# HG changeset patch
# User greg
# Date 1490208472 14400
# Node ID 7d07e0ebe8c98bb3f0101a8dbe0c424cefcd092e
# Parent  3296048d5ea0e8439df8d116f36c6b5b300f7eca
Uploaded

diff -r 3296048d5ea0 -r 7d07e0ebe8c9 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Wed Mar 22 14:47:44 2017 -0400
+++ b/phylogenomics_analysis.xml	Wed Mar 22 14:47:52 2017 -0400
@@ -24,6 +24,12 @@
                 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
                 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
                 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
+                #if str(input_format) == 'ptortho':
+                    #set sequence_type = 'protein'
+                #else:
+                    #set sequence_type = $phylogenetic_trees_cond.sequence_type
+                    #set orthogroup_fna = $input_format_cond.orthogroup_fna
+                #end if
             #end if
 
             python $__tool_directory__/phylogenomics_analysis.py
@@ -32,7 +38,9 @@
                 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
             #else:
                 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
-                --orthogroup_fna 'true'
+                #if str($orthogroup_fna) == 'yes':
+                    --orthogroup_fna 'true'
+                #end if
                 #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments
                 #if str($multiple_codon_alignments) == 'yes':
                     --codon_alignments 'true'
@@ -67,11 +75,7 @@
                     #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
+                    --sequence_type $sequence_type
                 #end if
 
                 #if str($remove_gappy_sequences) == 'yes':
@@ -130,6 +134,7 @@
             </when>
             <when value="ptorthocs">
                 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />
+                <expand macro="param_orthogroup_fna" />
                 <expand macro="param_scaffold" />
                 <expand macro="param_method" />
                 <conditional name="options_type_cond">