changeset 5:e3655a2755c1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 88130bb7c37cca7eff6df235ba17e0ae9f11df86-dirty"

--- a/data_manager/install_primer_scheme_bedfiles.py	Sat Apr 18 15:31:58 2020 +0000
+++ b/data_manager/install_primer_scheme_bedfiles.py	Sat Apr 18 15:35:45 2020 +0000
@@ -43,13 +43,16 @@
     return data
 
 
-def install_primer_file(output_directory, input_filename, primer_name, primer_description):
-    name = re.sub(r'\W', '', str(primer_name).replace(' ','_'))
-    output_filename = os.path.join(output_directory, name + '.bed')
+def install_primer_file(
+    output_directory, input_filename, primer_name, primer_description
+):
+    name = re.sub(r"\W", "", str(primer_name).replace(" ", "_"))
+    output_filename = os.path.join(output_directory, name + ".bed")
     shutil.copyfile(input_filename, output_filename)
     data = [dict(value=name, description=primer_description, path=output_filename)]
     return data
 
+
 class SplitArgs(argparse.Action):
     def __call__(self, parser, namespace, values, option_string=None):
         setattr(namespace, self.dest, values.split(","))
@@ -67,14 +70,16 @@
         "--primer_file", help="BED format file containing primer scheme"
     )
     primer_file.add_argument(
-        "--primer_name", help="Name of primer scheme (one word). Required if --primer_file is used"
+        "--primer_name",
+        help="Name of primer scheme (one word). Required if --primer_file is used",
     )
     primer_file.add_argument(
-        "--primer_description", help="Description of primer scheme. Required if --primer_file is used"
+        "--primer_description",
+        help="Description of primer scheme. Required if --primer_file is used",
     )
     artic = parser.add_argument_group()
     artic.add_argument(
-        "--primers",
+        "--artic_primers",
         action=SplitArgs,
         help="Comma separated list of primers to fetch",
     )
@@ -84,16 +89,26 @@
     )
     args = parser.parse_args()
 
-    if args.primers is None and args.primer_file is None:
-        print("One of --primers or --primer_file + --primer_name + --primer_description is required.", file=sys.stderr)
+    if args.artic_primers is None and args.primer_file is None:
+        print(
+            "One of --artic_primers or --primer_file + --primer_name + --primer_description is required.",
+            file=sys.stderr,
+        )
         exit(1)
-    elif args.primer_file is not None and (args.primer_name is None or args.primer_description is None):
-        print("If --primer_file is used --primer_name and --primer_description is also required", file=sys.stderr)
+    elif args.primer_file is not None and (
+        args.primer_name is None or args.primer_description is None
+    ):
+        print(
+            "If --primer_file is used --primer_name and --primer_description is also required",
+            file=sys.stderr,
+        )
         exit(1)
-    elif args.primer_file is not None and args.primers is not None:
-        print("Only one of --primers or --primer_file + --primer_name + --primer_description can be chosen")
+    elif args.primer_file is not None and args.artic_primers is not None:
+        print(
+            "Only one of --artic_primers or --primer_file + --primer_name + --primer_description can be chosen"
+        )
         exit(1)
-    
+
     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:
@@ -103,20 +118,24 @@
         os.makedirs(output_directory)
 
     data_manager_dict = {}
-    data_manager_dict["data_tables"] = json.load(open(args.galaxy_datamanager_filename)).get(
-        "data_tables", {}
-    )
+    data_manager_dict["data_tables"] = json.load(
+        open(args.galaxy_datamanager_filename)
+    ).get("data_tables", {})
     data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {})
     data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[
         "data_tables"
     ].get(DATA_TABLE_NAME, [])
 
-    if args.primers:
-        data = fetch_artic_primers(output_directory, args.primers)
+    if args.artic_primers:
+        data = fetch_artic_primers(output_directory, args.artic_primers)
     else:
-        data = install_primer_file(output_directory, args.primer_file, args.primer_name, args.primer_description)
+        data = install_primer_file(
+            output_directory,
+            args.primer_file,
+            args.primer_name,
+            args.primer_description,
+        )
 
     data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data)
     print(data_manager_dict)
     json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w"))
-

--- a/data_manager/install_primer_scheme_bedfiles.xml	Sat Apr 18 15:31:58 2020 +0000
+++ b/data_manager/install_primer_scheme_bedfiles.xml	Sat Apr 18 15:35:45 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.5" tool_type="manage_data" profile="19.05">
+<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.6" tool_type="manage_data" profile="19.05">
     <requirements>
         <requirement type="package">python</requirement>
         <requirement type="package" version="2.22.0">requests</requirement>