--- a/tool_dependencies.xml	Mon Jun 24 12:46:59 2013 -0400
+++ b/tool_dependencies.xml	Mon Jun 24 14:04:26 2013 -0400
@@ -1,48 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="SearchGUI" version="1.13.1">
-        <install version="1.0">
-            <actions>
-              <action type="download_by_url">http://searchgui.googlecode.com/files/SearchGUI-1.13.1_mac_and_linux.zip</action>
-	      <action type="shell_command">tar -xf SearchGUI-1.13.1_mac_and_linux.tar</action>
-	      <action type="shell_command">cd SearchGUI-1.13.1_mac_and_linux</action>
-	      <action type="shell_command">chmod -R o+w resources</action>
-              <action type="move_directory_files">
-                <source_directory>.</source_directory>
-                <destination_directory>$INSTALL_DIR/</destination_directory>
-              </action>
-	      <action type="shell_command">mkdir -p $BIN_DIR</action>
-              <action type="set_environment">
-                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-              </action>                
-            </actions>
-        </install>
-        <readme>
-          This package downloads and installs the SearchGUI scripts develped as part of the Peptideshaker tool.
-          (https://github.com/jmchilton/peptide-shaker).
-
-        </readme>
-    </package>
-    
+      <repository toolshed="http://toolshed.g2.bx.psu.edu" name="searchgui" owner="galaxyp" changeset_revision="57249f07debd" prior_installation_required="True"/>
+    </package>    
     <package name="PeptideShaker" version="0.20.1">
-        <install version="1.0">
-            <actions>
-              <action type="download_by_url">http://peptide-shaker.googlecode.com/files/PeptideShaker-0.20.1.zip</action>
-	      <action type="shell_command">chmod -R o+w resources</action>
-              <action type="move_directory_files">
-                <source_directory>.</source_directory>
-                <destination_directory>$INSTALL_DIR/</destination_directory>
-              </action>
-              <action type="shell_command">mkdir -p $BIN_DIR</action>
-              <action type="set_environment">
-                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-              </action>                
-            </actions>
-        </install>
-        <readme>
-          This package downloads and installs the peptideshaker tool as a part of the peptideshaker framework.
-          (https://github.com/jmchilton/peptide-shaker).
-
-        </readme>
+      <repository toolshed="http://toolshed.g2.bx.psu.edu" name="peptideshaker_0201" owner="galaxyp" changeset_revision="a92db19b2daa" prior_installation_required="True"/>
     </package>
 </tool_dependency>