<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>Merges bins from a Hi-C matrix</description>
    <macros>
        <token name="@BINARY@">hicMergeMatrixBins</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        ln -s '$matrix' input.npz.h5 &&

        hicMergeMatrixBins
            --matrix input.npz.h5
            --numBins $numBins
            $runningWindow
            --outFileName ./out.npz.h5

]]>
    </command>
    <inputs>
        <param argument="--matrix" type="data" format="h5" label="Matrix to reduce" />
        <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
        <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="small_test_matrix.h5" />
            <param name="numBins" value="5" />
            <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Merges neighboring bins in a Hi-C matrix.

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