<tool id="getWigProfile" name="get wig profile">
	<description>Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
	<command interpreter="python">
		../Java/Python/getWigProfile.py -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName == 'gff':
			-f gff	
		#elif $formatType.FormatInputFileName == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName == 'gff3':
			-f gff3
		#end if
		-w $inputWigFile
		-p $nbPoints
		-d $distance
		$strands
		-o $outputFilePNG
		#if $optionSMO.SMO == 'Yes':
			-m $optionSMO.smoothen
		#end if		

	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">
				<option value="bed">bed</option>
				<option value="gff">gff</option>
				<option value="gff2">gff2</option>
				<option value="gff3">gff3</option>
			</param>
			<when value="bed">
				<param name="inputFileName" format="bed" type="data" label="Input File"/>
			</when>
			<when value="gff">
				<param name="inputFileName" format="gff" type="data" label="Input File"/>
			</when>
			<when value="gff2">
				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
			</when>
			<when value="gff3">
				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
			</when>
		</conditional>
		
		<param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
		<param name="nbPoints" type="integer" value="1000" label="number of points on the x-axis"/>
		<param name="distance" type="integer" value="0" label="distance around genomic coordinates"/>
		<param name="strands" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately"/>
		
		<conditional name="optionSMO">
			<param name="SMO" type="select" label="smoothen the curve">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="smoothen" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
	</inputs>

	<outputs>
		<data name="outputFilePNG" format="png" label="[getWigProfile] out file"/>
	</outputs> 
	
	<help>
Computes the average distribution of the WIG data (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) along the transcripts given in input, and possibly before and after the transcripts.

The main inputs of the functions are a file containing a list of transcripts (or any sets of genomic interval) and a directory containing a set of WIG files (one file per chromosome, or one file per chromosome and per strand). The function then computes the WIG profile of each transcript. The user can also define a region around the transcripts that should also be plotted (in this case, the profile will include the WIG values which overlap with the transcript as well as the 5' and 3' regions). Since the transcript do not necessarily have the same sizes, all profiles will be extended or shrinked to fit in a size which is given by the user. If the resulting profile is a bit bumpy, the user can also smoothen the curve by using a linear smoothing function (the size of the smoothing window is given by the user). Finally, the user may want to plot the WIG data for the opposite strand too (if the strand specific WUG data are available).
	</help>
</tool>