--- a/SMART/galaxy/getDistribution.xml	Mon Apr 22 11:11:10 2013 -0400
+++ b/SMART/galaxy/getDistribution.xml	Mon Apr 29 03:20:15 2013 -0400
@@ -1,5 +1,8 @@
 <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>
 	<command interpreter="python">
 		../Java/Python/GetDistribution.py -i $formatType.inputFileName
 		#if $formatType.FormatInputFileName == 'bed':
@@ -10,8 +13,6 @@
 			-f gff2
 		#elif $formatType.FormatInputFileName == 'gff3':
 			-f gff3
-		#elif $formatType.FormatInputFileName == 'csv':
-			-f csv
 		#elif $formatType.FormatInputFileName == 'sam':
 			-f sam
 		#elif $formatType.FormatInputFileName == 'gtf':
@@ -59,8 +60,6 @@
 		$bothStrands
 		$average
 		$normalize
-		$csv $outputCSV
-		$gff $outputGFF
 		-m
 		-o $outputFile
 
@@ -225,13 +224,11 @@
 	</inputs>
 
 	<outputs>
-		<data name="outputFile" format="png" label="[getDistribution] out png file"/>
+		<data name="outputFile" format="png" label="[get distribution] output PNG file"/>
 	</outputs> 
 
     <help>
-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.
+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).