<tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>combines Hi-C matrices of the same size</description>
    <macros>
        <token name="@BINARY@">hicSumMatrices</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #for $counter, $m in enumerate($matrices):
            ln -s '$m' ${counter}.npz.h5 &&
        #end for

        #set $m = '" "'.join([ '%s.npz.h5' % $counter for $counter, $matrix in enumerate($matrices) ])
        hicSumMatrices
            --matrices "$m"
            --outFileName ./out.npz.h5
]]>
    </command>
    <inputs>
        <param argument="--matrices" type="data" format="h5" multiple="True"
            label="Matrices to combine" help="Needs to have the same shape"/>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
    </outputs>
    <tests>
        <test>
            <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/>
            <output name="outFileName" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
        </test>
    </tests>
    <help><![CDATA[
Summation of matrices
=====================

``hicSumMatrix`` is combining two (or more) contact matrices of the same size to one. 
This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to 
increase the power of the data. It is the nature of Hi-C that real contact cannot be distinguished
 from noise, especially with a low contact count. The more contacts are given, the more likely it is 
 that a high number of contacts are real contact or contain at least a high amount. Therefore it is 
 a common way to merge replicates of Hi-C experiments to increase the validity of the experiment.

Input
-----

Parameters
__________
- two or matrices of the same shape.

Output
------
The summed matrix.

| 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>