# HG changeset patch
# User dfornika
# Date 1636066371 0
# Node ID 4ee8002597d2a54bc38d7fb8e39836f5db24dfd5
# Parent  9c4f30740a71d0747076b4c59a3592e803f3b49b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3-dirty"

diff -r 9c4f30740a71 -r 4ee8002597d2 data_manager/bracken_build_database.py
--- a/data_manager/bracken_build_database.py	Thu Nov 04 22:49:26 2021 +0000
+++ b/data_manager/bracken_build_database.py	Thu Nov 04 22:52:51 2021 +0000
@@ -54,7 +54,7 @@
     parser.add_argument('--read-len', dest='read_len', help='Read length')
     parser.add_argument('--kraken-db', dest='kraken_database', help='Kraken Database')
     parser.add_argument('--database-name', dest='database_name', help='Database Name')
-    parser.add_argument('--prebuilt', dest='prebuilt', help='Use pre-built DB')
+    parser.add_argument('--prebuilt', action='store_true', dest='prebuilt', help='Use pre-built DB')
     args = parser.parse_args()
 
     with open(args.data_manager_json) as fh:
diff -r 9c4f30740a71 -r 4ee8002597d2 data_manager/bracken_build_database.xml
--- a/data_manager/bracken_build_database.xml	Thu Nov 04 22:49:26 2021 +0000
+++ b/data_manager/bracken_build_database.xml	Thu Nov 04 22:52:51 2021 +0000
@@ -11,7 +11,7 @@
         #set db_dir = os.path.basename($kraken_db.fields.path)
 
         mkdir '$db_dir' &&
-        ln -s '${kraken_db.fields.path}'/* '$db_dir/' &&
+        ln -s '${kraken_db.fields.path}/*' '$db_dir/' &&
         python '$__tool_directory__/bracken_build_database.py'
           '${out_file}'
           --kraken-db '$db_dir'