--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interprophet_wrapper.rb	Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,57 @@
+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
+
+interprophet_path=%x[which interprophet.rb]
+cmd << interprophet_path.chomp
+
+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}]
+