--- a/bismark_bowtie2_wrapper.xml	Wed Aug 21 05:19:54 2013 -0400
+++ b/bismark_bowtie2_wrapper.xml	Mon Apr 14 16:43:14 2014 -0400
@@ -1,5 +1,5 @@
-<tool id="bismark_bowtie2" name="Bismark" version="0.7.12.1">
-    <!-- Wrapper compatible with Bismark version 0.7.11 -->
+<tool id="bismark_bowtie2" name="Bismark" version="0.10.1">
+    <!-- Wrapper compatible with Bismark version 0.10 -->
     <description>bisulfite mapper (bowtie2)</description>
     <!--<version_command>bismark version</version_command>-->
     <requirements>
@@ -12,7 +12,7 @@
         bismark_wrapper.py
         
         ## Change this to accommodate the number of threads you have available.
-        --num-threads 24
+        --num-threads "\${GALAXY_SLOTS:-24}"
 
         --bismark_path \$SCRIPT_PATH
 
@@ -71,6 +71,9 @@
             -X $singlePaired.maxInsert
         #end if
 
+        #if $sort_bam:
+            --sort-bam
+        #end if
 
         ## for now hardcode the value for the required memory per thread in --best mode
         --chunkmbs 512
@@ -176,6 +179,7 @@
             </when>
         </conditional>
 
+        <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>
 
         <conditional name="params">
             <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
@@ -342,8 +346,6 @@
         </conditional>
       </actions>
     </data>
-        
-        
     </outputs>
 
     <tests>