Mercurial > repos > jjohnson > snpeff

diff data_manager_conf.xml @ 2:6ad9205c1307

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Update to SnpEff version 3.3
author Jim Johnson <jj@umn.edu>
date Fri, 04 Oct 2013 09:09:29 -0500
parents e1d9f6a0ad53
children
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--- a/data_manager_conf.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/data_manager_conf.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -4,8 +4,7 @@
     <data_table name="snpeff_databases">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="name" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
-        </column>
+        <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
       </output>
     </data_table>
   </data_manager>
@@ -13,15 +12,28 @@
     <data_table name="snpeff_genomedb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="name" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
+        <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="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/data</target>
+          </move>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/data</value_translation>
+          <value_translation type="function">abspath</value_translation>
         </column>
       </output>
     </data_table>
     <data_table name="snpeff_regulationdb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of 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" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
-        </column>
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+      </output>
+    </data_table>
+    <data_table name="snpeff_annotations">  <!-- Defines a Data Table to be modified. -->
+      <output> <!-- Handle the output of 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_manager>