Mercurial > repos > iuc > data_manager_build_bracken_database

diff data_manager_conf.xml @ 6:a0f18c07696a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
author iuc
date Wed, 05 Nov 2025 13:31:43 +0000
parents 5bc823e95ed3
children
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--- a/data_manager_conf.xml	Mon May 22 19:24:06 2023 +0000
+++ b/data_manager_conf.xml	Wed Nov 05 13:31:43 2025 +0000
@@ -4,8 +4,25 @@
             <output>
                 <column name="value"/>
                 <column name="name"/>
-                <column name="path" output_ref="out_file"/>
+                <column name="path" output_ref="out_file">
+                    <move type="directory" relativize_symlinks="True">
+                        <!-- we move the top level folder, since the path points to the bracken DB file -->
+		                <source>
+                        #import os
+                        #set base_dir = os.path.dirname($path)
+                        ${base_dir}
+                        </source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/${value}</target>
+                    </move>
+                    <!-- we store the path to the bracken DB file, since this is what bracken uses -->
+                <value_translation>
+                    #import os
+                    ${GALAXY_DATA_MANAGER_DATA_PATH}/bracken_databases/${value}/${os.path.basename($path)}
+                </value_translation>                    
+                <value_translation type="function">abspath</value_translation>
+                </column>
             </output>
+
         </data_table>
     </data_manager>
 </data_managers>