# HG changeset patch
# User tduigou
# Date 1749657637 0
# Node ID 40aa268ce07ff919efbca7f50b7922a2a815947c
# Parent  f103f5253a93ba90ca2d7bc6af685b4f1a99792a
planemo upload for repository https://github.com/brsynth commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty

diff -r f103f5253a93 -r 40aa268ce07f json_db_config_generating_boolean.xml
--- 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>
diff -r f103f5253a93 -r 40aa268ce07f output.html
--- a/output.html	Wed Jun 11 15:25:55 2025 +0000
+++ b/output.html	Wed Jun 11 16:00:37 2025 +0000
@@ -285,7 +285,7 @@
         var md = window.markdownit({
           html: true,
         });
-        target.innerHTML = md.render(atob('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+        target.innerHTML = md.render(atob('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'));
     </script>
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\ No newline at end of file
diff -r f103f5253a93 -r 40aa268ce07f output.json
--- a/output.json	Wed Jun 11 15:25:55 2025 +0000
+++ b/output.json	Wed Jun 11 16:00:37 2025 +0000
@@ -9,25 +9,25 @@
         {
             "data": {
                 "inputs": {
-                    "db_request|db_config|annotation_column": "annotation",
-                    "db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
-                    "db_request|db_config|fragment_column": "fragment",
-                    "db_request|db_config|sequence_column": "sequence",
-                    "db_request|db_config|table_name": "sample",
-                    "db_request|execution": true
+                    "db|db_request|db_config|annotation_column": "annotation",
+                    "db|db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
+                    "db|db_request|db_config|fragment_column": "fragment",
+                    "db|db_request|db_config|sequence_column": "sequence",
+                    "db|db_request|db_config|table_name": "sample",
+                    "db|db_request|execution": true
                 },
                 "job": {
-                    "command_line": "python3 -c \"import json; params = { 'execution': 'true', 'JSON_db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'JSON_table': 'sample', 'JSON_fragment_column': 'fragment', 'JSON_sequence_column': 'sequence', 'JSON_annotation_column': 'annotation' }; f = open('/tmp/tmpexzs2_xe/job_working_directory/000/1/outputs/dataset_0349192e-9e75-4498-b48a-0a53dbf83783.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpexzs2_xe/job_working_directory/000/1/outputs/dataset_0349192e-9e75-4498-b48a-0a53dbf83783.dat'",
+                    "command_line": "python3 -c \"import json; params = { 'execution': 'true', 'JSON_db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'JSON_table': 'sample', 'JSON_fragment_column': 'fragment', 'JSON_sequence_column': 'sequence', 'JSON_annotation_column': 'annotation' }; f = open('/tmp/tmpetlap50a/job_working_directory/000/1/outputs/dataset_adbe4688-ac5a-4157-9d00-bd44d8e5925a.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBUG && cat '/tmp/tmpetlap50a/job_working_directory/000/1/outputs/dataset_adbe4688-ac5a-4157-9d00-bd44d8e5925a.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-06-02T15:09:13.299180",
+                    "create_time": "2025-06-11T15:59:58.065310",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "282809",
+                    "external_id": "75561",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "a5a635de282655c8",
-                    "id": "a5a635de282655c8",
+                    "history_id": "6ee26cd2a9b017f6",
+                    "id": "6ee26cd2a9b017f6",
                     "inputs": {},
                     "job_messages": [],
                     "job_metrics": [],
@@ -38,30 +38,30 @@
                     "output_collections": {},
                     "outputs": {
                         "output_json": {
-                            "id": "a5a635de282655c8",
+                            "id": "6ee26cd2a9b017f6",
                             "src": "hda",
-                            "uuid": "0349192e-9e75-4498-b48a-0a53dbf83783"
+                            "uuid": "adbe4688-ac5a-4157-9d00-bd44d8e5925a"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
-                        "chromInfo": "\"/tmp/tmpexzs2_xe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-                        "db_request": "{\"__current_case__\": 0, \"db_config\": {\"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table_name\": \"sample\"}, \"execution\": true}",
+                        "chromInfo": "\"/tmp/tmpetlap50a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "db": "{\"db_request\": {\"__current_case__\": 0, \"db_config\": {\"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table_name\": \"sample\"}, \"execution\": true}}",
                         "dbkey": "\"?\""
                     },
                     "state": "ok",
                     "stderr": "",
-                    "stdout": "DEBG\n{\n    \"execution\": \"true\",\n    \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"JSON_table\": \"sample\",\n    \"JSON_fragment_column\": \"fragment\",\n    \"JSON_sequence_column\": \"sequence\",\n    \"JSON_annotation_column\": \"annotation\"\n}",
+                    "stdout": "DEBUG\n{\n    \"execution\": \"true\",\n    \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"JSON_table\": \"sample\",\n    \"JSON_fragment_column\": \"fragment\",\n    \"JSON_sequence_column\": \"sequence\",\n    \"JSON_annotation_column\": \"annotation\"\n}",
                     "tool_id": "json_db_config_generating",
                     "tool_stderr": "",
