# HG changeset patch
# User tduigou
# Date 1749655555 0
# Node ID f103f5253a93ba90ca2d7bc6af685b4f1a99792a
# Parent  8eb6c417d4f583625935cff8c4f2e93d0fe1fed4
planemo upload for repository https://github.com/brsynth commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty

diff -r 8eb6c417d4f5 -r f103f5253a93 json_db_config_generating.xml
--- a/json_db_config_generating.xml	Mon Jun 02 15:10:45 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-<tool id="json_db_config_generating" name="JSON DB_Config Generating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
-    <description>Genarate a JSON file used as DB config</description>
-    <macros>
-        <token name="@VERSION_SUFFIX@">2</token>
-        <token name="@TOOL_VERSION@">0.1.0</token>
-    </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('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$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" optional="false"/>
-            <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>
-    </inputs>   
-    <outputs>
-        <data name="output_json" format="json" label="JSON Conf" />
-    </outputs>
-    <tests>
-        <!--test execution is true -->
-        <test> 
-            <conditional name="db_request">
-                <param name="execution" value="true" />
-                <param name="db_config|db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
-                <param name="db_config|table_name" value="sample" />
-                <param name="db_config|fragment_column" value="fragment" />
-                <param name="db_config|sequence_column" value="sequence" />
-                <param name="db_config|annotation_column" value="annotation" />
-            </conditional>
-            <output name="output_json">
-                <assert_contents>
-                    <has_json_property_with_text property="execution" text="true" />
-                    <has_json_property_with_text property="JSON_db_uri" text="postgresql://postgres:RK17__at__localhost:5432/test_fragments_db" />
-                    <has_json_property_with_text property="JSON_table" text="sample" />
-                    <has_json_property_with_text property="JSON_fragment_column" text="fragment" />
-                    <has_json_property_with_text property="JSON_sequence_column" text="sequence" />
-                    <has_json_property_with_text property="JSON_annotation_column" text="annotation" />
-                </assert_contents>
-            </output>
-        </test>
-        <!--test execution is false -->
-        <test> 
-            <conditional name="db_request">
-                <param name="execution" value="false" />
-            </conditional>
-            <output name="output_json">
-                <assert_contents>
-                    <has_json_property_with_text property="execution" text="false" />
-                    <has_json_property_with_text property="JSON_db_uri" text="" />
-                    <has_json_property_with_text property="JSON_table" text="" />
-                    <has_json_property_with_text property="JSON_fragment_column" text="" />
-                    <has_json_property_with_text property="JSON_sequence_column" text="" />
-                    <has_json_property_with_text property="JSON_annotation_column" text="" />
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-
-    <help><![CDATA[
-JSON DB_Config Generating
-=========================
-
-Generate a JSON file to be used as a DB configuration. This JSON file can later be used to access the database via the specified URI, as well as the defined table and column names.
-This tool is primarily designed to control the execution of the save_to_db tool by enabling or disabling its execution and by providing the database configuration through a JSON file.
-
-**Parameters**:
----------------
-* **execution key**: The value of execution key in the JSON (true or false)
-* **DB Table Name**: Name of the target table in the PostgreSQL database.
-* **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN". 
-* **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file.
-* **DB IDs Column Name**: Column holding the unique fragment IDs.
-* **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name).
-* NOTE: This tool is designed to manage the execution of save_to_db within a workflow. If parameters are set directly in save_to_db via the user interface, the JSON file data will be ignored.
-    ]]></help>
-    <citations>
-        <citation type="bibtex">
-            @unpublished{json_db_config_generating
-                author = {Ramiz Khaled},
-                title = {{json_db_config_generating}},
-                url = {https://github.com/brsynth/},
-            }
-        </citation>
-    </citations>
-</tool>
\ No newline at end of file
diff -r 8eb6c417d4f5 -r f103f5253a93 json_db_config_generating_boolean.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/json_db_config_generating_boolean.xml	Wed Jun 11 15:25:55 2025 +0000
@@ -0,0 +1,109 @@
+<tool id="json_db_config_generating" name="JSON DB_Config Generating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>Genarate a JSON file used as DB config</description>
+    <macros>
+        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@TOOL_VERSION@">0.1.0</token>
+    </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()"
+    ]]></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>
+    </inputs>   
+    <outputs>
+        <data name="output_json" format="json" label="JSON Conf" />
+    </outputs>
+    <tests>
+        <!--test execution is true -->
+        <test> 
+            <conditional name="db_request">
+                <param name="execution" value="true" />
+                <param name="db_config|db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
+                <param name="db_config|table_name" value="sample" />
+                <param name="db_config|fragment_column" value="fragment" />
+                <param name="db_config|sequence_column" value="sequence" />
+                <param name="db_config|annotation_column" value="annotation" />
+            </conditional>
+            <output name="output_json">
+                <assert_contents>
+                    <has_json_property_with_text property="execution" text="true" />
+                    <has_json_property_with_text property="JSON_db_uri" text="postgresql://postgres:RK17__at__localhost:5432/test_fragments_db" />
+                    <has_json_property_with_text property="JSON_table" text="sample" />
+                    <has_json_property_with_text property="JSON_fragment_column" text="fragment" />
+                    <has_json_property_with_text property="JSON_sequence_column" text="sequence" />
+                    <has_json_property_with_text property="JSON_annotation_column" text="annotation" />
+                </assert_contents>
+            </output>
+        </test>
+        <!--test execution is false -->
+        <test> 
+            <conditional name="db_request">
+                <param name="execution" value="false" />
+            </conditional>
+            <output name="output_json">
+                <assert_contents>
+                    <has_json_property_with_text property="execution" text="false" />
+                    <has_json_property_with_text property="JSON_db_uri" text="" />
+                    <has_json_property_with_text property="JSON_table" text="" />
+                    <has_json_property_with_text property="JSON_fragment_column" text="" />
+                    <has_json_property_with_text property="JSON_sequence_column" text="" />
+                    <has_json_property_with_text property="JSON_annotation_column" text="" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+JSON DB_Config Generating
+=========================
+
+Generate a JSON file to be used as a DB configuration. This JSON file can later be used to access the database via the specified URI, as well as the defined table and column names.
+This tool is primarily designed to control the execution of the save_to_db tool by enabling or disabling its execution and by providing the database configuration through a JSON file.
+
+**Parameters**:
+---------------
+* **execution key**: The value of execution key in the JSON (true or false)
+* **DB Table Name**: Name of the target table in the PostgreSQL database.
+* **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN". 
+* **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file.
+* **DB IDs Column Name**: Column holding the unique fragment IDs.
+* **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name).
+* NOTE: This tool is designed to manage the execution of save_to_db within a workflow. If parameters are set directly in save_to_db via the user interface, the JSON file data will be ignored.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{json_db_config_generating
+                author = {Ramiz Khaled},
+                title = {{json_db_config_generating}},
+                url = {https://github.com/brsynth/},
+            }
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file