<tool id="hicExport" name="hicExport" version="1.0">
    <description>saves a HiC Matrix in text format</description>
    <macros>
        <token name="@BINARY@">hicExport</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
        hicExport
            #if $matrix and $matrix is not None:
                --matrix $matrix
            #end if
            --outputFormat $outputFormat
            $clearMaskedBins
            --outFileName $output

    ]]></command>
    <inputs>
        <param label="Matrix to use" name="matrix" type="data" help="(--matrix)" />
        <param label="Output format" name="outputFormat" type="select"
            help="There are two possibilities: &quot;dekker&quot; and &quot;ren&quot;.
            The dekker format outputs the whole matrix where the first column and first row are the bin widths and labels.
            The &quot;ren&quot; format is a list of tuples of the form chrom, bin_star, bin_end, values. (--outputFormat)">
            <option selected="true" value="dekker">Dekker (first column and first rows are labels)</option>
            <option value="ren">Ren (chrom, bin_star, bin_end, values)</option>
        </param>
        <param name="clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" label="If set, masked bins are removed from the matrix"
            help="Masked bins are those that do not have any values, mainly because they are repetitive regions of the genome (--clearMaskedBins)" />
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="hicBuildMatrix_result1.npz"/>
            <param name="outputFormat" value="dekker"/>
            <output name="output" file="hicExport_result1.txt" ftpye="txt"/>
        </test>
        <test>
            <param name="matrix" value="hicBuildMatrix_result1.npz"/>
            <param name="outputFormat" value="ren"/>
            <param name="clearMaskedBins" value="True"/>
            <output name="output" file="hicExport_result2.txt" ftpye="txt"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Saves a HiC Matrix in text format

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