<tool id="tt_baseline" name="Baseline toxicity calculator" version="0.1.0+galaxy0">
    <description>Toxicity prediction tool</description>
    <creator>
        <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology" url ="https://www.ufz.de/index.php?en=34241"/>
    </creator>
    <requirements>
        <requirement type="package" version="2.2.1">pandas</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
    python '$__tool_directory__/qsar1.py'
     --function '$function'
     --csv_input '$csv_input'
     #if $function == "apply_linear_functions"
     --functions_csv '$function_csv'
     #end if
     --output '$output'
    ]]></command>
 <inputs>
    <conditional name="function_cond">
        <param name="function" type="select" label="Process to execute" help="Select pre-set QSAR models or personal linear functions">
            <option value="calculate_baseline">Pre-defined QSARs</option>
            <option value="apply_linear_functions">Personal Linear Functions</option>
        </param>
        <when value="calculate_baseline">
        </when>
        <when value="apply_linear_functions">
            <param name="function_csv" type="data" label="Personal linear functions input" format="tabular" help="Input your logD data as tabular file"/>
        </when>
    </conditional>
    <param name="csv_input" type="data" label="logD data input" format="tabular" help="Input your logD data as tabular file"/>
</inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
        <tests>
        <test>
            <param name="function" value="calculate_baseline"/>
            <param name="csv_input" value="qsar.tabular"/>
            <output name="output" value="qsar_result.tsv" ftype="tabular"/>
        </test>
        <test>
            <param name="function" value="apply_linear_functions"/>
            <param name="csv_input" value="qsar.tabular"/>
            <param name="function_csv" value="functions.tabular"/>
            <output name="output" value="qsar_result_2.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help>
        Features:
        *calculate_baseline*
        *** Estimate the EC50 for four different species. EC50 are expressed in mol/L ***
        + Danio rerio log(1/EC50)= 0.99 * logDlipw + 0.78
        + Caenorhabditis elegans log(1/EC50)= 0.81 * logDlipw + 1.15
        + Daphnia magna log(1/EC50)= 0.82 * logDlipw + 1.48
        + Generic Human Cell log(1/EC50)= 0.026 / (10**logDlipw) * (1 + 10**(0.7*logDlipw+0.34) * 3 * 0.001 + 10**(3) * 0.07 * 0.001)
        *apply_linear_functions*
        *** Estimate the EC50 or based on user input linear functions (assuming the format 'ax+b' or 'ax-b') ***

        Input format: Tabular file with column  header and integers values for rows
        Functions input: Tabular file with one column header and linear function in the format 'ax+b' or 'ax-b' for rows
    </help>
    <citations>
    <citation type="doi">10.1021/acs.est.2c05217</citation>
    <citation type="doi">10.1016/j.aquatox.2018.12.003</citation>
    <citation type="doi">10.1016/S0048-9697(98)00157-0</citation>
    </citations>
</tool>