diff json_db_config_generating.xml @ 0:95757ea6c333 draft

planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae

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+++ b/json_db_config_generating.xml	Mon Jun 02 13:39:41 2025 +0000
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+<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@">1</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>
+        <param name="execution" type="boolean" label="execution key" checked="False" help="If True the execution key in the json file will be true" optional="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" />
+    </inputs>   
+    <outputs>
+        <data name="output_json" format="json" label="JSON Conf" />
+    </outputs>
+    <tests>
+        <!--test execution is true -->
+        <test> 
+            <param name="execution" value="True" />
+            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
+            <param name="table_name" value="sample" />
+            <param name="fragment_column" value="fragment" />
+            <param name="sequence_column" value="sequence" />
+            <param name="annotation_column" value="annotation" />
+            <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> 
+            <param name="execution" value="False" />
+            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
+            <param name="table_name" value="sample" />
+            <param name="fragment_column" value="fragment" />
+            <param name="sequence_column" value="sequence" />
+            <param name="annotation_column" value="annotation" />
+            <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="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>
+    </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>
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