--- a/computeGCBias.xml	Mon Aug 05 11:36:11 2013 -0400
+++ b/computeGCBias.xml	Tue Aug 06 08:20:47 2013 -0400
@@ -1,5 +1,6 @@
 <tool id="computeGCBias" name="computeGCBias" version="1.0.1">
-  <description></description>
+  <description>to see whether your samples should be normalized for GC bias</description>
+  
   <requirements>
     <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
@@ -51,13 +52,17 @@
 
   #end if
 
-  #if $output.showOutputSettings == "yes"
-      #if $output.saveBiasPlot:
-        --biasPlot biasPlot.png ;
-        mv biasPlot.png $biasPlot
-      #end if
+  #if $saveBiasPlot:
+    --biasPlot $biasPlot
   #end if
 
+##  #if $output.showOutputSettings == "yes"
+##      #if $output.saveBiasPlot:
+##        --biasPlot biasPlot.png ;
+##        mv biasPlot.png $biasPlot
+##      #end if
+##  #end if
+
   ; rm $temp_dir -rf
 
   </command>
@@ -123,6 +128,8 @@
         </when>
     </conditional>
 
+    <param name="saveBiasPlot" type="boolean" truevalue="--biasPlot" falsevalue="" checked="True" label="Save a diagnostic image summarizing the GC bias found on the sample"/>
+    <!--
     <conditional name="output" >
         <param name="showOutputSettings" type="select" label="Show additional output options" >
         <option value="no" selected="true">no</option>
@@ -133,6 +140,7 @@
         <param name="saveBiasPlot" type="boolean" label="Save a diagnostic image summarizing the GC bias found on the sample"/>
       </when>
     </conditional>
+    -->
   </inputs>
   <outputs>
     <data format="tabular" name="outFileName" />
@@ -144,8 +152,8 @@
 
 **What it does**
 
-Computes the GC bias ussing Benjamini's method [citation]. The resulting GC
-bias can later be used to plot the bias or to correct the bias.
+This tool computes the GC bias ussing the method proposed by Benjamini and Speed (2012). Nucleic Acids Res. 
+The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias.
 
 -----