--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peptide_prophet_wrapper.rb	Mon Jul 23 00:20:58 2012 -0400
@@ -0,0 +1,38 @@
+require 'pathname'
+
+$VERBOSE=nil
+
+peptide_prophet_path=%x[which peptide_prophet.rb]
+
+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 << peptide_prophet_path.chomp
+
+
+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"
+
+%x[#{cmd}]