Mercurial > repos > tduigou > get_db_info

comparison get_DB_data.xml @ 12:ee28ec28140d draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 23 May 2025 12:45:20 +0000
parents 6c1e564bb278
children 5b16f2911491
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11:6c1e564bb278 12:ee28ec28140d
75 Implemented a system to generate GenBank (.gb) files from CSV input, based on data retrieved from a PostgreSQL database via URI requests. 75 Implemented a system to generate GenBank (.gb) files from CSV input, based on data retrieved from a PostgreSQL database via URI requests.
76 The tool is tested on a locally hosted PostgreSQL database running in a Docker container. 76 The tool is tested on a locally hosted PostgreSQL database running in a Docker container.
77 77
78 **Parameters**: 78 **Parameters**:
79 --------------- 79 ---------------
80 * **Input CSV File**: Contains construct IDs in the column 'ID' and their corresponding fragments in the following columns. 80 * **Input CSV File**: Contains construct IDs in the first column and their corresponding fragments in the following columns. (Without Header)
81 * **DB Table Name**: Name of the target table in the PostgreSQL database. 81 * **DB Table Name**: Name of the target table in the PostgreSQL database.
82 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN". 82 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
83 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, starting with "FEATURES" and including "LOCUS" information. Other metadata is optional. 83 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, starting with "FEATURES" and including "LOCUS" information. Other metadata is optional.
84 * **DB IDs Column Name**: Column holding the unique fragment IDs. 84 * **DB IDs Column Name**: Column holding the unique fragment IDs.
85 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name). 85 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name).