# HG changeset patch
# User greg
# Date 1504879512 14400
# Node ID 5873a9420e03ba57f36b646fe04f05fad56c4afa
# Parent  97a298d2fc363aab17420f3ebd3e306f6e9f48fb
Uploaded

diff -r 97a298d2fc36 -r 5873a9420e03 macros.xml
--- a/macros.xml	Fri Aug 25 13:26:29 2017 -0400
+++ b/macros.xml	Fri Sep 08 10:05:12 2017 -0400
@@ -67,12 +67,6 @@
             <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="Multiple sequence alignment method">
@@ -114,6 +108,10 @@
                         <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
                     </when>
                 </conditional>
+                <param name="output_pristine_alignments" type="select" display="radio" label="Output non-filtered, non-trimmed alignemnts?" help="In addition to trimmed/filtered alignments">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
             </when>
         </conditional>
     </xml>