# HG changeset patch
# User greg
# Date 1490196567 14400
# Node ID 60d375f35e2411b9056475bd7a0ca183bc64c6a4
# Parent  063a39e397059a8bb84561ddf909607719a82d4f
Uploaded

diff -r 063a39e39705 -r 60d375f35e24 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Wed Mar 22 11:29:09 2017 -0400
+++ b/phylogenomics_analysis.xml	Wed Mar 22 11:29:27 2017 -0400
@@ -33,10 +33,9 @@
             #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
+                #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments
                 #if str($multiple_codon_alignments) == 'yes':
-                    --sequence_type $multiple_codon_alignments_cond.sequence_type
+                    --codon_alignments 'true'
                 #end if
             #end if
             --config_dir '$scaffold.fields.path'
@@ -68,6 +67,11 @@
                     #end if
                     --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size
                     --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size
+                    #if str($input_format) == 'ptortho':
+                        --sequence_type 'protein'
+                    #else:
+                        --sequence_type $phylogenetic_trees_cond.sequence_type
+                    #end if
                 #end if
 
                 #if str($remove_gappy_sequences) == 'yes':
@@ -119,7 +123,7 @@
                     <when value="basic" />
                     <when value="advanced">
                         <expand macro="cond_multiple_sequence_alignments" />
-                        <expand macro="cond_phylogenomic_trees" />
+                        <expand macro="cond_phylogenomic_trees_ptortho" />
                         <expand macro="cond_remove_gappy_sequences" />
                     </when>
                 </conditional>
@@ -133,9 +137,9 @@
                     <when value="basic" />
                     <when value="advanced">
                         <expand macro="cond_multiple_sequence_alignments" />
-                        <expand macro="cond_phylogenomic_trees" />
+                        <expand macro="cond_phylogenomic_trees_ptorthocs" />
                         <expand macro="cond_remove_gappy_sequences" />
-                        <expand macro="cond_multiple_codon_alignments" />
+                        <expand macro="param_multiple_codon_alignments" />
                     </when>
                 </conditional>
             </when>