--- a/data_managers/data_manager_conf.xml	Wed Oct 11 16:31:13 2017 -0400
+++ b/data_managers/data_manager_conf.xml	Wed Oct 11 16:43:22 2017 -0400
@@ -35,6 +35,7 @@
       <output>
         <column name="value" />
         <column name="name" />
+	<column name="dbkey" />
         <column name="path" output_ref="out_file">
           <move type="directory" relativize_symlinks="True">
             <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${path}</target>

--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 16:31:13 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 16:43:22 2017 -0400
@@ -11,17 +11,17 @@
 DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"]
 
 
-def mentalist_download_pubmlst( data_manager_dict, database_name, kmer_size, scheme, output, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
-    args = [ 'mentalist', 'download_pubmlst', '--db', database_name, '-k', str(kmer_size), '-s', scheme, '-o', output]
+def mentalist_download_pubmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
+    database_path = scheme.lower().replace(" ", "_").translate(None, string.punctuation) + "_k" + str(kmer_size) + "_pubmlst"
+    database_name = data_table_path + ".h5"
+    display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)"
+    args = [ 'mentalist', 'download_pubmlst', '--db', database_name, '-k', str(kmer_size), '-s', scheme, '-o', database_path]
     proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
     if return_code:
         print("Error building database.", file=sys.stderr)
         sys.exit( return_code )
-    data_table_path = scheme.lower().replace(" ", "_").translate(None, string.punctuation) + "_k" + str(kmer_size) + "_pubmlst"
-    data_table_value = data_table_path + ".h5"
-    data_table_name = scheme.lower() + " k=" + str(kmer_size) + " (PubMLST)"
-    data_table_entry = dict( value=data_table_value, dbkey='PubMLST', name=data_table_name, path=database_name )
+    data_table_entry = dict( value=database_name, dbkey='PubMLST', name=display_name, path=database_path )
     for data_table_name in data_table_names:
         _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
 
@@ -36,10 +36,8 @@
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('params')
-    parser.add_argument( '-d', '--db', dest='database_name', default=None, help='Database Name' )
     parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' )
     parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help='Scheme' )
-    parser.add_argument( '-o', '--output', dest='output', default=None, help='Output' )
     args = parser.parse_args()
 
     params = loads( open( args.params ).read() )
@@ -56,7 +54,7 @@
     data_manager_dict = {}
 
     # build the index
-    mentalist_download_pubmlst( data_manager_dict, args.database_name, args.kmer_size, args.scheme, args.output, params, target_directory, DEFAULT_DATA_TABLE_NAMES )
+    mentalist_download_pubmlst( data_manager_dict, args.kmer_size, args.scheme, params, target_directory, DEFAULT_DATA_TABLE_NAMES )
 
     # save info to json file
     open( args.params, 'wb' ).write( dumps( data_manager_dict ) )