# HG changeset patch
# User greg
# Date 1490271387 14400
# Node ID 5f64fcf4437a9f1f02694321f1d415928d56dcad
# Parent  6154253af2639392ddb1cc1b5655c20147d2be8f
Uploaded

diff -r 6154253af263 -r 5f64fcf4437a macros.xml
--- a/macros.xml	Thu Mar 23 08:16:20 2017 -0400
+++ b/macros.xml	Thu Mar 23 08:16:27 2017 -0400
@@ -43,9 +43,8 @@
                     <expand macro="param_options_type" />
                     <when value="basic" />
                     <when value="advanced">
-                        <expand macro="cond_multiple_sequence_alignments" />
+                        <expand macro="cond_remove_gappy_sequences" />
                         <expand macro="cond_phylogenetic_trees_ptorthocs" />
-                        <expand macro="cond_remove_gappy_sequences" />
                         <expand macro="param_multiple_codon_alignments" />
                     </when>
                 </conditional>
@@ -55,9 +54,8 @@
                     <expand macro="param_options_type" />
                     <when value="basic" />
                     <when value="advanced">
-                        <expand macro="cond_multiple_sequence_alignments" />
+                        <expand macro="cond_remove_gappy_sequences" />
                         <expand macro="cond_phylogenetic_trees_ptorthocs" />
-                        <expand macro="cond_remove_gappy_sequences" />
                     </when>
                 </conditional>
             </when>
@@ -162,7 +160,9 @@
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
-            <when value="no" />
+            <when value="no">
+                <expand macro="cond_multiple_sequence_alignments" />
+            </when>
             <when value="yes">
                 <conditional name="trim_type_cond">
                     <param name="trim_type" type="select" label="Select process used for gap trimming">
@@ -183,6 +183,7 @@
                     <when value="yes">
                         <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
                         <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/>
+                        <expand macro="cond_multiple_sequence_alignments" />
                     </when>
                 </conditional>
             </when>