# HG changeset patch
# User greg
# Date 1488298080 18000
# Node ID 43252277cb238be46a36139dbca4ea39febd8742
# Parent  6d93b214ec55ae557126781a800c59e0f967e5c0
Uploaded

diff -r 6d93b214ec55 -r 43252277cb23 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Tue Feb 28 09:55:36 2017 -0500
+++ b/phylogenomics_analysis.xml	Tue Feb 28 11:08:00 2017 -0500
@@ -16,15 +16,6 @@
             #import os
             #import sys
 
-            #set input_format = $input_format_cond.input_format
-            #if str($input_format) == 'ptorthocs':
-                #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
-                #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
-                #if str($multiple_codon_alignments) == 'yes':
-                    --sequence_type $multiple_codon_alignments_cond.sequence_type
-                #end if
-            #end if
-
             #if str($options_type.options_type_selector) == 'advanced':
                 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond
                 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
@@ -35,23 +26,29 @@
                 #else:
                     #set generate_output_aln = False
                 #end if
+                #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
+                    #set generate_output_tree = True
+                #else:
+                    #set generate_output_tree = False
+                #end if
             #else:
                 #set generate_output_aln = False
-            #end if
-
-            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
-                #set generate_output_tree = True
-            #else:
                 #set generate_output_tree = False
             #end if
 
             python $__tool_directory__/phylogenomics_analysis.py
             --num_threads \${GALAXY_SLOTS:-4}
+            #set input_format = $input_format_cond.input_format
             #if str($input_format) == 'ptortho':
                 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
             #else:
                 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
                 --orthogroup_fna 'true'
+                #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
+                #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
+                #if str($multiple_codon_alignments) == 'yes':
+                    --sequence_type $multiple_codon_alignments_cond.sequence_type
+                #end if
             #end if
             --config_dir '$scaffold.fields.path'
             --scaffold '$scaffold.fields.path'