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(-) [+]
line wrap: on
line diff
--- 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>