--- a/bamCompare.xml	Tue Feb 04 08:56:19 2014 -0500
+++ b/bamCompare.xml	Tue Feb 04 09:02:21 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.3">
+<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.4">
     <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -47,8 +47,8 @@
           #end if
       #end if
 
-      #if str(region).strip() != '':
-          --region 'region'
+      #if str($region).strip() != '':
+          --region '$region'
       #end if
 
       #if $advancedOpt.showAdvancedOpt == "yes":
@@ -74,10 +74,10 @@
     </command>
 
     <inputs>
-        <param name="bamFile1" format="bam" type="data" label="Treatment BAM file"
+        <param name="bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
             help="The BAM file must be sorted."/>
 
-        <param name="bamFile2" format="bam" type="data" label="BAM file"
+        <param name="bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
             help="The BAM file must be sorted."/>
 
         <param name="fragmentLength" type="integer" value="300" min="1"
@@ -92,7 +92,7 @@
             <param name="method" type="select" 
                 label="Method to use for scaling the largest sample to the smallest">
                 <option value="readCount" selected="true">read count</option>
-                <option value="SES">signal extraction scaling (SES)</option>
+                <option value="SES">signal extraction scaling (SES), check the bamFingerprint plot before using it!</option>
                 <option value="own">enter own scaling factors</option>
             </param>
             <when value="SES">
@@ -205,9 +205,7 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
-You can find more details in the `bamCompare wiki`_.
-
-.. _bamCompare wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
+You can find more details on the bamCompare wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
 
 
 **Output files**: