# HG changeset patch
# User sanbi-uwc
# Date 1587069935 0
# Node ID 59b3556d9ec8a30e821dfe17e39d7c3630f2715c
# Parent  c401f63b3d124875dc1b11ee44776c94f5a9f047
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"

diff -r c401f63b3d12 -r 59b3556d9ec8 data_manager/fetch_artic_primers.py
--- a/data_manager/fetch_artic_primers.py	Thu Apr 16 14:06:59 2020 +0000
+++ b/data_manager/fetch_artic_primers.py	Thu Apr 16 20:45:35 2020 +0000
@@ -19,13 +19,16 @@
         }
 
     if not os.path.isdir(output_directory):
-        os.makedirs(output_directory)    
-    data_manager_dict = json.load(open(output_filename))
+        os.makedirs(output_directory)
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = json.load(open(output_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, [])
     
     data = []
     for name, url in primer_sets.items():
+        if name not in primers:
+            continue
         response = requests.get(url)
         if response.status_code != 200:
             print('Error: download of', url, 'failed with code', response.status_code, file=sys.stderr)
diff -r c401f63b3d12 -r 59b3556d9ec8 data_manager/fetch_artic_primers.xml
--- a/data_manager/fetch_artic_primers.xml	Thu Apr 16 14:06:59 2020 +0000
+++ b/data_manager/fetch_artic_primers.xml	Thu Apr 16 20:45:35 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="fetch_artic_primers" name="ARTIC primer data manager" version="0.0.1" tool_type="manage_data" profile="19.05">
+<tool id="fetch_artic_primers" name="ARTIC primer data manager" version="0.0.2" tool_type="manage_data" profile="19.05">
     <requirements>
         <requirement type="package">python</requirement>
         <requirement type="package" version="2.22.0">requests</requirement>
@@ -7,6 +7,7 @@
     <command detect_errors="exit_code">
     python '$__tool_directory__/fetch_artic_primers.py'
         --galaxy_datamanager_filename '${output_file}'
+        --primers '${primers}'
     </command>
     <inputs>
         <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch">
diff -r c401f63b3d12 -r 59b3556d9ec8 data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Apr 16 14:06:59 2020 +0000
+++ b/data_manager_conf.xml	Thu Apr 16 20:45:35 2020 +0000
@@ -8,9 +8,9 @@
                 <column name="path" output_ref="output_file" >
                     <move type="file">
                         <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">artic_primers/#echo str($name).bed#</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">artic_primers/#echo str($value).bed#</target>
                     </move>
-                    <value_translation>artic_primers/#echo str($name).bed#</value_translation>
+                    <value_translation>artic_primers/#echo str($value).bed#</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>