diff --git a/tools/sr_mapping/bowtie2_wrapper.py b/tools/sr_mapping/bowtie2_wrapper.py
index 4b132d53393..c4971686de2 100644
--- a/tools/sr_mapping/bowtie2_wrapper.py
+++ b/tools/sr_mapping/bowtie2_wrapper.py
@@ -25,6 +25,12 @@ def __main__():
     parser.add_option( '', '--local', dest='local', action="store_true" )
     parser.add_option( '', '--preset-alignment', dest='preset_alignment')
 
+    # Read group options.
+    parser.add_option( '', '--rgid', dest='rgid', help='Read group identifier' )
+    parser.add_option( '', '--rglb', dest='rglb', help='Library name' )
+    parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' )
+    parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
+
     (options, args) = parser.parse_args()
     
     # Creat bowtie index if necessary.
@@ -86,7 +92,16 @@ def __main__():
         if options.local:
             opts += ' --local'
         if options.preset_alignment:
-            opts += " --" + options.preset_alignment
+            opts += ' --' + options.preset_alignment
+
+    # Read group options.
+    if options.rgid:
+        if not options.rglb or not options.rgpl or not options.rgsm:
+            stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
+        opts += ' --rg-id %s' % options.rgid
+        opts += ' --rg %s:%s' % ( 'LB', options.rglb )
+        opts += ' --rg %s:%s' % ( 'PL', options.rgpl )
+        opts += ' --rg %s:%s' % ( 'SM', options.rgsm )
         
     # Final command:
     cmd = cmd % ( opts, index_path, reads, options.output )
diff --git a/tools/sr_mapping/bowtie2_wrapper.xml b/tools/sr_mapping/bowtie2_wrapper.xml
index 416fdc0f0bf..f74526a631e 100644
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -44,6 +44,14 @@
                 --local --preset-alignment=$params.preset.align_preset_select-local
             #end if
         #end if
+
+        ## Read group information.
+        #if $params.readGroup.specReadGroup == "yes"
+          --rgid="$params.readGroup.rgid"
+          --rglb="$params.readGroup.rglb"
+          --rgpl="$params.readGroup.rgpl"
+          --rgsm="$params.readGroup.rgsm"
+        #end if
     </command>
     <inputs>
         <conditional name="singlePaired">
@@ -80,7 +88,7 @@
           </when>  <!-- history -->
         </conditional>  <!-- refGenomeSource -->
         <conditional name="params">
-            <param name="settingsType" type="select" label="Bowtie settings to use" help="You can use the default settings or set custom values for any of Bowtie's parameters.">
+            <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for any of Bowtie's parameters.">
               <option value="preSet">Use Defaults</option>
               <option value="full">Full parameter list</option>
             </param>
@@ -104,9 +112,21 @@
                             <option value="very-sensitive">Very sensitive</option>
                         </param>
                     </when>
-                    <!-- TODO: -->
                     <when value="No" />
                 </conditional>
+                <conditional name="readGroup">
+                <param name="specReadGroup" type="select" label="Specify the read group for this file?">
+                    <option value="yes">Yes</option>
+                    <option value="no" selected="True">No</option>
+                </param>
+                <when value="yes">
+                    <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." />
+                    <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
+                    <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" />
+                    <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
+                </when>
+                <when value="no" />
+            </conditional>
             </when>  <!-- full -->
       </conditional>  <!-- params -->
     </inputs>