annotate hicMergeMatrixBins.xml @ 3:5186eda61ca4 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

<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[
        hicMergeMatrixBins
            --matrix '$matrix_h5_cooler'
            --numBins $numBins
            $runningWindow
            --outFileName ./out.npz.h5

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />

        <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_h5_cooler" 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[

Change matrix resolution
========================

``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb 
contact matrix a 1000 kb one:

Number of bins to merge = 10

100 kb * 10 = 1000 kb = 1 Mb

This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is
to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but 
to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it 
difficult to interpret, especially if the read depth of the Hi-C data is not high.

Input
-----

Parameters
__________
- contact matrix to change the resolution on
- Number of bins to merge
- running window

Output
------

A contact matrix with the resolution ``original resolution * number of bins``.

| 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>