " #{a}" 
-}
-
-cmd << " -o peptide_prophet_output.pep.xml"
-
-# Finally we need to fix up the output file so any references to the temporary working file are changed to refs to the original input file
-cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}')\" peptide_prophet_output.pep.xml"
-cmd << ";ruby -pi -e \"gsub('#{full_tmp_output_path_string}', '#{actual_output_path_string}')\" peptide_prophet_output.pep.xml"
-
-p %x[#{cmd}]

--- a/protein_prophet_wrapper.rb	Tue Mar 11 20:50:51 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-require 'pathname'
-
-$VERBOSE=nil
-
-actual_output_path_string=ARGV.shift
-
-# Second argument is the original input file name ... we'll change this below
-original_input_file=ARGV[0]
-
-# Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input 
-# name because peptide prophet can't handle anything else
-
-wd= Dir.pwd
-
-original_input_path=Pathname.new("#{original_input_file}")
-actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml"
-
-cmd = "ln -s #{original_input_file} #{actual_input_path_string};"
-
-cmd << "rvm 1.9.3@protk-1.2.0 do protein_prophet.rb"
-
-
-ARGV[0]="#{actual_input_path_string}"
-
-ARGV.each { |a| 
-    
-  cmd << " #{a}" 
-}
-
-cmd << " -o protein_prophet_results.prot.xml"
-
-cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}.pep.xml')\" protein_prophet_results.prot.xml"
-
-%x[#{cmd}]
-