<tool id="scater_plot_exprs_freq" name="Scater: plot expression frequency" version="@TOOL_VERSION@">
    <description>Plot the frequency of expression against the mean expression level for SCE</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="0.2.1">r-ggpubr</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/scater-plot-exprs-freq.R'
-i '$input_loom'
-o '$output_plot'
    ]]></command>
    <inputs>
        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
    </inputs>
    <outputs>
        <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
            <output name="output_plot" file="scater_exprs_freq.pdf" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Plot the frequency of expression (i.e., percentage of expressing cells) against the mean expression level for each feature in a SingleCellExperiment object.
    ]]></help>
    <expand macro="citations" />
</tool>