<tool id="get_DB_data" name="get data from DB" version="0.1.0" profile="21.09">
    <description>Import data from Sorbonne Biofondry DB</description>
    <requirements>
        <requirement type="package" version="2.2.3">pandas</requirement>
        <requirement type="package" version="2.0.40">sqlalchemy</requirement>
        <requirement type="package" version="2.9.9">psycopg2</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/get_db_info.py' 
            --input '$input' 
            --db_uri '$db_uri' 
            --table '$table' 
            --fragment_column '$fragment_column'
            --output '$output'
    ]]></command>
    <inputs> 
        <param name="input" type="data" format="csv" label="Input CSV file" />
        <param name="table" type="text" label="Database Table Name" 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" />
    </inputs>    
    <outputs>
        <data name="output" format="json" label="DB Annotated Fragments (json)">
        </data>
    </outputs>
    <!--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'-->
    <tests>
        <test> 
            <param name="input" value="test_input.csv" />
            <param name="table" value="sample" />
            <param name="fragment_column" value="fragment" />
            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
            <output name="output" file="output_annotations.json" ftype="json" />
        </test>
    </tests>
    <help><![CDATA[
Pick Data From DB
===================

DBget data from SQL DB in docker container.
    ]]></help>
    <citations>
        <citation type="bibtex">
            @unpublished{get_DB_data
                author = {Ramiz Khaled},
                title = {{get_DB_data}},
                url = {https://github.com/brsynth/},
            }
        </citation>
    </citations>
</tool>