<tool id="schicexplorer_schicconsensusmatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>creates per cluster one average matrix</description>
    <macros>
        <token name="@BINARY@">scHicConsensusMatrices</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @BINARY@

        --matrix '$matrix_scooler'
        --clusters $clusters

        --outFileName consensus_matrix.scool

        --threads @THREADS@



    ]]></command>
    <inputs>
        
        <expand macro="matrix_scooler_macro"/>
        <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>
        
        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="consensus_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Consensus matrices"/>
    </outputs>
    <tests>
        <test>
            <param name='matrix_scooler' value='test_matrix.scool' />
            <param name='clusters' value='scHicConsensusMatrices/cluster_kmeans.txt' />
            <output name="outFileName" ftype="scool">
                <assert_contents>
                    <has_h5_keys keys='consensus_matrix_cluster_0, 
                                        consensus_matrix_cluster_0/bins, consensus_matrix_cluster_0/bins/chrom, 
                                        consensus_matrix_cluster_0/bins/end, consensus_matrix_cluster_0/bins/start,
                                        consensus_matrix_cluster_0/chroms, consensus_matrix_cluster_0/chroms/length, 
                                        consensus_matrix_cluster_0/chroms/name, consensus_matrix_cluster_0/indexes, 
                                        consensus_matrix_cluster_0/indexes/bin1_offset, consensus_matrix_cluster_0/indexes/chrom_offset,
                                        consensus_matrix_cluster_0/pixels, consensus_matrix_cluster_0/pixels/bin1_id,
                                        consensus_matrix_cluster_0/pixels/bin2_id, consensus_matrix_cluster_0/pixels/count, 
                                        consensus_matrix_cluster_1, consensus_matrix_cluster_1/bins, consensus_matrix_cluster_1/bins/chrom, 
                                        consensus_matrix_cluster_1/bins/end, consensus_matrix_cluster_1/bins/start, consensus_matrix_cluster_1/chroms,
                                        consensus_matrix_cluster_1/chroms/length, consensus_matrix_cluster_1/chroms/name, consensus_matrix_cluster_1/indexes,
                                        consensus_matrix_cluster_1/indexes/bin1_offset, consensus_matrix_cluster_1/indexes/chrom_offset, 
                                        consensus_matrix_cluster_1/pixels, consensus_matrix_cluster_1/pixels/bin1_id, consensus_matrix_cluster_1/pixels/bin2_id,
                                        consensus_matrix_cluster_1/pixels/count, consensus_matrix_cluster_2, consensus_matrix_cluster_2/bins, 
                                        consensus_matrix_cluster_2/bins/chrom, consensus_matrix_cluster_2/bins/end, consensus_matrix_cluster_2/bins/start, 
                                        consensus_matrix_cluster_2/chroms, consensus_matrix_cluster_2/chroms/length, consensus_matrix_cluster_2/chroms/name,
                                        consensus_matrix_cluster_2/indexes, consensus_matrix_cluster_2/indexes/bin1_offset, consensus_matrix_cluster_2/indexes/chrom_offset, 
                                        consensus_matrix_cluster_2/pixels, consensus_matrix_cluster_2/pixels/bin1_id, consensus_matrix_cluster_2/pixels/bin2_id, 
                                        consensus_matrix_cluster_2/pixels/count'/>
                </assert_contents>
            </output>
        </test>
       
    </tests>
    <help><![CDATA[

Consensus matrices
==================

scHicConsensusMatrices creates one consensus matrix for each cluster based on the clustered samples. The consensus matrices are normalized to an equal read coverage level and are all stored in one s
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>