--- a/SMART/galaxy/getDistribution.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/getDistribution.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,8 +1,5 @@
 <tool id="getDistribution" name="get distribution">
-	<description>Get Distribution: Get the distribution of the genomic coordinates along a genome.</description>
-    <requirements>
-        <requirement type="set_environment">PYTHONPATH</requirement>
-    </requirements>
+	<description>Get Distribution: Get the distribution of the genomic coordinates on a genome.</description>
 	<command interpreter="python">
 		../Java/Python/GetDistribution.py -i $formatType.inputFileName
 		#if $formatType.FormatInputFileName == 'bed':
@@ -13,6 +10,8 @@
 			-f gff2
 		#elif $formatType.FormatInputFileName == 'gff3':
 			-f gff3
+		#elif $formatType.FormatInputFileName == 'csv':
+			-f csv
 		#elif $formatType.FormatInputFileName == 'sam':
 			-f sam
 		#elif $formatType.FormatInputFileName == 'gtf':
@@ -60,6 +59,8 @@
 		$bothStrands
 		$average
 		$normalize
+		$csv $outputCSV
+		$gff $outputGFF
 		-m
 		-o $outputFile
 
@@ -72,6 +73,7 @@
 				<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>
@@ -87,6 +89,9 @@
 			<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>
@@ -98,7 +103,7 @@
 		<param name="refFile" format="fasta" type="data" label="reference genome file"/>
 		
 		<conditional name="optionNbBin">
-			<param name="Nb" type="select" label="number of points">
+			<param name="Nb" type="select" label="number of bins">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -109,20 +114,8 @@
 			</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="if you wish to plot only one locus, mention its start position">
+			<param name="start" type="select" label="start from a given region">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -134,7 +127,7 @@
 		</conditional>
 
 		<conditional name="optionEnd">
-			<param name="end" type="select" label="if you wish to plot only one locus, mention its end position">
+			<param name="end" type="select" label="end from a given region">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -146,7 +139,7 @@
 		</conditional>
 
 		<conditional name="optionHeight">
-			<param name="height" type="select" label="height of the figure">
+			<param name="height" type="select" label="height of the graphics">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -158,7 +151,7 @@
 		</conditional>
 
 		<conditional name="optionWidth">
-			<param name="width" type="select" label="width of the figure">
+			<param name="width" type="select" label="width of the graphics">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -193,6 +186,18 @@
 			</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>
@@ -205,8 +210,9 @@
 			</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="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot plot average (instead of sum)"/>
 
 		<conditional name="optionNames">
 			<param name="names" type="select" label="name for the tags (separated by commas and no space)">
@@ -220,18 +226,23 @@
 			</when>
 		</conditional>
 
-		<param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panel sizes are different)"/>
+		<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."/>
 	</inputs>
 
 	<outputs>
-		<data name="outputFile" format="png" label="[get distribution] output PNG file"/>
+		<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>
-Print a density profile of the data for each chromosome. 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.
+        This script gives a .tar out file, if you want to take look at the results, you have to download it.
     </help>	
 </tool>