diff data_manager_conf.xml @ 15:367b0d693b0c draft default tip

Uploaded

--- a/data_manager_conf.xml	Fri Dec 15 15:53:28 2017 -0500
+++ b/data_manager_conf.xml	Mon Apr 30 16:17:37 2018 -0400
@@ -1,39 +1,20 @@
 <?xml version="1.0"?>
 <data_managers>
-    <data_manager tool_file="data_manager/add_ctat_ref_lib.xml" id="ctat_genome_ref_lib_data_manager"> 
-        <data_table name="ctat_genome_ref_libs">
+    <data_manager tool_file="data_manager/add_ctat_centrifuge_index.xml" id="ctat_centrifuge_index_data_manager"> 
+        <data_table name="ctat_centrifuge_indexes">
             <output>
                 <column name="value" />
                     <!-- value is used to uniquely identify this entry in the table.
-                    For now id is also the name of the environment variable that is used within tools to
-                    access a CTAT Resource Library. 
-                    FIX - Need to get rid of that and use command line params...
                     -->
                 <column name="name" />
                     <!-- name is used as the selector in the pull down lists for items in this table.
                     -->
                 <column name="path" />
-                    <!-- path is the absolute path of the corresponding CTAT Genome Reference Library.
-                    -->
-                <!-- <column name="path" output_ref="out_file"> -->
-                    <!-- It is typical to move the data file, but because our tool gets the destination
-                    location from the user, we do not want to move the data from that location.
-                    The full path of the CTAT Resource library is returned in location. 
-                    So no need to change the value either.
+                    <!-- path is the absolute path of the directory containing the centrifuge index files.
                     -->
-                    <!-- <move type="file" relativize_symlinks="False"> -->
-                        <!--<source>${path}</source> -->
-                        <!--<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ctat_genome_lib_build_dir</target> -->
-                    <!--</move> -->
-                    <!--
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ctat_genome_lib_build_dir
-                    </value_translation>
-                    -->
-                    <!-- The location returned by the tool should already be an absolute path.
-                    <value_translation type="function">abspath</value_translation>
-                    -->
-                <!--</column> -->
+                <!-- Same as the Genome Reference Library, we create the Centrifuge Index files where we want them.
+                -->
             </output>
         </data_table>
     </data_manager>
-</data_managers>
\ No newline at end of file
+</data_managers>