diff save_to_db.xml @ 3:eca0d710bbe9 draft

planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 23 May 2025 08:51:50 +0000
parents 81e9e1d803fa
children c7a7520afb4b
line wrap: on
line diff
--- a/save_to_db.xml	Fri May 16 09:34:35 2025 +0000
+++ b/save_to_db.xml	Fri May 23 08:51:50 2025 +0000
@@ -24,11 +24,11 @@
     ]]></command>
     <inputs>
         <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
-        <param name="table" type="text" label="Database Table Name" optional="false" />
-        <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" optional="false" />
-        <param name="annotation_column" type="text" label="DB column contains annotation for ganbank file" optional="false" />
-        <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" />
-        <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
+        <param name="table" type="text" label="DB Table Name" optional="false" />
+        <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" />
+        <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" />
+        <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" />
+        <param name="db_uri" type="text" label="DB Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
     </inputs>   
     <outputs>
         <data name="output" format="txt" label="saving report" />
@@ -68,7 +68,17 @@
 Save Data To DB
 ===================
 
-Save GanDank data in SQL DB.
+Implemented a system to save GenBank (.gb) files in SQL DB, based on a connection via URI requests.
+The tool is tested on a locally hosted PostgreSQL database running in a Docker container.
+
+**Parameters**:
+---------------
+* **GenBank File(s)**: List of GenBaks files.
+* **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).
     ]]></help>
     <citations>
         <citation type="bibtex">