--- a/peptide_prophet_wrapper.rb	Mon Mar 04 18:41:22 2013 -0500
+++ b/peptide_prophet_wrapper.rb	Mon Mar 04 19:04:16 2013 -0500
@@ -33,4 +33,4 @@
 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}]
+p %x[#{cmd}]

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pepxml_to_table.xml	Mon Mar 04 19:04:16 2013 -0500
@@ -0,0 +1,29 @@
+<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.0">
+
+	<requirements>
+	    <requirement type="package" version="1.1.9">galaxy_protk</requirement>
+   </requirements>
+
+
+
+  <description>Converts a pepXML file to a tab delimited text file</description>
+
+
+<!-- Note .. the input file is assumed to be the first argument -->
+<command>rvm 1.9.3@protk-1.1.9 do pepxml_to_table.rb $input_file -o $output</command>
+
+
+<inputs>
+
+	<param name="input_file" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
+
+</inputs>
+<outputs>
+	<data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" />
+</outputs>
+
+<help>
+	Convert a pepXML file to Tab delimited text
+</help>
+
+</tool>

--- a/repository_dependencies.xml	Mon Mar 04 18:41:22 2013 -0500
+++ b/repository_dependencies.xml	Mon Mar 04 19:04:16 2013 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <repositories description="Proteomics datatypes and the TPP">
 
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/>
 
 	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>