--- a/SMART/galaxy/plotTranscriptList.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/plotTranscriptList.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -2,16 +2,12 @@
 	<description>Plot some information from a list of transcripts. </description>
 	<command interpreter="python">
 		../Java/Python/plotTranscriptList.py  -i $formatType.inputFileName
-		#if $formatType.FormatInputFileName == 'bed':
-			-f bed
-		#elif $formatType.FormatInputFileName == 'gff':
+		#if $formatType.FormatInputFileName == 'gff':
 			-f gff	
 		#elif $formatType.FormatInputFileName == 'gff2':
 			-f gff2
 		#elif $formatType.FormatInputFileName == 'gff3':
 			-f gff3
-		#elif $formatType.FormatInputFileName == 'sam':
-			-f sam
 		#elif $formatType.FormatInputFileName == 'gtf':
 			-f gtf
 		#end if
@@ -33,10 +29,7 @@
 			-m $optionyLab.labVal
 		#end if	
 
-		#if $optionyLog.log == 'Yes':
-			-l $optionyLog.logVal
-		#end if	
-					
+		$optionLog.log
 		-s $shape
 		-b $bucket
 		
@@ -46,16 +39,11 @@
 	<inputs>
 		<conditional name="formatType">
 			<param name="FormatInputFileName" type="select" label="Input File Format">
-				<option value="bed">bed</option>
 				<option value="gff">gff</option>
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
-				<option value="sam">sam</option>
 				<option value="gtf">gtf</option>
 			</param>
-			<when value="bed">
-				<param name="inputFileName" format="bed" type="data" label="Input File"/>
-			</when>
 			<when value="gff">
 				<param name="inputFileName" format="gff" type="data" label="Input File"/>
 			</when>
@@ -65,16 +53,13 @@
 			<when value="gff3">
 				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
 			</when>
-			<when value="sam">
-				<param name="inputFileName" format="sam" 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 [compulsory option]"/>
-		<param name="yVal" type="text" value="None" label="tag for the y value [compulsory option]"/>
+		<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 ">
@@ -92,7 +77,7 @@
 		
 		<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"/>
+		<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 ">
@@ -117,16 +102,13 @@
 			</when>
 		</conditional>	
 
-		<conditional name="optionyLog">
+		<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>
+					<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>
-			<when value="Yes">
-				<param name="logVal" type="text" value=" "/>
-			</when>
-			<when value="No">
-			</when>
 		</conditional>	
 		
 		<param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
@@ -138,4 +120,15 @@
 		<data name="outputFilePNG" format="png" label="[plotTranscriptList]out 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>