-                    "tool_stdout": "DEBG\n{\n    \"execution\": \"true\",\n    \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"JSON_table\": \"sample\",\n    \"JSON_fragment_column\": \"fragment\",\n    \"JSON_sequence_column\": \"sequence\",\n    \"JSON_annotation_column\": \"annotation\"\n}",
-                    "update_time": "2025-06-02T15:09:19.180152",
+                    "tool_stdout": "DEBUG\n{\n    \"execution\": \"true\",\n    \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"JSON_table\": \"sample\",\n    \"JSON_fragment_column\": \"fragment\",\n    \"JSON_sequence_column\": \"sequence\",\n    \"JSON_annotation_column\": \"annotation\"\n}",
+                    "update_time": "2025-06-11T16:00:13.304790",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "a5a635de282655c8"
+                    "user_id": "6ee26cd2a9b017f6"
                 },
                 "status": "success",
                 "test_index": 0,
-                "time_seconds": 6.056678056716919,
+                "time_seconds": 15.370232105255127,
                 "tool_id": "json_db_config_generating",
                 "tool_version": "0.1.0+galaxy2"
             },
@@ -70,21 +70,19 @@
         },
         {
             "data": {
-                "inputs": {
-                    "db_request|execution": false
-                },
+                "inputs": {},
                 "job": {
-                    "command_line": "python3 -c \"import json; params = { 'execution': 'false', 'JSON_db_uri': '', 'JSON_table': '', 'JSON_fragment_column': '', 'JSON_sequence_column': '', 'JSON_annotation_column': '' }; f = open('/tmp/tmpexzs2_xe/job_working_directory/000/2/outputs/dataset_1d7dac23-dc24-4747-901c-6441a3b1807a.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpexzs2_xe/job_working_directory/000/2/outputs/dataset_1d7dac23-dc24-4747-901c-6441a3b1807a.dat'",
+                    "command_line": "python3 -c \"import json; params = { 'execution': 'false', 'JSON_db_uri': '', 'JSON_table': '', 'JSON_fragment_column': '', 'JSON_sequence_column': '', 'JSON_annotation_column': '' }; f = open('/tmp/tmpetlap50a/job_working_directory/000/2/outputs/dataset_c331c972-0356-4042-917b-f63fe99f938d.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBUG && cat '/tmp/tmpetlap50a/job_working_directory/000/2/outputs/dataset_c331c972-0356-4042-917b-f63fe99f938d.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-06-02T15:09:19.474779",
+                    "create_time": "2025-06-11T16:00:13.510772",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "282881",
+                    "external_id": "75631",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "1d721e33ec06790c",
-                    "id": "1d721e33ec06790c",
+                    "history_id": "39ef7b54816acc5a",
+                    "id": "39ef7b54816acc5a",
                     "inputs": {},
                     "job_messages": [],
                     "job_metrics": [],
@@ -95,30 +93,30 @@
                     "output_collections": {},
                     "outputs": {
                         "output_json": {
-                            "id": "1d721e33ec06790c",
+                            "id": "39ef7b54816acc5a",
                             "src": "hda",
-                            "uuid": "1d7dac23-dc24-4747-901c-6441a3b1807a"
+                            "uuid": "c331c972-0356-4042-917b-f63fe99f938d"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
-                        "chromInfo": "\"/tmp/tmpexzs2_xe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-                        "db_request": "{\"__current_case__\": 1, \"db_config\": {\"annotation_column\": null, \"db_uri\": null, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null}, \"execution\": false}",
+                        "chromInfo": "\"/tmp/tmpetlap50a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "db": "{\"db_request\": {\"__current_case__\": 1, \"db_config\": {\"annotation_column\": null, \"db_uri\": null, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null}, \"execution\": false}}",
                         "dbkey": "\"?\""
                     },
                     "state": "ok",
                     "stderr": "",
-                    "stdout": "DEBG\n{\n    \"execution\": \"false\",\n    \"JSON_db_uri\": \"\",\n    \"JSON_table\": \"\",\n    \"JSON_fragment_column\": \"\",\n    \"JSON_sequence_column\": \"\",\n    \"JSON_annotation_column\": \"\"\n}",
+                    "stdout": "DEBUG\n{\n    \"execution\": \"false\",\n    \"JSON_db_uri\": \"\",\n    \"JSON_table\": \"\",\n    \"JSON_fragment_column\": \"\",\n    \"JSON_sequence_column\": \"\",\n    \"JSON_annotation_column\": \"\"\n}",
                     "tool_id": "json_db_config_generating",
                     "tool_stderr": "",
-                    "tool_stdout": "DEBG\n{\n    \"execution\": \"false\",\n    \"JSON_db_uri\": \"\",\n    \"JSON_table\": \"\",\n    \"JSON_fragment_column\": \"\",\n    \"JSON_sequence_column\": \"\",\n    \"JSON_annotation_column\": \"\"\n}",
-                    "update_time": "2025-06-02T15:09:25.155850",
+                    "tool_stdout": "DEBUG\n{\n    \"execution\": \"false\",\n    \"JSON_db_uri\": \"\",\n    \"JSON_table\": \"\",\n    \"JSON_fragment_column\": \"\",\n    \"JSON_sequence_column\": \"\",\n    \"JSON_annotation_column\": \"\"\n}",
+                    "update_time": "2025-06-11T16:00:19.478490",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "a5a635de282655c8"
+                    "user_id": "6ee26cd2a9b017f6"
                 },
                 "status": "success",
                 "test_index": 1,
-                "time_seconds": 6.073927402496338,
+                "time_seconds": 6.3762428760528564,
                 "tool_id": "json_db_config_generating",
                 "tool_version": "0.1.0+galaxy2"
             },