<tool id="scater_plot_dist_scatter" name="Scater: plot library QC" version="@TOOL_VERSION@">
    <description>Create plots to visualise library size, feature counts and mito gene expression</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="0.2.2">r-ggpubr</requirement>
        <requirement type="package" version="1.0.0">r-scales</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/scater-plot-dist-scatter.R'
-i '$input_loom'
-o '$output_plot'
$plot_log
    ]]></command>
    <inputs>
        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
        <param name="plot_log" type="boolean" truevalue="--log-scale" falsevalue="" label="Plot on log scale" help="Recommended for large datasets" />
    </inputs>
    <outputs>
        <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
            <param name="plot_log" value="false"/>
            <output name="output_plot" file="scater_reads_genes_dist.pdf" compare="sim_size" />
        </test>
        <test>
            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
            <param name="plot_log" value="true"/>
            <output name="output_plot" file="scater_reads_genes_dist_log.pdf" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Plot distribution of reads and features for single-cell RNA-seq analysis using Scater.
    ]]></help>
    <expand macro="citations" />
</tool>