mkdir ./QCfolder &&
        mkdir '$qc.files_path' &&
        hicBuildMatrix
            --samFiles
            #for $repeat in $samFiles:
                '${repeat.samFile}'
            #end for

            --restrictionCutFile '$restrictionCutFile'

            #if $restrictionSequence:
                --restrictionSequence $restrictionSequence
            #end if
            #if $danglingSequence:
                --danglingSequence $danglingSequence
            #end if
            #if $minDistance:
            --minDistance $minDistance
            #end if
            #if $maxLibraryInsertSize:
                --maxLibraryInsertSize $maxLibraryInsertSize
            #end if

            #if $binSizes:
                --binSize
                #for $repeat in $binSizes
                    '${repeat.binSize}'
                #end for
            #end if

            #if $chromosomeSizes:
                --chromosomeSizes '$chromosomeSizes'
            #end if
            #if $dbKey:
                --genomeAssembly '$dbKey'
            #else
                --genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
            #end if

            #if $region:
                --region '$region'
            #end if

            --outFileName 'matrix.$outputFormat'

            #if $outBam:
                $outBam ./unsorted.bam
            #end if

            $keepSelfCircles
            $keepSelfLigation
            $skipDuplicationCheck

            #if $minMappingQuality and $minMappingQuality is not None:
                --minMappingQuality $minMappingQuality
            #end if

            --threads \${GALAXY_SLOTS:-4}

            --QCfolder ./QCfolder
        &&
        mv ./QCfolder/* $qc.files_path/
        &&
        mv '$qc.files_path/hicQC.html' '$qc'
        && mv "$qc.files_path"/*.log raw_qc
        && mv matrix.$outputFormat matrix
        #if $outBam:
            && samtools sort -@ \${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
        #end if