# HG changeset patch # User sanbi-uwc # Date 1587123779 0 # Node ID 6114f017f8199b0a278da92b7310c27ea0bd0126 # Parent 119f459fc35ff6effdad09690bd79b535c66c66c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397" diff -r 119f459fc35f -r 6114f017f819 data_manager/fetch_artic_primers.py --- a/data_manager/fetch_artic_primers.py Thu Apr 16 20:51:27 2020 +0000 +++ b/data_manager/fetch_artic_primers.py Fri Apr 17 11:42:59 2020 +0000 @@ -52,4 +52,9 @@ parser.add_argument('--galaxy_datamanager_filename', help='Galaxy JSON format file describing data manager inputs') parser.add_argument('--primers', default='ARTCIv1,ARTICv2,ARTICv3', action=SplitArgs, help='Comma separated list of primers to fetch') args = parser.parse_args() - fetch_artic_primers(args.galaxy_datamanager_filename, args.output_directory, args.primers) \ No newline at end of file + + config = json.load(open(args.galaxy_datamanager_filename)) + output_directory = config.get('output_data', [{}])[0].get('extra_files_path', None) + if output_directory is None: + output_directory = args.output_directory + fetch_artic_primers(args.galaxy_datamanager_filename, output_directory, args.primers) \ No newline at end of file diff -r 119f459fc35f -r 6114f017f819 data_manager/fetch_artic_primers.xml --- a/data_manager/fetch_artic_primers.xml Thu Apr 16 20:51:27 2020 +0000 +++ b/data_manager/fetch_artic_primers.xml Fri Apr 17 11:42:59 2020 +0000 @@ -1,4 +1,4 @@ - + python requests