annotate dose_response.xml @ 3:2aa9da0a84a4 draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses commit 707eca86fc2de2e563fb5c89889f54eb13f529d0

<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@">4</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'
            '$replicate_column'
            '$plot_output'
            '$ec_output'
            '$compound_name'
            '$concentration_unit'
        ]]>
    </command>
    <inputs>
        <param name="input_csv" type="data" format="tabular" label="Dose-Response Tabular Input"/>
        <param name="concentration_column" type="data_column" data_ref="input_csv" label="Dose/Concentration Column Index" help="Index of the column for concentration values"/>
        <param name="response_column" type="data_column" data_ref="input_csv" label="Response Column Index" help="Index of the column for response values"/>
        <param name="replicate_column" type="data_column" data_ref="input_csv" label="Replicate Column Index" help="Index of the column for replicate values"/>
        <param name="compound_name" type="text" label="Compound Name" help="Name of the compound to analyze">
            <validator type="regex" message="Enter a valid compound name">^^[a-zA-Z0-9\[\]()_-]+$</validator>
        </param>
        <param name="concentration_unit" type="text" label="Concentration Unit (i.e. mg/L, µM)">
            <validator type="regex" message="Enter a valid concentration unit">^(\S+/\S+)</validator>
        </param>
    </inputs>
    <outputs>
        <data name="plot_output" format="jpg" label="${tool.name} on ${on_string}: ${compound_name} - Dose Response Plot"/>
        <data name="ec_output" format="tabular" label="${tool.name} on ${on_string}: ${compound_name} - EC Values"/>
    </outputs>
        <tests>
        <test>
            <param name="input_csv" value="drc_input.tsv"/>
            <param name="concentration_column" value="2"/>
            <param name="response_column" value="3"/>
            <param name="replicate_column" value="1"/>
            <param name="compound_name" value="test-chemical"/>
            <param name="concentration_unit" value="mg/L"/>
            <output name="plot_output" value="image_output.jpg" 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/TSV file,
        generates a dose-response plot, and calculates three Effect Concentrations (EC) values (EC10, EC25, EC50).
        The tool further calculate the AIC and the model summary.

        The tool need three inputs from the CSV/TSV file:
        - One column with the replicate number
        - One column with concentrations values
        - One column with biological response

        An exemplary input might look like:

      +------------+---------------+---------------+
      | rep        | conc          | resp          |
      +============+===============+===============+
      | 1          | 0             | 0             |
      +------------+---------------+---------------+
      | 2          | 10            | 50            |
      +------------+---------------+---------------+
      | 1          | 5             | 10            |
      +------------+---------------+---------------+

        **NOTE: Input Table must have column headers!**


    ]]></help>
        <citations>
    <citation type="doi">10.1371/journal.pone.0146021</citation>
    </citations>
</tool>