# HG changeset patch
# User dfornika
# Date 1551748147 18000
# Node ID 1601703ae5117b9667dc018590c559849b311e0c
# Parent  f53064ca5398ac25b1f4c5e61b4e5ae53e0da43c
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty

diff -r f53064ca5398 -r 1601703ae511 data_manager/kraken2_build_special.py
--- a/data_manager/kraken2_build_special.py	Mon Mar 04 19:24:23 2019 -0500
+++ b/data_manager/kraken2_build_special.py	Mon Mar 04 20:09:07 2019 -0500
@@ -96,13 +96,15 @@
         else:
             raise
 
+    data_manager_output = {}
+    
     kraken2_build_standard(
-        data_manager_input,
+        data_manager_output,
         kraken2_args,
         target_directory,
     )
 
-    open(args.data_manager_json, 'wb').write(json.dumps(data_manager_input))
+    open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
 
 
 if __name__ == "__main__":
diff -r f53064ca5398 -r 1601703ae511 data_manager/kraken2_build_standard.py
--- a/data_manager/kraken2_build_standard.py	Mon Mar 04 19:24:23 2019 -0500
+++ b/data_manager/kraken2_build_standard.py	Mon Mar 04 20:09:07 2019 -0500
@@ -93,13 +93,15 @@
         else:
             raise
 
+    data_manager_output = {}
+    
     kraken2_build_standard(
-        data_manager_input,
+        data_manager_output,
         kraken2_args,
         target_directory,
     )
 
-    open(args.data_manager_json, 'wb').write(json.dumps(data_manager_input))
+    open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
 
 
 if __name__ == "__main__":
diff -r f53064ca5398 -r 1601703ae511 data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Mar 04 19:24:23 2019 -0500
+++ b/data_manager_conf.xml	Mon Mar 04 20:09:07 2019 -0500
@@ -5,11 +5,11 @@
 		<column name="value"/>
 		<column name="name"/>
 		<column name="path" output_ref="out_file">
-		    <move type="directory" relativize_symlinks="True">
-			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases</target>
+		    <move type="directory">
+		        <source>${path}</source>
+			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target>
 		    </move>
-		    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases</value_translation>
-		    <value_translation type="function">abspath</value_translation>
+		    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation>
 		</column>
 	    </output>
 	</data_table>
@@ -20,11 +20,11 @@
 		<column name="value"/>
 		<column name="name"/>
 		<column name="path" output_ref="out_file">
-		    <move type="directory" relativize_symlinks="True">
-			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases</target>
+		    <move type="directory">
+		        <source>${path}</source>
+			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target>
 		    </move>
-		    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases</value_translation>
-		    <value_translation type="function">abspath</value_translation>
+		    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation>
 		</column>
 	    </output>
 	</data_table>
@@ -35,11 +35,11 @@
 		<column name="value"/>
 		<column name="name"/>
 		<column name="path" output_ref="out_file">
-		    <move type="directory" relativize_symlinks="True">
-			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases</target>
+		    <move type="directory">
+		        <source>${path}</source>
+			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target>
 		    </move>
-		    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases</value_translation>
-		    <value_translation type="function">abspath</value_translation>
+		    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation>
 		</column>
 	    </output>
 	</data_table>