#if $reference_source.reference_source_selector == "cached":
            ln -s $reference_source.ref_file.fields.path reference.fasta &&
        #else:
            ln -s $reference_source.ref_file reference.fasta &&
        #end if

       ln -s '$input_sortedAlignBAM' ./infile.bam &&
       ln -s '${input_sortedAlignBAM.metadata.bam_index}' infile.bai &&

        MethylDackel
            $main_task.task

            -@ \${GALAXY_SLOTS:-4}
            #if $main_task.task == 'extract':
                -o output
                $main_task.mergeContext
                #if str($main_task.OT).strip() != '':
                    --OT $main_task.OT
                #end if
                #if str($main_task.OB).strip() != '':
                    --OB $main_task.OB
                #end if
                #if str($main_task.CTOT).strip() != '':
                    --CTOT $main_task.CTOT
                #end if
                #if str($main_task.CTOB).strip() != '':
                    --CTOB $main_task.CTOB
                #end if
                #if str($main_task.mappability_options.mappability_status) == 'True':
                    -M '${main_task.mappability_options.mappability}'
                    --mappabilityThreshold $main_task.mappability_options.mappabilityThreshold
                    --minMappableBases $main_task.mappability_options.minMappableBases            
                #end if
            #end if
            #if $advanced_options.mbias_regionString:
                -r $advanced_options.mbias_regionString
            #end if
            #if $regionBed_options.regionBed_status == 'True':
                -l '$regionBed_options.regionBed'
                $regionBed_options.keepStrand
            #end if
            $advanced_options.keepDupes
            $advanced_options.keepSingleton
            $advanced_options.keepDiscordant
            -q $advanced_options.min_mapq
            -p $advanced_options.min_phred
            #if $advanced_options.methylation_metrics
                #for $context_methylation in $advanced_options.methylation_metrics:
                    $context_methylation
                #end for
            #end if
            #if $main_task.task == 'extract':
                --minOppositeDepth $advanced_options.minOppositeDepth
                --maxVariantFrac $advanced_options.maxVariantFrac
                -d $advanced_options.min_pbdepth
                --ignoreFlags $advanced_options.ignoreFlags
                --requireFlags $advanced_options.requireFlags
                #if $main_task.extract_outputs
                    $main_task.extract_outputs
                #end if
                #if str($advanced_options.nOT).strip() != '':
                    --nOT $advanced_options.nOT
                #end if
                #if str($advanced_options.nOB).strip() != '':
                    --nOB $advanced_options.nOB
                #end if
                #if str($advanced_options.nCTOT).strip() != '':
                    --nCTOT $advanced_options.nCTOT
                #end if
                #if str($advanced_options.nCTOB).strip() != '':
                    --nCTOB $advanced_options.nCTOB
                #end if
            #end if


            reference.fasta

            ./infile.bam

            #if $main_task.task == 'mbias':
                out_mbias $main_task.tsv > out_mbias.tsv &&
                touch out_mbias_OT.svg &&
                touch out_mbias_OB.svg &&
                touch out_mbias_CTOT.svg &&
                touch out_mbias_CTOB.svg
            #end if