## single to single case

        #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
            #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional

            #if $xml_path.inputFormat_selector == 'optionCool':
                ln -s '$xml_path.matrix_h5_cooler' "matrix.cool" &&

            #end if
            #if $xml_path.inputFormat_selector == 'optionH5':
                ln -s '$xml_path.matrix_h5_cooler' "matrix.h5" &&

            #end if
            #if $xml_path.inputFormat_selector == 'optionHomer':
               ln -s '$xml_path.matrixHomer' "matrix.homer" &&

            #end if

            #if $xml_path.inputFormat_selector == 'optionHicpro':
                ln -s '$xml_path.matrixHicpro' "matrix.hicpro" &&
                ln -s '$xml_path.bedHicpro' "matrix.bed" &&
            #end if
            #if $xml_path.inputFormat_selector == 'option2Dtext':
               ln -s '$xml_path.matrix2Dtext' "matrix.2Dtext" &&

               ln -s '$xml_path.chromosomeSizes' "chromosomeSizes.txt" &&

            #end if
            #if $xml_path.inputFormat_selector == 'optionHic':
                ln -s '$xml_path.matrixHic' "matrix.hic" &&
            #end if

            hicConvertFormat
            
            #if $xml_path.inputFormat_selector == 'optionCool':
                --matrices 'matrix.cool'
                --inputFormat cool
                #if $xml_path.correctionName:
                    --correction_name '$xml_path.correctionName'
                #end if

                #if $xml_path.correctionDivision:
                    --correction_division
                #end if

                #if $xml_path.chromosome:
                    #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($xml_path.chromosome).split(' ') ])

                    --chromosome $chromosome
                #end if

                #if $xml_path.loadRawValues:
                    --load_raw_values
                #end if
            #end if
            #if $xml_path.inputFormat_selector == 'optionH5':
                --matrices "matrix.h5"
                --inputFormat h5

            #end if
            #if $xml_path.inputFormat_selector == 'optionHomer':
                --matrices "matrix.homer"
                --inputFormat homer

            #end if
            #if $xml_path.inputFormat_selector == 'optionHicpro':
                --matrices "matrix.hicpro"
                --bedFileHicpro "matrix.bed"
                --inputFormat hicpro
            #end if
            #if $xml_path.inputFormat_selector == 'option2Dtext':
                --matrices "matrix.2Dtext"
                #if $xml_path.resolutions:
                    #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])
                    --resolutions $resolutions
                #end if
                --chromosomeSizes "chromosomeSizes.txt"
                --inputFormat 2D-text
            #end if
            #if $xml_path.inputFormat_selector == 'optionHic':
                --matrices "matrix.hic"
                #if $xml_path.resolutions:
                    #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])

                    --resolutions $resolutions
                #end if
                --inputFormat hic
            #end if
        

            --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
            --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
            #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'hicpro':
                --bedFileHicpro intervalls.bed
            #end if

        ### Set up links to matrices to have correct ending
        #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
            #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
                #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
                #if $xml_path.inputFormat_selector == 'optionCool':
                    ln -s '$xml_path.matrix_h5_cooler' "matrix.cool" &&
                #end if

                #if $xml_path.inputFormat_selector == 'optionH5':
                    ln -s '$xml_path.matrix_h5_cooler' "matrix.h5" &&
                #end if

                #if $xml_path.inputFormat_selector == 'optionHomer':
                    ln -s '$xml_path.matrix_h5_cooler' "matrix.homer" &&
                #end if

                #if $xml_path.inputFormat_selector == 'optionHicpro':
                    ln -s '$xml_path.matrix_h5_cooler' "matrix.hicpro" &&
                    ln -s '$xml_path.bedHicpro' "matrix.bed" &&
                #end if
                #if $xml_path.inputFormat_selector == 'option2Dtext':
                    ln -s '$xml_path.chromosomeSizes' "chromosomeSizes.txt" &&

