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comparison get_DB_data.xml @ 10:703fda6c48c5 draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 23 May 2025 08:39:47 +0000
parents 6401a277ee72
children 6c1e564bb278
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9:6401a277ee72 10:703fda6c48c5
1 <tool id="get_DB_data" name="get data from DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="get_DB_data" name="get data from DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Import data from Sorbonne Biofondry DB</description> 2 <description>Import GenBank data from a PostgreSQL database running in a Docker container and export it as .gb files</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">0.1.0</token> 5 <token name="@TOOL_VERSION@">0.1.0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
20 --table '$table' 20 --table '$table'
21 --fragment_column '$fragment_column' 21 --fragment_column '$fragment_column'
22 --output 'outdir' 22 --output 'outdir'
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param name="input" type="data" format="csv" label="Input CSV file" /> 25 <param name="input" type="data" format="csv" label="Input CSV File" />
26 <param name="table" type="text" label="Database Table Name" optional="false" /> 26 <param name="table" type="text" label="DB Table Name" optional="false" />
27 <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" optional="false" /> 27 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" />
28 <param name="annotation_columns" type="text" label="DB column contains annotation for ganbank file" optional="false" /> 28 <param name="annotation_columns" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" />
29 <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" /> 29 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" />
30 <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" /> 30 <param name="db_uri" type="text" label="DB Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
31 </inputs> 31 </inputs>
32 <outputs> 32 <outputs>
33 <collection name="output_gb" type="list" label="GenBank Files collection" > 33 <collection name="output_gb" type="list" label="GenBank Files collection" >
34 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" /> 34 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
35 </collection> 35 </collection>
36 </outputs> 36 </outputs>
37 <tests> 37 <tests>
38 <!--python get_db_info.py -input 'test-data/test_input.tsv' -sequence_column 'sequence' -annotation_column 'annotation' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output'--> 38 <!--python get_db_info.py -input 'test-data/test_input.csv' -sequence_column 'sequence' -annotation_column 'annotation' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output'-->
39 <test> 39 <test>
40 <param name="input" value="test_input.csv" /> 40 <param name="input" value="test_input.csv" />
41 <param name="table" value="sample" /> 41 <param name="table" value="sample" />
42 <param name="sequence_column" value="sequence" /> 42 <param name="sequence_column" value="sequence" />
43 <param name="annotation_columns" value="annotation" /> 43 <param name="annotation_columns" value="annotation" />
70 70
71 <help><![CDATA[ 71 <help><![CDATA[
72 Pick Data From DB 72 Pick Data From DB
73 =================== 73 ===================
74 74
75 generate GanDank files from csv file based on SQL DB. 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.
77
78 **Parameters**:
79 ---------------
80 * **Input CSV File**: Contains construct IDs in the column 'ID' and their corresponding fragments in the following columns.
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".
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.
85 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name).
76 ]]></help> 86 ]]></help>
77 <citations> 87 <citations>
78 <citation type="bibtex"> 88 <citation type="bibtex">
79 @unpublished{get_DB_data 89 @unpublished{get_DB_data
80 author = {Ramiz Khaled}, 90 author = {Ramiz Khaled},