annotate dose_response.xml @ 1:8a1b524ed9d8 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit dca5f947ae4c9697ac0cfce0b313170b541124e5

<tool id="dr_curve" name="Dose Response Curve for Toxicological Risk Assessment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>for Toxicological Risk Assessment</description>
    <macros>
        <token name="@TOOL_VERSION@">3.0.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <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="@TOOL_VERSION@">r-drc</requirement>
        <requirement type="package" version="4.3.3">r-base</requirement>
        <requirement type="package" version="3.5.1">r-ggplot2</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
        Rscript '$__tool_directory__'/dose_response.R
            '$input_csv'
            '$concentration_column'
            '$response_column'
            '$plot_output'
            '$ec_output'
        ]]>
    </command>
    <inputs>
        <param name="input_csv" type="data" format="tabular" label="Concentration - Response Tabular Input"/>
        <param name="concentration_column" type="data_column" data_ref="input_csv" label="Concentration Column" help="Name of the column for concentration values"/>
        <param name="response_column" type="data_column" data_ref="input_csv" label="Response Column" help="Name of the column for response values"/>
    </inputs>
    <outputs>
        <data name="plot_output" format="jpg" label="Dose Response Plot"/>
        <data name="ec_output" format="tabular" label="${tool.name} on ${on_string}: EC Values"/>
    </outputs>
        <tests>
        <test>
            <param name="input_csv" value="drc_input.tsv"/>
            <param name="concentration_column" value="1"/>
            <param name="response_column" value="2"/>
            <output name="plot_output" ftype="jpg">
                <assert_contents>
                    <has_image_width width="480"/>
                    <has_image_height height="480"/>
                </assert_contents>
            </output>
            <output name="ec_output" value="drc_EC_output.tsv" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
        This tool performs dose-response analysis on the provided CSV file,
        generates a dose-response plot, and calculates EC values (EC10, EC25, EC50).

        - `input_csv`: A TSV file containing the dose-response data.
        - `concentration_column`: The name of the column in the CSV file that contains the concentration values.
        - `response_column`: The name of the column in the CSV file that contains the response values
        - `plot_output`: A JPG image file of the dose-response plot.
        - `ec_output`: A tabular file containing the calculated EC values.
    ]]></help>
        <citations>
    <citation type="doi">10.1371/journal.pone.0146021</citation>
    </citations>
</tool>