--- a/macros.xml	Mon Apr 10 14:46:51 2017 -0400
+++ b/macros.xml	Tue Apr 11 14:21:35 2017 -0400
@@ -70,6 +70,12 @@
             <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
         </param>
     </xml>
+    <xml name="param_sequence_type">
+        <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
+            <option value="protein" selected="true">Amino acid based</option>
+            <option value="dna">Nucleotide based</option>
+        </param>
+    </xml>
     <xml name="cond_alignment_method">
         <conditional name="alignment_method_cond">
             <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
@@ -96,7 +102,7 @@
                         <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
                     </param>
                     <when value="gap_trimming">
-                        <param name="gap_trimming" type="float" value="0" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="Zero value has no affect" />
+                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Remove sites in alignments with gaps of" />
                     </when>
                     <when value="automated_trimming" />
                 </conditional>
@@ -107,8 +113,8 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="remove_sequences_with_gaps_of" type="float" value="0" min="0" max="1" label="Remove sequences with gaps of" help="Zero value has no affect" />
-                        <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
+                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Remove sequences with gaps of" />
+                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Maximum number of iterations" />
                     </when>
                 </conditional>
             </when>