# HG changeset patch
# User rhpvorderman
# Date 1530779056 14400
# Node ID 9a265f7c4a2e20adafe150405dc8677771fe40fc
# Parent  d4c529a7df9e2a7e22fc9c094773aea96ea7c41f
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 71ea714f0481e240e14f4fd0272ad7df891d7756

diff -r d4c529a7df9e -r 9a265f7c4a2e data_manager/__pycache__/path_name_value_key_manager.cpython-35.pyc
Binary file data_manager/__pycache__/path_name_value_key_manager.cpython-35.pyc has changed
diff -r d4c529a7df9e -r 9a265f7c4a2e data_manager/__pycache__/test_path_name_value_key_manager.cpython-35-PYTEST.pyc
Binary file data_manager/__pycache__/test_path_name_value_key_manager.cpython-35-PYTEST.pyc has changed
diff -r d4c529a7df9e -r 9a265f7c4a2e data_manager/data_manager_select_index_by_path.xml
--- a/data_manager/data_manager_select_index_by_path.xml	Thu Jul 05 03:46:12 2018 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml	Thu Jul 05 04:24:16 2018 -0400
@@ -14,7 +14,7 @@
         --data_table_name "${data_table_set.data_table}"
         --json_output_file "${json_output_file}"
         #if $data_table_set.data_table == "rnastar_index2"
-        --extra-columns {'with-gtf': '$data_table_set.with_gtf'}
+        --extra-columns '{"with-gtf": "$data_table_set.with_gtf"}'
         #end if
         ]]></command>
     <inputs>
diff -r d4c529a7df9e -r 9a265f7c4a2e data_manager/path_name_value_key_manager.py
--- a/data_manager/path_name_value_key_manager.py	Thu Jul 05 03:46:12 2018 -0400
+++ b/data_manager/path_name_value_key_manager.py	Thu Jul 05 04:24:16 2018 -0400
@@ -61,8 +61,8 @@
         self.data_table_name = data_table_name
         self.name = name if name else str(self.index_path.with_suffix(
             '').name)
-        self.value = value if value is not None else self.name
-        self.dbkey = dbkey if dbkey is not None else self.value
+        self.value = value if value else self.name
+        self.dbkey = dbkey if dbkey else self.value
         self.extra_columns = extra_columns if extra_columns is not None else {}
         self.indexes_properties_file = indexes_properties_file
 
@@ -170,8 +170,7 @@
     options = argument_parser().parse_args()
 
     if options.json_output_file.exists():
-        raise FileExistsError(
-            "\'{0}\' already exists.".format(str(options.json_output_file)))
+        pass # Do not raise error.
 
     if options.extra_columns is None:
         extra_columns = dict()