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Allow speficying columns by name for attribute_value_splitter filter

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This commit is contained in:
Nicola Soranzo
2018-05-09 17:58:55 +01:00
parent 993f5f52db
commit 88202fbc57
1 changed files with 6 additions and 5 deletions
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lib/galaxy/tools/parameters/dynamic_options.py
+6 -5
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@@ -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: