# HG changeset patch
# User greg
# Date 1483626192 18000
# Node ID 26f5584ab88a96ea979e7e904639b92a44bfbf04
# Parent  37b56c1befaa40afecde63336e7ac7bef36e58cb
Uploaded

diff -r 37b56c1befaa -r 26f5584ab88a phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Jan 05 09:11:57 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Jan 05 09:23:12 2017 -0500
@@ -21,18 +21,20 @@
             --scaffold "$scaffold"
             --method $method
             #if str($options_type.options_type_selector) == 'advanced':
-                #if str($options_type.multiple_sequence_alignments_cond) == 'yes':
-                    #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond
+                #if str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes':
                     #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
-                    #if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'create_alignments':
+                    #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
+                    #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond
+                    #set multiple_codon_alignments = multiple_codon_alignments_cond.multiple_codon_alignments
+                    #if str($multiple_sequence_alignments_option) == 'create_alignments':
                         --create_alignments
-                    #else if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'add_alignments':
+                    #else if str($multiple_sequence_alignments_option) == 'add_alignments':
                         --add_alignments
-                    #else if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'pasta_alignments':
+                    #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
                         --pasta_alignments
                         --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
                     #end if
-                    #if str($multiple_codon_alignments_cond.multiple_codon_alignments) == 'yes':
+                    #if str($multiple_codon_alignments) == 'yes':
                         --codon_alignments
                         --orthogroup_fna "$orthogroup_fna"
                         --sequence_type $multiple_codon_alignments_cond.sequence_type
@@ -89,7 +91,7 @@
             <when value="basic" />
             <when value="advanced">
                 <conditional name="multiple_sequence_alignments_cond">
-                    <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignemnts options?">
+                    <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
                         <option value="no" selected="true">No</option>
                         <option value="yes">Yes</option>
                     </param>