# HG changeset patch
# User iuc
# Date 1619297733 0
# Node ID fca4564d83ae58739292a018847857c8b0f5ff7b
# Parent  ea8b9716313339e38a2ea86de75254327d19c705
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 68adfad76cdb5ff13ec9fb49895a3cde2c502514"

diff -r ea8b97163133 -r fca4564d83ae data_manager/install_primer_scheme_bedfiles.py
--- a/data_manager/install_primer_scheme_bedfiles.py	Mon Oct 12 13:46:40 2020 +0000
+++ b/data_manager/install_primer_scheme_bedfiles.py	Sat Apr 24 20:55:33 2021 +0000
@@ -135,7 +135,8 @@
         )
         exit(1)
 
-    config = json.load(open(args.galaxy_datamanager_filename))
+    with open(args.galaxy_datamanager_filename) as fh:
+        config = json.load(fh)
     output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
     if output_directory is None:
         output_directory = args.output_directory
@@ -144,10 +145,7 @@
         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"] = data_manager_dict.get("data_tables", {})
+    data_manager_dict["data_tables"] = config.get("data_tables", {})
     data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[
         "data_tables"
     ].get(DATA_TABLE_NAME, [])
@@ -163,5 +161,5 @@
         )
 
     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"))
+    with open(args.galaxy_datamanager_filename, "w") as fh:
+        json.dump(data_manager_dict, fh, sort_keys=True)
diff -r ea8b97163133 -r fca4564d83ae data_manager/install_primer_scheme_bedfiles.xml
--- a/data_manager/install_primer_scheme_bedfiles.xml	Mon Oct 12 13:46:40 2020 +0000
+++ b/data_manager/install_primer_scheme_bedfiles.xml	Sat Apr 24 20:55:33 2021 +0000
@@ -3,7 +3,7 @@
         <requirement type="package" version="2.24.0">requests</requirement>
     </requirements>
     <!-- fetch all the primers in one go -->
-    <command detect_errors="exit_code">
+    <command detect_errors="exit_code"><![CDATA[
     python '$__tool_directory__/install_primer_scheme_bedfiles.py'
         '${output_file}'
         #if $input.input_type == "ARTIC"
@@ -13,7 +13,7 @@
             --primer_name '${input.primer_name}'
             --primer_description '${input.primer_description}'
         #end if
-    </command>
+    ]]></command>
     <inputs>
         <conditional name="input">
             <param name="input_type" label="Choose the source for primer schemes" type="select">