diff data_manager/rna_star_index_builder.py @ 6:64deddb6a8ec draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"

--- a/data_manager/rna_star_index_builder.py	Thu Aug 15 11:30:16 2019 -0400
+++ b/data_manager/rna_star_index_builder.py	Thu Nov 28 15:48:56 2019 -0500
@@ -6,26 +6,42 @@
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument( '--config-file' )
-    parser.add_argument( '--value' )
-    parser.add_argument( '--dbkey' )
-    parser.add_argument( '--name' )
-    parser.add_argument( '--subdir' )
-    parser.add_argument( '--data-table' )
-    parser.add_argument( '--with-gene-model', action='store_true' )
-    parser.add_argument( '--index-version' )
+    parser.add_argument('--config-file')
+    parser.add_argument('--value')
+    parser.add_argument('--dbkey')
+    parser.add_argument('--name')
+    parser.add_argument('--subdir')
+    parser.add_argument('--data-table')
+    parser.add_argument('--with-gene-model', action='store_true')
+    parser.add_argument('--index-version')
 
     args = parser.parse_args()
 
-    if args.dbkey in [ None, '', '?' ]:
-        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( args.dbkey ) )
+    if args.dbkey in [None, '', '?']:
+        raise Exception(
+            '"%s" is not a valid dbkey. You must specify a valid dbkey.'
+            % (args.dbkey)
+        )
 
     with_gene_model = "0"
     if args.with_gene_model:
         with_gene_model = "1"
 
-    data_manager_dict = {'data_tables': {args.data_table: [dict({"value": args.value, "dbkey": args.dbkey, "name": args.name, "path": args.subdir, "with_gene_model": with_gene_model, "version": args.index_version} )]}}
-    open( args.config_file, 'w' ).write( json.dumps( data_manager_dict ) )
+    data_manager_dict = {
+        'data_tables': {
+            args.data_table: [
+                {
+                    "value": args.value,
+                    "dbkey": args.dbkey,
+                    "name": args.name,
+                    "path": args.subdir,
+                    "with_gene_model": with_gene_model,
+                    "version": args.index_version
+                }
+            ]
+        }
+    }
+    open(args.config_file, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
 
 
 if __name__ == "__main__":