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comparison get_DB_data.xml @ 0:41ac63b5d221 draft

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planemo upload for repository https://github.com/brsynth commit 15dbdd1f0a222a8e1b0fb5c16b36885520a3d005
author tduigou
date Thu, 10 Apr 2025 08:45:18 +0000
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1 <tool id="get_DB_data" name="get data from DB" version="0.1.0" profile="21.09">
2 <description>Import data from Sorbonne Biofondry DB</description>
3 <requirements>
4 <requirement type="package" version="2.2.3">pandas</requirement>
5 <requirement type="package" version="2.0.40">sqlalchemy</requirement>
6 <requirement type="package" version="2.9.9">psycopg2</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 python '$__tool_directory__/get_db_info.py'
10 --input '$input'
11 --db_uri '$db_uri'
12 --table '$table'
13 --fragment_column '$fragment_column'
14 --output '$output'
15 ]]></command>
16 <inputs>
17 <param name="input" type="data" format="csv" label="Input CSV file" />
18 <param name="table" type="text" label="Database Table Name" optional="false" />
19 <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" />
20 <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
21 </inputs>
22 <outputs>
23 <data name="output" format="json" label="DB Annotated Fragments (json)">
24 </data>
25 </outputs>
26 <!--python get_DB_info.py -input 'test-data/test_input.csv' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output.json'-->
27 <tests>
28 <test>
29 <param name="input" value="test_input.csv" />
30 <param name="table" value="sample" />
31 <param name="fragment_column" value="fragment" />
32 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
33 <output name="output" file="output_annotations.json" ftype="json" />
34 </test>
35 </tests>
36 <help><![CDATA[
37 Pick Data From DB
38 ===================
39
40 DBget data from SQL DB in docker container.
41 ]]></help>
42 <citations>
43 <citation type="bibtex">
44 @unpublished{get_DB_data
45 author = {Ramiz Khaled},
46 title = {{get_DB_data}},
47 url = {https://github.com/brsynth/},
48 }
49 </citation>
50 </citations>
51 </tool>