Mercurial > repos > sanbi-uwc > data_manager_fetch_artic_primers
changeset 3:6114f017f819 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
author | sanbi-uwc |
---|---|
date | Fri, 17 Apr 2020 11:42:59 +0000 |
parents | 119f459fc35f |
children | |
files | data_manager/fetch_artic_primers.py data_manager/fetch_artic_primers.xml |
diffstat | 2 files changed, 7 insertions(+), 2 deletions(-) [+] |
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--- 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
--- 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 @@ -<tool id="fetch_artic_primers" name="ARTIC primer data manager" version="0.0.3" tool_type="manage_data" profile="19.05"> +<tool id="fetch_artic_primers" name="ARTIC primer data manager" version="0.0.4" tool_type="manage_data" profile="19.05"> <requirements> <requirement type="package">python</requirement> <requirement type="package" version="2.22.0">requests</requirement>