--- a/hyphy_fade.xml	Fri Nov 16 15:41:48 2018 -0500
+++ b/hyphy_fade.xml	Sun Nov 18 22:57:28 2018 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
-  <description>: FUBAR* Approach to Directional Selection (*Fast
+  <description>: FUBAR* Approach to Directional Evolution (*Fast
   Unconstrained Bayesian Approximation)</description>
   <macros>
     <import>macros.xml</import>
@@ -11,10 +11,11 @@
   <command detect_errors="exit_code"><![CDATA[
     ln -s '$input_file' fade_input.fa &&
     ln -s '$input_nhx' fade_input.nhx &&
-    echo $substitutionmodel > tool_params &&
     echo `pwd`/fade_input.fa >> tool_params &&
     echo `pwd`/fade_input.nhx >> tool_params &&
+    echo '$branches' >> tool_params &&
     echo '$grid_points' >> tool_params &&
+    echo $substitutionmodel > tool_params &&
     echo '$mcmc' >> tool_params &&
     echo '$chain_length' >> tool_params &&
     echo '$samples' >> tool_params &&
@@ -26,6 +27,12 @@
   <inputs>
     <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
     <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
+    <param name="branches" type="select" label="Set of branches to test">
+      <option value="1">All branches</option>
+      <option value="2">Internal branches</option>
+      <option value="3">Leaf branches</option>
+      <option value="4">Unlabeled branches</option>
+    </param>
     <param name="substitutionmodel" type="select" label="Substitution Model">
       <option value="1">LG (Generalist empirical model from Le and
       Gascuel 2008)</option>
@@ -79,7 +86,7 @@
     </test>
   </tests>
   <help><![CDATA[
-FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect site evolving under directional evolution in protien alignments. 
+FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect sites evolving under directional evolution in protien alignments. 
         ]]></help>
   <expand macro="citations">
     <citation type="doi">10.1093/molbev/msv022</citation>