<tool id="getWigData" name="get WIG data">
    <description>Compute the average data for some genomic coordinates using WIG files</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
    <command interpreter="python">
		../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile
	</command>
	
    <inputs>
    	<param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/>
   		<param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
		<param name="tagName" type="text" value="None" label="tag option" help="choose a tag name to write the wig information to output file."/>
		<param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/>    
    </inputs>
        
    <outputs>
        <data format="gff3" name="outputFile" label="[get WIG data] output file"/>       
    </outputs> 

	<help>
Reads a transcript list, computes the average value of some WIG data (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) for each transcript and adds a tag corresponding to this average value to the transcript.

The script finds all the data which correspond to the genomic coordinates of a transcript, average these data and store the result into a tag. Then, the transcripts are written in an output file, together with the tag.

You can then plot your data using *plotTranscriptList.py*.
	</help>
</tool>