<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>normalize and compare two HiC matricies</description>
    <macros>
        <token name="@BINARY@">hicCompareMatrices</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

    @BINARY@
    --matrices '$matrix1' '$matrix2'
    --operation $operation
    --outFileName matrix.$outputFormat

    && mv matrix.$outputFormat matrix
]]>
    </command>
    <inputs>
        <param name='matrix1' type="data" format="h5,cool"
            label="First matrix"/>
        <param name='matrix2' type="data" format="h5,cool"
            label="Second matrix to compare against the first"/>

        <param name='operation' type='select' label="Operation to be used for the comparison">
            <option value='diff'>diff</option>
            <option value="ratio">ratio</option>
            <option value="log2ratio">log2ratio</option>
        </param>
        <param name='outputFormat' type='select' label="Output file format">
            <option value='h5'>HiCExplorer format</option>
            <option value="cool">cool</option>
        </param>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
            <change_format>
                <when input="outputFormat" value="cool" format="cool" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix1" value="small_test_matrix.h5"/>
            <param name="matrix2" value="small_test_matrix.h5"/>
            <param name="operation" value='log2ratio' />
            <param name="outputFormat" value="h5" />
            <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='2000'/>
        </test>
        <test>
            <param name="matrix1" value="pearson_small_50kb.cool"/>
            <param name="matrix2" value="pearson_small_50kb.cool"/>
            <param name="operation" value='ratio' />
            <param name="outputFormat" value="cool" />
            <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/>
        </test>

    </tests>
    <help><![CDATA[
Comparison of HiC matrices
==========================
`hicCompareMatrices` takes two matrices, normalizes them and appliesthe given operation. To
normalize the matrices each element is divided by sum of the matrix.

Input
-----
- the matricies to be compared



| For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]></help>
    <expand macro="citations" />
</tool>