# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1372075308 18000
# Node ID b649c729be4c7a32f2fba756f7db747e845fc253
# Parent  1af6f32ff592a708385103f872ca02dc340ec14b
Change tool data table to defuse_reference

diff -r 1af6f32ff592 -r b649c729be4c data_manager_conf.xml
--- a/data_manager_conf.xml	Fri Jun 21 14:46:11 2013 -0500
+++ b/data_manager_conf.xml	Mon Jun 24 07:01:48 2013 -0500
@@ -3,10 +3,10 @@
   <data_manager tool_file="datamanager_create_reference.xml" id="data_manager_defuse_reference" >
     <data_table name="defuse_reference">  <!-- Defines a Data Table to be modified. -->
             <output> <!-- Handle the output of the Data Manager Tool -->
-                <column name="unique_id" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
                 <column name="dbkey" />
                 <column name="name" />
-                <column name="config" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
+                <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 -->
                     </move>
diff -r 1af6f32ff592 -r b649c729be4c datamanager_create_reference.py
--- a/datamanager_create_reference.py	Fri Jun 21 14:46:11 2013 -0500
+++ b/datamanager_create_reference.py	Mon Jun 24 07:01:48 2013 -0500
@@ -83,12 +83,12 @@
     except Exception, e:
         stop_err( 'Error creating defuse reference:\n' + str( e ) )
     config_dict = get_config_dict(config, dataset_directory=target_directory)
-    data_table_entry = dict(unique_id=dbkey, dbkey=dbkey, name=description, path=config_name)
+    data_table_entry = dict(value=dbkey, dbkey=dbkey, name=description, path=config_name)
     _add_data_table_entry( data_manager_dict, data_table_entry )
 def _add_data_table_entry( data_manager_dict, data_table_entry ):
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
-    data_manager_dict['data_tables']['defuse'] = data_manager_dict['data_tables'].get( 'defuse', [] )
-    data_manager_dict['data_tables']['defuse'].append( data_table_entry )
+    data_manager_dict['data_tables']['defuse_reference'] = data_manager_dict['data_tables'].get( 'defuse_reference', [] )
+    data_manager_dict['data_tables']['defuse_reference'].append( data_table_entry )
     return data_manager_dict
 
 def main():
diff -r 1af6f32ff592 -r b649c729be4c tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Jun 24 07:01:48 2013 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="defuse_reference" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/defuse_reference.loc" />
+    </table>
+</tables>