<tool id="plotCoverage" name="plot coverage">
	<description>Plot the coverage of the first data with respect to the second one.</description>
	<command interpreter="python">
		../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
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName1" type="select" label="Input File Format 1">
				<option value="bed">bed</option>
				<option value="gff">gff</option>
				<option value="gff2">gff2</option>
				<option value="gff3">gff3</option>
				<option value="sam">sam</option>
				<option value="gtf">gtf</option>
			</param>
			<when value="bed">
				<param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
			</when>
			<when value="gff">
				<param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
			</when>
			<when value="gff2">
				<param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
			</when>
			<when value="gff3">
				<param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
			</when>
			<when value="sam">
				<param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
			</when>
			<when value="gtf">
				<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
			</when>
		</conditional>

		<conditional name="formatType2">
			<param name="FormatInputFileName2" type="select" label="Input File Format 2">
				<option value="bed">bed</option>
				<option value="gff">gff</option>
				<option value="gff2">gff2</option>
				<option value="gff3">gff3</option>
				<option value="gff2">sam</option>
				<option value="gff3">gtf</option>
			</param>
			<when value="bed">
				<param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
			</when>
			<when value="gff">
				<param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
			</when>
			<when value="gff2">
				<param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
			</when>
			<when value="gff3">
				<param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
			</when>
			<when value="sam">
				<param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
			</when>
			<when value="gtf">
				<param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
			</when>
		</conditional>

		<conditional name="optionRef">
			<param name="Ref" type="select" label="reference sequence file">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="inputSequenceFile" format="fasta" type="data" value="None"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		


		<conditional name="optionwidth">
			<param name="width" type="select" label="width of the plots (in px)">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="widthVal" type="integer" value="1500"  />
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="optionheight">
			<param name="height" type="select" label="height of the plots (in px)">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="heightVal" type="integer" value="1000" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optiontitle">
			<param name="title" type="select" label="title of the plots ">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="titleVal" type="text" value=" " />
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="optionXlab">
			<param name="Xlab" type="select" label="label on the x-axis">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="XlabVal" type="text" value=" "/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionYlab">
			<param name="Ylab" type="select" label="label on the y-axis">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="YlabVal" type="text" value=" " />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionplusColor">
			<param name="plusColor" type="select" label="color for the elements on the plus strand">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="plusColorVal" type="text" value="red"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionminusColor">
			<param name="minusColor" type="select" label="color for the elements on the minus strand">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="minusColorVal" type="text" value="blue"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionsumColor">
			<param name="sumColor" type="select" label="color for 2 strands coverage line">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="sumColorVal" type="text" value="black"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionlineColor">
			<param name="lineColor" type="select" label="color for the lines">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="lineColorVal" type="text" value="black"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<param name="merge" type="boolean" truevalue="-1" falsevalue="" checked="false" label="merge the 2 plots in 1"/>
	</inputs>

	<outputs>
		<data name="outputFile" format="tar" label="[plotCoverage] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
	</outputs> 
	
    <help>
        This script gives a .tar out file, if you want to take look at the results, you have to download it.
    </help>		
</tool>