# HG changeset patch
# User dfornika
# Date 1564610886 14400
# Node ID f25264bb7d6d133b60128715f89c97952f91eb07
# Parent  0a2f97661db356ae0efb6242ac467ea9ffa0a28a
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit 324b55b24e9d403b04a1cc6aba362b03bad98368-dirty

diff -r 0a2f97661db3 -r f25264bb7d6d data_manager/bracken_build_database.py
--- a/data_manager/bracken_build_database.py	Fri Jul 26 17:18:22 2019 -0400
+++ b/data_manager/bracken_build_database.py	Wed Jul 31 18:08:06 2019 -0400
@@ -25,7 +25,7 @@
 
     database_name = database_name
 
-    database_path = database_value
+    database_path = bracken_build_args['kraken_database']
 
     try:
         os.mkdir( os.path.join(target_directory, database_path) )
@@ -35,8 +35,7 @@
         else:
             raise
 
-    
-          
+
     bracken_build_args_list = [
         '-t', bracken_build_args['threads'],
         '-k', bracken_build_args['kmer_len'],
@@ -46,12 +45,7 @@
 
     subprocess.check_call(['bracken-build'] + bracken_build_args_list,
                           cwd=os.path.join(target_directory, database_path))
-    
-    bagit_args_list = [
-        database_path,
-    ]
 
-    subprocess.call(['bagit.py'] + bagit_args_list, cwd=target_directory)
     
     data_table_entry = {
         "data_tables": {
@@ -59,7 +53,7 @@
                 {
                     "value": database_value,
                     "name": database_name,
-                    "path": os.path.join(database_path, 'data'),
+                    "path": os.path.join(database_path),
                 }
             ]
         }
diff -r 0a2f97661db3 -r f25264bb7d6d data_manager_conf.xml
--- a/data_manager_conf.xml	Fri Jul 26 17:18:22 2019 -0400
+++ b/data_manager_conf.xml	Wed Jul 31 18:08:06 2019 -0400
@@ -6,8 +6,8 @@
                 <column name="name"/>
                 <column name="path" output_ref="out_file">
                     <move type="file">
-                        <source>#import os#${os.path.dirname($path)}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/#import os#${os.path.dirname($path)}</target>
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/${path}</target>
                    </move>
                       <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bracken_databases/${path}</value_translation>
                       <value_translation type="function">abspath</value_translation>