<tool id="scater_plot_tsne" name="Scater: t-SNE plot" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>of two components</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="0.15">r-rtsne</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/scater-plot-tsne.R'
-i '$input_loom'
#if str($colour_by).strip():
    --colour-by '$colour_by'
#end if
#if str($size_by).strip():
    --size-by '$size_by'
#end if
#if str($shape_by).strip():
    --shape-by '$shape_by'
#end if
-o '$output_plot'
    ]]></command>
    <inputs>
        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
        <param name="colour_by" argument="--colour-by" type="text" optional="true" label="Feature (from annotation file) to colour t-SNE plot points by" help="The values represented in this options should be categorical" />
        <param name="size_by" argument="--size-by" type="text" optional="true" label="Feature (from annotation file) to size t-SNE plot points by" help="The values represented in this options should be numerical and not categorical" />
        <param name="shape_by" argument="--shape-by" type="text" optional="true" label="Feature (from annotation file) to shape t-SNE plot points by" help="The values represented in this options should be categorical" />
    </inputs>
    <outputs>
        <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
            <param name="colour_by" value="Treatment" />
            <param name="shape_by" value="Mutation_Status" />
            <output name="output_plot" file="scater_tsne_plot.pdf" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Creates a t-SNE plot of a normalised SingleCellLoomExperiment object using Scater.
    ]]></help>
    <expand macro="citations" />
</tool>