--- a/SMART/galaxy/getDistribution.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/getDistribution.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -1,5 +1,5 @@
 <tool id="getDistribution" name="get distribution">
-	<description>Get Distribution: Get the distribution of the genomic coordinates on a genome.</description>
+	<description>Get Distribution: Get the distribution of the genomic coordinates along a genome.</description>
 	<command interpreter="python">
 		../Java/Python/GetDistribution.py -i $formatType.inputFileName
 		#if $formatType.FormatInputFileName == 'bed':
@@ -58,7 +58,6 @@
 
 		$bothStrands
 		$average
-		-n $names
 		$normalize
 		$csv $outputCSV
 		$gff $outputGFF
@@ -74,7 +73,6 @@
 				<option value="gff">gff</option>
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
-				<option value="csv">csv</option>
 				<option value="sam">sam</option>
 				<option value="gtf">gtf</option>
 			</param>
@@ -90,9 +88,6 @@
 			<when value="gff3">
 				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
 			</when>
-			<when value="csv">
-				<param name="inputFileName" format="csv" type="data" label="Input File"/>
-			</when>
 			<when value="sam">
 				<param name="inputFileName" format="sam" type="data" label="Input File"/>
 			</when>
@@ -104,7 +99,7 @@
 		<param name="refFile" format="fasta" type="data" label="reference genome file"/>
 		
 		<conditional name="optionNbBin">
-			<param name="Nb" type="select" label="number of bins">
+			<param name="Nb" type="select" label="number of points">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -115,8 +110,20 @@
 			</when>
 		</conditional>
 
+		<conditional name="optionChrom">
+			<param name="chrom" type="select" label="if you wish to plot only one chromosome, mention the chromosome name">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="chromValue" type="text" value="chromName" />
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+
 		<conditional name="optionStart">
-			<param name="start" type="select" label="start from a given region">
+			<param name="start" type="select" label="if you wish to plot only one locus, mention its start position">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -128,7 +135,7 @@
 		</conditional>
 
 		<conditional name="optionEnd">
-			<param name="end" type="select" label="end from a given region">
+			<param name="end" type="select" label="if you wish to plot only one locus, mention its end position">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -140,7 +147,7 @@
 		</conditional>
 
 		<conditional name="optionHeight">
-			<param name="height" type="select" label="height of the graphics">
+			<param name="height" type="select" label="height of the figure">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -152,7 +159,7 @@
 		</conditional>
 
 		<conditional name="optionWidth">
-			<param name="width" type="select" label="width of the graphics">
+			<param name="width" type="select" label="width of the figure">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -187,18 +194,6 @@
 			</when>
 		</conditional>
 
-		<conditional name="optionChrom">
-			<param name="chrom" type="select" label="plot only one given chromosome">
-				<option value="Yes">Yes</option>
-				<option value="No" selected="true">No</option>
-			</param>
-			<when value="Yes">
-				<param name="chromValue" type="text" value="chromName" />
-			</when>
-			<when value="No">
-			</when>
-		</conditional>
-
 		<conditional name="optionColor">
 			<param name="color" type="select" label="color of the lines (separated by commas and no space)">
 				<option value="Yes">Yes</option>
@@ -211,27 +206,35 @@
 			</when>
 		</conditional>
 
+		<param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/>
+		<param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot the number of element per bin (instead of sum)"/>
 
-		<param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/>
-		<param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot plot average (instead of sum)"/>
-		<param name="names" type="text" value="nbElements" label="name for the tags (separated by commas and no space)"/>
-		<param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panels are different)"/>
-		<param name="csv" type="boolean" truevalue="-x" falsevalue="" checked="false" label="write a .csv file."/>
-		<param name="gff" type="boolean" truevalue="-g" falsevalue="" checked="false" label="write a .gff file."/>
+		<conditional name="optionNames">
+			<param name="names" type="select" label="name for the tags (separated by commas and no space)">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="namesValue" type="text" value="nbElements" />
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+
+		<param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panel sizes are different)"/>
 	</inputs>
 
 	<outputs>
 		<data name="outputFile" format="png" label="[getDistribution] out png file"/>
-		<data name="outputCSV" format="csv" label="[getDistribution] output csv file">
-			<filter>csv</filter>
-		</data>
-
-		<data name="outputGFF" format="gff" label="[getDistribution] output gff file">
-			<filter>gff</filter>
-		</data>
 	</outputs> 
 
     <help>
-        This script gives a .tar out file, if you want to take look at the results, you have to download it.
+This script gives a .tar out file, if you want to take look at the results, you have to download it.
+
+Print a density profile of the data for each chromosome, see Figure~\ref{fig:getDistribution}. You have to provide the reference genome, to know the sizes of the chromosomes. You can also provide the number of points (called *bins*) you want per chromosome.
+
+By default, only one curve is plotted per chromosome, but you can plot one curve per strand and per chromosome (the minus strand will be plotted with non-positive values on the *y*-axis).
+
+If you want, you can also plot a specific region, by mentionning the chromosome, the start and the end positions of the region.
     </help>	
 </tool>