Mercurial > repos > jjohnson > data_manager_snpeff

diff data_manager_conf.xml @ 5:78bcf4ac437c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
author Jim Johnson <jj@umn.edu>
date Tue, 13 Jan 2015 12:54:20 -0600
parents 6a378d0f4856
children
line wrap: on
line diff
--- a/data_manager_conf.xml	Thu Oct 23 05:43:46 2014 -0500
+++ b/data_manager_conf.xml	Tue Jan 13 12:54:20 2015 -0600
@@ -1,36 +1,44 @@
 <?xml version="1.0"?>
 <data_managers>
-  <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff4_databases" >
-    <data_table name="snpeff4_databases">  <!-- Defines a Data Table to be modified. -->
+  <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff_databases" >
+    <data_table name="snpeffv_databases">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="version" /> <!-- 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="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff4_download" >
-    <data_table name="snpeff4_genomedb">  <!-- Defines a Data Table to be modified. -->
+  <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff_download" >
+    <data_table name="snpeffv_genomedb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="version" /> <!-- 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="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="path" output_ref="out_file" >
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4/data</target>
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4_0/data</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4/data</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4_0/data</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
     </data_table>
-    <data_table name="snpeff4_regulationdb">  <!-- Defines a Data Table to be modified. -->
+    <data_table name="snpeffv_regulationdb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="genome" /> <!-- 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="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
       </output>
     </data_table>
-    <data_table name="snpeff4_annotations">  <!-- Defines a Data Table to be modified. -->
+    <data_table name="snpeffv_annotations">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="genome" /> <!-- 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="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->