--- a/data_manager_conf.xml	Mon Jun 24 08:12:05 2013 -0500
+++ b/data_manager_conf.xml	Thu Jun 27 13:11:50 2013 -0500
@@ -8,12 +8,14 @@
                 <column name="name" />
                 <column name="path" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
                     <move type="directory"> <!-- Moving a file from the extra files path of "out_file" -->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/defuse</target> <!-- Target Location to store the file, directories are created as needed -->
+                        !-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/defuse</target> <!-- Target Location to store the file, directories are created as needed -->
                     </move>
                     <!-- datamanager_create_reference.py should have copied the defuse config file to the working directory.  
                          so if we put the ${dbkey}.config path in this column,  defuse.xml can set the data_directory to this this directory.
                      -->
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/defuse/${dbkey}.config</value_translation> <!-- Store this value in the final Data Table -->
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/defuse/${value}.config</value_translation> <!-- Store this value in the final Data Table -->
+                    <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
         </data_table>