<tool id="scater_normalize" name="Scater: normalize SCE" version="@TOOL_VERSION@">
    <description>Compute normalised expression values for SCE</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/scater-normalize.R'
-i '$input_loom'
-o '$output_loom'
    ]]></command>
    <inputs>
        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset to normalize" />
    </inputs>
    <outputs>
        <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_loom" value="scater_manual_filtered.loom" ftype="loom" />
            <output name="output_loom" file="scater_filtered_normalised.loom" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Normalize a SingleCellLoomExperiment object using Scater. Adds 'logcounts' to assays slot.
    ]]></help>
    <expand macro="citations" />
</tool>