diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py index b957527c2b3..e62e5a54fe8 100644 --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -277,7 +277,7 @@ class MultipleSplitterFilter(Filter): Filter.__init__(self, d_option, elem) self.separator = elem.get("separator", ",") columns = elem.get("column", None) - assert columns is not None, "Required 'columns' attribute missing from filter" + assert columns is not None, "Required 'column' attribute missing from filter" self.columns = [d_option.column_spec_to_index(column) for column in columns.split(",")] def filter_options(self, options, trans, other_values): @@ -306,9 +306,9 @@ class AttributeValueSplitterFilter(Filter): Filter.__init__(self, d_option, elem) self.pair_separator = elem.get("pair_separator", ",") self.name_val_separator = elem.get("name_val_separator", None) - self.columns = elem.get("column", None) - assert self.columns is not None, "Required 'columns' attribute missing from filter" - self.columns = [int(column) for column in self.columns.split(",")] + columns = elem.get("column", None) + assert columns is not None, "Required 'column' attribute missing from filter" + self.columns = [d_option.column_spec_to_index(column) for column in columns.split(",")] def filter_options(self, options, trans, other_values): attr_names = [] @@ -510,7 +510,8 @@ class DynamicOptions(object): full_path = os.path.join(self.tool_param.tool.app.config.tool_data_path, data_file) if os.path.exists(full_path): self.index_file = data_file - self.file_fields = self.parse_file_fields(open(full_path)) + with open(full_path) as fh: + self.file_fields = self.parse_file_fields(fh) else: self.missing_index_file = data_file elif dataset_file is not None: