diff json_db_config_generating_boolean.xml @ 5:40aa268ce07f draft default tip

planemo upload for repository https://github.com/brsynth commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty

--- a/json_db_config_generating_boolean.xml	Wed Jun 11 15:25:55 2025 +0000
+++ b/json_db_config_generating_boolean.xml	Wed Jun 11 16:00:37 2025 +0000
@@ -6,36 +6,38 @@
     </macros>
     <command detect_errors="exit_code"><![CDATA[
         python3 -c "import json; params = {
-        'execution': '$execution',
-        'JSON_db_uri': '$db_uri',
-        'JSON_table': '$table_name',
-        'JSON_fragment_column': '$fragment_column',
-        'JSON_sequence_column': '$sequence_column',
-        'JSON_annotation_column': '$annotation_column'
-        }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()"
+        'execution': '$db.execution',
+        'JSON_db_uri': '$db.db_uri',
+        'JSON_table': '$db.table_name',
+        'JSON_fragment_column': '$db.fragment_column',
+        'JSON_sequence_column': '$db.sequence_column',
+        'JSON_annotation_column': '$db.annotation_column'
+        }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBUG && cat '$output_json'
     ]]></command>
     <inputs>
-        <conditional name="db_request">
-            <param name="execution" type="boolean" label="Save To DB ?" checked ='false' help="If True the execution key in the json file will be true" />
-            <when value='true'>
-                <section name='db_config' title='DB config' expanded='true'>
-                    <param name="db_uri" type="text" label="DB Connection URI" optional="true" />
-                    <param name="table_name" type="text" label="DB Table Name" optional="true" />
-                    <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" />
-                    <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" />
-                    <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" />
-                </section>
-            </when>
-            <when value='false'>
-                <section name='db_config' title='DB config' expanded='false'>
-                    <param name="db_uri" type="text" label="DB Connection URI" optional="true" />
-                    <param name="table_name" type="text" label="DB Table Name" optional="true" />
-                    <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" />
-                    <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" />
-                    <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" />
-                </section>
-            </when>
-        </conditional>
+        <section name="db" title="DB request" expanded="false">
+            <conditional name="db_request">
+                <param name="execution" type="boolean" label="Save To DB ?" checked ='false' help="If True the execution key in the json file will be true" />
+                <when value='true'>
+                    <section name='db_config' title='DB config' expanded='true'>
+                        <param name="db_uri" type="text" label="DB Connection URI" optional="true" />
+                        <param name="table_name" type="text" label="DB Table Name" optional="true" />
+                        <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" />
+                        <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" />
+                        <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" />
+                    </section>
+                </when>
+                <when value='false'>
+                    <section name='db_config' title='DB config' expanded='false'>
+                        <param name="db_uri" type="text" label="DB Connection URI" optional="true" />
+                        <param name="table_name" type="text" label="DB Table Name" optional="true" />
+                        <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" />
+                        <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" />
+                        <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" />
+                    </section>
+                </when>
+            </conditional>
+        </section>
     </inputs>   
     <outputs>
         <data name="output_json" format="json" label="JSON Conf" />
@@ -65,7 +67,7 @@
         <!--test execution is false -->
         <test> 
             <conditional name="db_request">
-                <param name="execution" value="false" />
+                <param name="db|execution" value="false" />
             </conditional>
             <output name="output_json">
                 <assert_contents>