<tool id="plot" name="Plot">
	<description>Plot some information from a list of transcripts.</description>
	<command interpreter="python">
		../Java/Python/plot.py -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'gff':
			-f gff
		#elif $formatType.FormatInputFileName == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName == 'gff3':
			-f gff3
		#end if
		
		-x $xLabel
		
                -y $yLabel

	        -X $XVal
                -Y $YVal

	        #if $optionLog.log == 'Yes' :
		    -l $optionLog.logOnAxisLabel
                #end if
                
                -s $shape
		-o $outputFile

	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">
				<option value="gff">gff</option>
				<option value="gff2">gff2</option>
				<option value="gff3">gff3</option>
			</param>
			<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="xLabel" type="text" value="value1" label="x label option" help="Choose one of the tags of 9th column in GFF file to be plotted as X-axis. Warning: You can only choose the tag value is digital."/>
                <param name="yLabel" type="text" value="value2" label="y label option" help="Choose one of the tags of 9th column in GFF file to be plotted as Y-axis. You can only choose the tag value is digital."/>
                <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/>
		
		<param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>


                <conditional name="optionLog">
			<param name="log" type="select" label="calculate log option" help="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="logOnAxisLabel" type="text" value="y" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"/>
			</when>
			<when value="No">
			</when>
		</conditional>
                <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
	</inputs>
	
	<outputs>
		<data name="outputFile" format="png" label="[plot] Output file"/>
	</outputs>
</tool>