<tool id="plotTranscriptList" name="plot transcript list">
	<description>Plot some information from a list of transcripts. </description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python">
		../Java/Python/plotTranscriptList.py  -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'gff':
			-f gff	
		#elif $formatType.FormatInputFileName == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName == 'gff3':
			-f gff3
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf
		#end if
		
		-x $xVal
		-y $yVal
		#if $optionz.z == 'Yes':
			-z $optionz.zVal
		#end if		
			
		-X $XVal
		-Y $YVal
		-Z $ZVal
			
		#if $optionxLab.xLab == 'Yes':
			-n $optionxLab.labVal
		#end if
		#if $optionyLab.yLab == 'Yes':
			-m $optionyLab.labVal
		#end if	

		$log
		-s $shape
		-b $bucket
		
		-o $outputFilePNG
	</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>
				<option value="gtf">gtf</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>
			<when value="gtf">
				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
			</when>
		</conditional>
		
		<param name="xVal" type="text" value="None" label="tag for the x value"/>
		<param name="yVal" type="text" value="None" label="tag for the y value"/>
			
		<conditional name="optionz">
			<param name="z" type="select" label="tag for the z value ">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="zVal" type="text" value="None"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<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"/>

		<param name="ZVal" type="float" value="0.0" label="value for z when tag is not present (if applicable)"/>
			
		<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="labVal" 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="labVal" type="text" value=" "/>
			</when>
			<when value="No">
			</when>
		</conditional>	

		<param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
				<option value="" selected="true">No</option>
				<option value="-l x">log on the x-axis</option>
				<option value="-l y">log on the y-axis</option>
				<option value="-l xy">log on the x- and y-axis</option>
		</param>
		
		<param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
		<param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/>
		
	</inputs>

	<outputs>
		<data name="outputFilePNG" format="png" label="[plot transcript list] output file"/>
	</outputs> 
	
	<help>
Plot the data attached as tags in a transcript list. This can be used for displaying the comparison of different sets of sliding windows, for instance.
  
The tool reads the tags of a transcript file (actually, a GFF3 file). It considers more specifically the tag names that you specify as parameter. If you use only one tag name, you can display a line plot. In this case, you have to specify a bucket size *s* (which is by defaut 1) and a point (*x*, *y*) tells you that there are *y* transcripts with tag values *x* to *x + s*.

You can display could plots if you use two tag names. Each point represents the values of the two tags of a transcript. If you use three variables, the third variable will be the color of the point. You can also use a log scale and name the axes of the plot.

Each transcript must contain the tags which are specified. If not, you should provide a default value, which is used when the tag is not present.

If you use a cloud plot, you can compute the Spearman's rho to quantify a correlation between your two tag values.
	</help>
</tool>