<tool id="plotCoverage" name="plot coverage">
	<description>Plot the coverage of the first data with respect to the second one.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<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="sam">sam</option>
				<option value="gtf">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 for the figure">
					<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="[plot coverage] tar output file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
	</outputs> 
	
    <help>
Plot the coverage of the first set of genomic coordinates with respect to the second set of genomic coordinates. For each element of the second set (we will suppose that they are annotated genes), it computes the number of  elements of the first set (reads, for instance) which overlap it.

Alternatively, if the first file is in GFF format, and contains the **Target** file, you can omit the second file. However, a fasta file corresponding to the second file should be given (to compute the size of the reference elements).

The tool produces two plots per gene. The first plot gives the coverage: a point (*x*, *y*) means that *y* reads cover the *x* th nucleotide of the gene. The second figure displays the (possibly spliced) gene in black, and the overlapping reads (blue is colinear, red is anti-sense).

This script gives a .tar out file, if you want to take look at the results, you have to download it.
    </help>		
</tool>