<tool id="schicexplorer_schicnormalize" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
    <description>normalize single-cell Hi-C interaction matrices to the same read coverage</description>
    <macros>
        <token name="@BINARY@">scHicNormalize</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @BINARY@

        --matrix '$matrix_scooler'

        --outFileName normalized_matrix.scool

        --threads @THREADS@



    ]]></command>
    <inputs>
        
        <expand macro="matrix_scooler_macro"/>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="normalized_matrix.scool" format="scool" label="${tool.name} on ${on_string}: normalized matrix"/>
    </outputs>
    <tests>
        <test>
            <param name='matrix_scooler' value='test_matrix.scool' />
            <output name="outFileName" ftype="scool">
                <assert_contents>
                    <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/bin1_offset, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/bin2_id, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz, 
                    Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/chrom,
                    Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/end, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/start, 
                    Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms/length, 
                    Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms/name, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/indexes, 
                    Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/indexes/bin1_offset, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/indexes/chrom_offset,
                    Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/pixels, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/pixels/bin1_id,
                    Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/pixels/bin2_id, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/pixels/count, 
                    Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz, Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/bins, 
                    Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/bins/end,
                    Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/bins/start, Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/chroms, 
                    Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/chroms/name,
                    Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/indexes, Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/indexes/bin1_offset,
                    Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/pixels, 
                    Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/pixels/bin2_id, 
                    Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz, 
                    Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/bins, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/bins/chrom, 
                    Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/bins/end, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/bins/start, 
                    Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/chroms, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/chroms/length,
                    Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/chroms/name, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/indexes, 
                    Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/indexes/bin1_offset, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/indexes/chrom_offset, 
                    Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/pixels, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/pixels/bin1_id,
                    Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/pixels/bin2_id, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/pixels/count,
                    Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/bins, 
                    Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/bins/end,
                    Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/bins/start, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/chroms,
                    Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/chroms/name,
                    Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/indexes, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/indexes/bin1_offset, 
                    Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/pixels, 
                    Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/pixels/bin2_id,
                    Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz, 
                    Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/bins, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/bins/chrom,
                    Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/bins/end, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/bins/start,
                    Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/chroms, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/chroms/length,
                    Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/chroms/name, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/indexes,
                    Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/indexes/bin1_offset, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/indexes/chrom_offset, 
                    Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/pixels, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/pixels/bin1_id, 
                    Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/pixels/bin2_id, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/pixels/count, 
                    Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz, Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/bins, Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/bins/chrom, 
                    Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/bins/end, Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/bins/start, 
                    Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/chroms, Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/chroms/length, 
                    Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/chroms/name, Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/indexes, 
                    Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/indexes/bin1_offset, Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/indexes/chrom_offset, 
                    Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/pixels, Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/pixels/bin1_id, 
                    Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/pixels/bin2_id, Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz/pixels/count, 
                    Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/bins, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/bins/chrom, 
                    Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/bins/end, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/bins/start, 
                    Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/chroms, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/chroms/length, 
                    Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/chroms/name, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/indexes, 
                    Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/indexes/chrom_offset,
                    Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/pixels, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/pixels/bin1_id, 
                    Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/pixels/bin2_id, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/pixels/count, 
                    Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/bins, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/bins/chrom, 
                    Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/bins/end, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/bins/start,
                    Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/chroms, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/chroms/length, 
                    Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/chroms/name, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/indexes, 
                    Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/indexes/bin1_offset, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/indexes/chrom_offset,
                    Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/bin1_id, 
                    Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/bin2_id, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/count, 
                    Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz, Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/bins, 
                    Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/bins/chrom, Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/bins/end, 
                    Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/bins/start, Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/chroms, 
                    Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/chroms/length, Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/chroms/name,
                    Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/indexes, Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/indexes/bin1_offset,
                    Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/indexes/chrom_offset, Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/pixels, 
                    Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/pixels/bin2_id,
                    Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz/pixels/count, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz, 
                    Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/chrom, 
                    Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/end, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/start, 
                    Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/length, 
                    Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/name, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes,
                    Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/bin1_offset, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/chrom_offset, 
                    Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin1_id, 
                    Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin2_id, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/count,
                    Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz, Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/bins, 
                    Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/bins/end, 
                    Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/chroms, 
                    Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/chroms/name,
                    Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/indexes, Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/indexes/bin1_offset,
                    Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/pixels,
                    Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/pixels/bin2_id,
                    Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz, 
                    Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/bins, Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/bins/chrom,
                    Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/bins/start,
                    Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/chroms, Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/chroms/length,
                    Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/indexes, 
                    Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/indexes/chrom_offset, 
                    Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/pixels, Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/pixels/bin1_id, 
                    Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz/pixels/count,
                    Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins, 
                    Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/end,
                    Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms,
                    Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/name,
                    Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/bin1_offset,
                    Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels, 
                    Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin2_id,
                    Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz, 
                    Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/bins, Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/bins/chrom, 
                    Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/bins/start, 
                    Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/chroms, Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/chroms/length, 
                    Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/indexes,
                    Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/indexes/chrom_offset,
                    Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/pixels, Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/pixels/bin1_id,
                    Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz/pixels/count, 
                    Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz, Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/bins,
                    Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/bins/end, 
                    Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/chroms,
                    Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/chroms/name, 
                    Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/indexes/bin1_offset,
                    Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/pixels,
                    Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/pixels/bin2_id,
                    Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz,
                    Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/bins, Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/bins/chrom,
                    Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/bins/start, 
                    Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/chroms, Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/chroms/length,
                    Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/indexes, 
                    Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/indexes/chrom_offset, 
                    Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/pixels, Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/pixels/bin1_id,
                    Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz/pixels/count,
                    Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz, Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/bins,
                    Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/bins/end,
                    Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/chroms, 
                    Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/chroms/name,
                    Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/indexes/bin1_offset, 
                    Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/pixels,
                    Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/pixels/bin2_id,
                    Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz, 
                    Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/chrom, 
                    Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/start, 
                    Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/length, 
                    Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes, 
                    Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/chrom_offset,
                    Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin1_id, 
                    Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/count, 
                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/bins, 
                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/bins/end,
                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/bins/start, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms, 
                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms/length, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms/name,
                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes/bin1_offset,
                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels, 
                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/bin2_id, 
                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/count'/>
                </assert_contents>
            </output>
        </test>
       
    </tests>
    <help><![CDATA[

Normalize matrices
==================

scHicNormalize scales the read coverage of all matrices stored in the provided scool file to the matrix displaying the lowest read coverage in the said file.
This is a highly parallelized version of HiCExplorer's ̀ hicNormalize`, for more information, you can refer to this page:
https://hicexplorer.readthedocs.io/en/latest/content/tools/hicNormalize.html

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

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

</tool>