<tool id="plotRepartition" name="plot repartition">
	<description>Plot the repartition of different data on a whole genome. (This tool uses only 1 input file, the different values are stored in the tags. )</description>
	<command interpreter="python">
		../Java/Python/WrappPlotRepartition.py -i $inputFileName
		-n $names
		$normalize
		#if $optionColor.Color == 'Yes':
			-c $optionColor.colValue
		#end if		
		-f $format
		
		#if $optionLog.log == 'Yes':
			-l $optionLog.logVal
		#end if	
		
		-o $outputFilePNG
	</command>

	<inputs>
		<param name="inputFileName" type="data" label="Input Gff3 File" format="gff3"/>
		<param name="names" type="text" value="None" label="name for the tags (separated by commas and no space) [compulsory option]"/>
		<param name="normalize" type="boolean" truevalue="-r" falsevalue="" checked="false" label="normalize data (when panels are different)"/>
		<param name="format" type="text" value="png" label="format of the output file[default: png]"/>
		
		<conditional name="optionColor">
			<param name="Color" type="select" label="scolor of the lines (separated by commas and no space) ">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="colValue" type="text" value="None"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="optionLog">
			<param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="logVal" type="text" value=" "/>
			</when>
			<when value="No">
			</when>
		</conditional>	
		
	</inputs>

	<outputs>
		<data name="outputFilePNG" format="tar" label="[plotRepartition]out 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>