<tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0">
    <description>generating a principal component analysis (PCA) plot from bamCorrelate or bigwigCorrelate output</description>
    <macros>
        <token name="@BINARY@">plotPCA</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
<![CDATA[
        @BINARY@
            --corData "$corData"
            --plotTitle "$plotTitle"
            --plotFile "$outFileName"
            --plotFileFormat "$outFileFormat"
]]>
    </command>
    <inputs>
        <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the bamCorrelate tool"/>
        <expand macro="image_file_format" />
        <expand macro="plotTitle" />
    </inputs>
    <outputs>
        <expand macro="output_image_file_format" />
    </outputs>
    <tests>
        <test>
            <param name="corData" value="bamCorrelate_result2.npz" ftype="deeptools_coverage_matrix" />
            <param name="plotTitle" value="Test Plot" />
            <param name="outFileFormat" value="png" />
            <output name="outFileName" file="plotPCA_result1.png" compare="sim_size" delta="100" />
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

Tool for generating a principal component analysis (PCA)
plot from bamCorrelate or bigwigCorrelate output.

-----

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>