Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
changeset 30:9a265f7c4a2e draft
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 71ea714f0481e240e14f4fd0272ad7df891d7756
| author | rhpvorderman |
|---|---|
| date | Thu, 05 Jul 2018 04:24:16 -0400 |
| parents | d4c529a7df9e |
| children | b212c0b89a6a |
| files | data_manager/__pycache__/path_name_value_key_manager.cpython-35.pyc data_manager/__pycache__/test_path_name_value_key_manager.cpython-35-PYTEST.pyc data_manager/data_manager_select_index_by_path.xml data_manager/path_name_value_key_manager.py |
| diffstat | 4 files changed, 4 insertions(+), 5 deletions(-) [+] |
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Binary file data_manager/__pycache__/test_path_name_value_key_manager.cpython-35-PYTEST.pyc has changed
--- 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>
--- 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()