../Java/Python/WrappPlotCoverage.py -i $formatType.inputFileName1
		#if $formatType.FormatInputFileName1 == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName1 == 'gff':
			-f gff	
		#elif $formatType.FormatInputFileName1 == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName1 == 'gff3':
			-f gff3
		#elif $formatType.FormatInputFileName1 == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName1 == 'gtf':
			-f gtf
		#end if
			
		-j $formatType2.inputFileName2
		#if $formatType2.FormatInputFileName2 == 'bed':
			-g bed
		#elif $formatType2.FormatInputFileName2 == 'gff':
			-g gff	
		#elif $formatType2.FormatInputFileName2 == 'gff2':
			-g gff2
		#elif $formatType2.FormatInputFileName2 == 'gff3':
			-g gff3
		#elif $formatType2.FormatInputFileName2 == 'sam':
			-g sam
		#elif $formatType2.FormatInputFileName2 == 'gtf':
			-g gtf
		#end if


		#if $optionRef.Ref == 'Yes':
			-q $optionRef.inputSequenceFile
		#end if

		#if $optionwidth.width == 'Yes':
			-w $optionwidth.widthVal
		#end if
		#if $optionheight.height == 'Yes':
			-e $optionheight.heightVal
		#end if
		#if $optionXlab.Xlab == 'Yes':
			-x $optionXlab.XlabVal
		#end if
		#if $optionYlab.Ylab == 'Yes':
			-y $optionYlab.YlabVal
		#end if
		#if $optiontitle.title == 'Yes':
			-t $optiontitle.titleVal
		#end if	
	
		#if $optionplusColor.plusColor == 'Yes':
			-p $optionplusColor.plusColorVal
		#end if
		#if $optionminusColor.minusColor == 'Yes':
			-m $optionminusColor.minusColorVal
		#end if

		#if $optionsumColor.sumColor == 'Yes':
			-s $optionsumColor.sumColorVal
		#end if
		#if $optionlineColor.lineColor == 'Yes':
			-l $optionlineColor.lineColorVal
		#end if	

		$merge
		-o $outputFile