<tool id="schicexplorer_schiccreatebulkmatrix" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
    <description>creates the bulk matrix out of  single-cell Hi-C interaction matrices</description>
    <macros>
        <token name="@BINARY@">scHicCreateBulkMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @BINARY@

        --matrix '$matrix_scooler'

        --outFileName bulk_matrix.cool

        --threads @THREADS@

    ]]></command>
    <inputs>
        
        <expand macro="matrix_scooler_macro"/>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="bulk_matrix.cool" format="scool" label="${tool.name} on ${on_string}: Bulk matrix"/>
    </outputs>
    <tests>
        <test>
            <param name='matrix_scooler' value='test_matrix.scool' />
            <output name="outFileName" file="scHicCreateBulkMatrix/bulk_matrix.cool" ftype="scool" compare="sim_size" delta="4000"/>
        </test>
    </tests>
    <help><![CDATA[

Create bulk matrix
==================

scHicCreateBulkMatrix adds all available single-cell matrices of a scool file together and writes it as a single matrix to a cool file.

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

.. _readthedocs.io: http://schicexplorer.readthedocs.io/
]]></help>
    <expand macro="citations" />

</tool>