<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>distance vs HiC counts plot per chromosome</description>
    <macros>
        <token name="@BINARY@">hicPlotDistVsCounts</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[


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

        @BINARY@

            --matrix input_matrix.npz.h5
            $skipDiagonal
            --plotFile plot.png
            #if $plotTitle and $plotTitle is not None:
                --plotTitle '$plotTitle'
            #end if

            ## special: --chromosomeExclude is optional, but if given needs at least one argument
            #set chroms = '" "'.join([ str($var.chromosomeExclude) for $var in $chromosomeExclude ])
            #if $chromosomeExclude:
                --chromosomeExclude $chroms
            #end if

]]>
    </command>
    <inputs>
        <param argument="--matrix" type="data" format="h5" label="Hi-C normalized/corrected matrix"/>

        <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" />
        <param argument="--plotTitle" type="text" optional="true" label="Plot title"/>
        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude">
            <param argument="--chromosomeExclude" type="text" value="" />
        </repeat>

    </inputs>
    <outputs>
        <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/>
            <param name="skipDiagonal" value="False"/>
            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/>
            <param name="skipDiagonal" value="False"/>
            <param name="plotTitle" value="Excluded chrUextra"/>
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chrUextra"/>
            </repeat>
            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

This program makes a distance vs. hi-c counts plot per chromosome.


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