Mercurial > repos > tduigou > save_to_db
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 |
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--- 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">
