--- a/bowtie2_wrapper.xml	Wed Nov 18 09:52:21 2015 -0500
+++ b/bowtie2_wrapper.xml	Fri Dec 18 18:50:22 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="bowtie2" name="Bowtie2" version="2.2.6">
+<tool id="bowtie2" name="Bowtie2" version="2.2.6.1">
     <description>- map reads against reference genome</description>
     <macros>
         <import>read_group_macros.xml</import>
@@ -167,6 +167,11 @@
             ${analysis_type.cline}
         #end if
 
+        ## mapping stats (i.e. stderr from bowtie2)
+        #if $save_mapping_stats
+	  2&gt; "$mapping_stats"
+        #end if
+
         ## output file
         #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
           | samtools view -Su - | samtools sort -o - - &gt; $output
@@ -430,6 +435,7 @@
                 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
             </when>
         </conditional>
+        <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
     </inputs>
 
     <!-- define outputs -->
@@ -517,6 +523,9 @@
             </conditional>
           </actions>
         </data>
+        <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
+          <filter>save_mapping_stats is True</filter>
+        </data>
 
     </outputs>
 
@@ -550,6 +559,21 @@
             <param name="own_file" value="bowtie2-ref.fasta" />
             <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
         </test>
+        <test>
+            <!-- basic test on single paired default run with stats-->
+            <param name="type" value="paired"/>
+            <param name="selection" value="no"/>
+            <param name="paired_options_selector" value="no"/>
+            <param name="unaligned_file" value="false"/>
+            <param name="analysis_type_selector" value="simple"/>
+            <param name="source" value="history" />
+            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
+            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
+            <param name="own_file" value="bowtie2-ref.fasta" />
+            <param name="save_mapping_stats" value="true" />
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
+            <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
+        </test>
     </tests>
 
     <help>