--- a/tophat2/tophat2_wrapper.xml	Wed Jun 22 13:52:52 2016 -0400
+++ b/tophat2/tophat2_wrapper.xml	Wed Jun 22 14:00:45 2016 -0400
@@ -1,14 +1,49 @@
-<tool id="tophat2" name="TopHat" version="0.9">
+<tool id="tophat2" name="TopHat" version="2.1.0">
     <!-- Wrapper compatible with Tophat version 2.0.0+ -->
     <description>Gapped-read mapper for RNA-seq data</description>
-    <version_command>tophat2 --version</version_command>
+    <macros>
+      <import>tophat_macros.xml</import>
+      <xml name="paired_parameters">
+        <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>
+        <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs"  help="--mate-std-dev; The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp."/>
+        <!-- Discordant pairs. -->
+        <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?" help="--no-discordant">
+            <option value="No">No</option>
+            <option selected="True" value="Yes">Yes</option>
+        </param>
+      </xml>
+      <macro name="dbKeyActions">
+        <actions>
+          <conditional name="refGenomeSource.genomeSource">
+            <when value="indexed">
+              <action type="metadata" name="dbkey">
+                <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
+                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                </option>
+              </action>
+            </when>
+            <when value="history">
+              <action type="metadata" name="dbkey">
+                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+              </action>
+            </when>
+          </conditional>
+        </actions>
+      </macro>
+    </macros>
     <requirements>
         <requirement type="package" version="2.2.5">bowtie2</requirement>
         <requirement type="package" version="2.1.0">tophat</requirement>
     </requirements>
+    <stdio>
+        <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
+        <regex match=".*" source="both" level="log" description="tool progress"/>
+    </stdio>
+    <version_command>tophat2 --version</version_command>
 
     <command>
-        ##
+         ##
         ## Set path to index, building the reference if necessary.
         ##
 
@@ -195,10 +230,12 @@
               <expand macro="own_junctionsConditional" />
               <!-- Coverage search. -->
               <conditional name="coverage_search">
-                <param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.">
-                    <option selected="true" value="No">No</option>
-                    <option value="Yes">Yes</option>
+                <param name="use_search" type="select" label="Use coverage-based search for junctions" help="Select 'Auto' to let TopHat decide when to enable coverage search (e.g. disable it for reads 75bp or longer). Select 'Yes' to enforce maximum sensitivity and to specify minimum and maximum intron length">
+                    <option selected="true" value="auto">Auto</option>
+                    <option value="No">No (--no-coverage-search)</option>
+                    <option value="Yes">Yes (--coverage-search)</option>
                 </param>
+                <when value="auto" />
                 <when value="Yes">
                     <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" help="--min-coverage-intron; The minimum intron length that may be found during coverage search. The default is 50."/>
                     <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" help="--max-coverage-intron; The maximum intron length that may be found during coverage search. The default is 20000."/>
@@ -272,11 +309,6 @@
       </conditional> <!-- readGroup -->
     </inputs>
 
-    <stdio>
-        <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
-        <regex match=".*" source="both" level="log" description="tool progress"/>
-    </stdio>
-
     <outputs>
         <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/>
         <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out">
@@ -301,38 +333,6 @@
 
     </outputs>
 
-    <macros>
-      <import>tophat_macros.xml</import>
-      <xml name="paired_parameters">
-        <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>
-        <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs"  help="--mate-std-dev; The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp."/>
-        <!-- Discordant pairs. -->
-        <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?" help="--no-discordant">
-            <option value="No">No</option>
-            <option selected="True" value="Yes">Yes</option>
-        </param>
-      </xml>
-      <macro name="dbKeyActions">
-        <actions>
-          <conditional name="refGenomeSource.genomeSource">
-            <when value="indexed">
-              <action type="metadata" name="dbkey">
-                <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
-                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                </option>
-              </action>
-            </when>
-            <when value="history">
-              <action type="metadata" name="dbkey">
-                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-              </action>
-            </when>
-          </conditional>
-        </actions>
-      </macro>
-    </macros>
-
     <tests>
         <!-- Test base-space single-end reads with pre-built index and preset parameters -->
         <test>