                #end if
                #if $xml_path.inputFormat_selector == 'optionHic':
                    ln -s '$xml_path.matrix_h5_cooler' "matrix.hic" &&
                #end if
            #else:
                #set xml_manyToOne = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional
                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
                    #for $counter, $m in enumerate($xml_manyToOne.matrix_h5_cooler_multiple):
                        ln -s '$m' "${counter}_matrix.cool" &&
                    #end for
                    #set $m = ' '.join([ '"%s_matrix"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix_h5_cooler_multiple) ])

                #end if
                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionH5':
                    #for $counter, $m in enumerate($xml_manyToOne.matrix_h5_cooler_multiple):
                        ln -s '$m' "${counter}_matrix.h5" &&
                    #end for
                    #set $m = ' '.join([ '"%s_matrix"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix_h5_cooler_multiple) ])
                #end if
                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
                    #for $counter, $m in enumerate($xml_manyToOne.matrixHomer):
                        ln -s '$m' "${counter}_matrix.homer" &&
                    #end for
                    #set $m = ' '.join([ '"%s_matrix.homer"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHomer) ])
                #end if
                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'option2Dtext':
                    #for $counter, $m in enumerate($xml_manyToOne.matrix2Dtext):
                        ln -s '$m' "${counter}_matrix.matrix2Dtext" &&
                    #end for
                    #set $m = ' '.join([ '"%s_matrix.matrix2Dtext"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix2Dtext) ])
                    #if $xml_manyToOne.resolutions:
                        #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_manyToOne.resolutions).split(" ") ])
                    --resolutions $resolutions
                    #end if
                    --chromosomeSizes "chromosomeSizes.txt"

                #end if
                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
                    #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro):
                        ln -s '$m' "${counter}_matrix.hicpro" &&
                    #end for
                    #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ])

                    #for $counter, $bed in enumerate($xml_manyToOne.bedHicpro):
                        ln -s '$bed' "${counter}_matrix.bed" &&
                    #end for
                    #set $bed = ' '.join([ '"%s_matrix.bed"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.bedHicpro) ])
                    --bedFileHicpro '$bed'
                #end if
            #end if


        hicConvertFormat
            --outputFormat mcool

            #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
                #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutions).split(" ") ])

                --resolutions $resolutions
                 #if $xml_path.inputFormat_selector == 'optionCool':
                    --matrices "matrix.cool"
                    --inputFormat cool
                #end if
                #if $xml_path.inputFormat_selector == 'optionH5':
                    --matrices "matrix.h5"
                    --inputFormat h5
                #end if
                #if $xml_path.inputFormat_selector == 'optionHomer':
                    --matrices "matrix.homer"
                    --inputFormat homer
                #end if
                #if $xml_path.inputFormat_selector == 'optionHicpro':
                    --matrices "matrix.hicpro"
                    --bedFileHicpro "matrix.bed"
                    --inputFormat hicpro
                #end if
                #if $xml_path.inputFormat_selector == 'option2Dtext':
                    --matrices "matrix.2Dtext"
                    --chromosomeSizes "chromosomeSizes.txt"
                    --inputFormat 2D-text
                #end if
                #if $xml_path.inputFormat_selector == 'optionHic':
                    --matrices "matrix.hic"
                    --inputFormat hic
                #end if
            #end if

            #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'manyToOne_option':
                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
                    --inputFormat cool
                #end if

                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionH5':
                    --inputFormat h5
                #end if

                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
                    --inputFormat homer
                #end if
                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'option2Dtext':
                    
                    --inputFormat 2D-text
                #end if
                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
                    --inputFormat hicpro
                    --bedFileHicpro '$bed'
                #end if

                --matrices $m
            #end if
            --outFileName matrix.mcool
        #end if
        $storeAppliedCorrection
        $enforceInteger

        #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
            #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
                && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
            #else if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'hicpro':
                && mv matrix.hicpro matrix_out
            #else:
                && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
            #end if
        #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
            && mv matrix.mcool matrix_out
        #end if