--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/plotTranscriptList.xml	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,132 @@
+<tool id="plotTranscriptList" name="plot transcript list">
+	<description>Plot some information from a list of transcripts. </description>
+	<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>