# HG changeset patch
# User greg
# Date 1484059887 18000
# Node ID e19872abae29ea048152aa7d2080de2677cc947e
# Parent  61c90d75c7cd4d2f48a9ff581ed4335945bd6b02
Uploaded

diff -r 61c90d75c7cd -r e19872abae29 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Sat Jan 07 10:09:32 2017 -0500
+++ b/phylogenomics_analysis.xml	Tue Jan 10 09:51:27 2017 -0500
@@ -118,7 +118,7 @@
                         --remove_sequences $remove_gappy_sequences_cond.remove_sequences
                         #if str($trim_type_cond.trim_type) == 'automated_trimming':
                             --automated_trimming
-                        else:
+                        #else:
                             --gap_trimming $trim_type_cond.gap_trimming
                         #end if
                     #end if
@@ -259,8 +259,8 @@
                                 <param name="remove_sequences" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps"/>
                                 <conditional name="trim_type_cond">
                                     <param name="trim_type" type="select" label="Select process used for gap trimming">
-                                        <option value="automated_trimming" selected="true">Trim alignments using trimAl's ML heuristic trimming approach</option>
-                                        <option value="gap_trimming">Nucleotide based</option>
+                                        <option value="gap_trimming" selected="true">Nucleotide based</option>
+                                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
                                     </param>
                                     <when value="automated_trimming"/>
                                     <when value="gap_trimming">