#import re

        mkdir interactionFiles &&
        mkdir targetFolder &&
        mkdir significantFilesFolder &&

        #if $tar_input_conditional.tar_input_selector == 'tar_input':
            ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 
            tar -C interactionFiles -xvf viewpoints.tar &&
        #else:
            #for $file in $tar_input_conditional.interactionFiles:
                #set identifier = re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))                
                ln -s '$file' 'interactionFiles/$identifier' &&
            #end for
        #end if
    
        #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
            #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % re.sub('[^\s\w\-\.]', '_', str($file.element_identifier)) for $file in $interactionFiles ])
        #end if
        chicSignificantInteractions
            #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
                --interactionFile $interactonfileslist
                --computeSampleNumber $batchmode_conditional.computeSampleNumber
            #else:
                --interactionFile '$batchmode_conditional.interactionFilesOrderFile'
                --interactionFileFolder interactionFiles
                --batchMode
                --targetFileList targetListFile.txt
                --writeFileNamesToFile significantFiles.txt
                --computeSampleNumber $batchmode_conditional.computeSampleNumber
            #end if

            --pValue $pvalue

            #if $filter_conditional.filter_selector == 'optionXfold':
                --xFoldBackground $filter_conditional.xfold
            #else:
                --loosePValue $filter_conditional.loosePvalue

            #end if
            --backgroundModelFile '$backgroundModelFile'
            --resolution $resolution
            --peakInteractionsThreshold $peakInteractionsThreshold
            --range $rangeUpstream $rangeDownstream
            --targetFolder targetFolder
            --outputFolder significantFilesFolder
            $truncateZeroPvalues
            --fixateRange $fixateRange
            -suffix significant_interactions.txt
            --threads \${GALAXY_SLOTS:-4}

            #if $tar:
                && cd targetFolder
                && tar -cvf ../targetFolder.tar *
                && cd ..
                && rm -rf targetFolder

                && cd significantFilesFolder
                && tar -cvf ../significantFilesFolder.tar *
                && cd ..
                && rm -rf significantFilesFolder

            #end if