# HG changeset patch
# User greg
# Date 1490628026 14400
# Node ID e0fa1e2105f6ae5e01a321694568677339ce5386
# Parent  4d78ec10c07ed6255366e62d4682c1df8a1b31ae
Uploaded

diff -r 4d78ec10c07e -r e0fa1e2105f6 macros.xml
--- a/macros.xml	Mon Mar 27 11:00:32 2017 -0400
+++ b/macros.xml	Mon Mar 27 11:20:26 2017 -0400
@@ -129,6 +129,18 @@
         --min_orthogroup_size $min_orthogroup_size
         --max_orthogroup_size $max_orthogroup_size
     </token>
+    <token name="@OUTPUT_ALN@">
+        #if str($input_format_cond['options_type_cond']['options_type']) == 'advanced' and ((str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['remove_gappy_sequences']) == 'yes' and str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments']) == 'yes') or (str($input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes') and str($input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments']) == 'yes')):
+            --output_aln '$output_aln'
+            --output_aln_dir '$output_aln.files_path'
+        #end if
+    </token>
+    <token name="@OUTPUT_TREE@">
+        #if str($input_format_cond['options_type_cond']['options_type']) == 'advanced' and str($input_format_cond['options_type_cond']['phylogenetic_trees_cond']['phylogenetic_trees']) == 'yes':
+            --output_tree '$output_tree'
+            --output_tree_dir '$output_tree.files_path'
+        #end if
+    </token>
     <xml name="param_scaffold">
         <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
             <options from_data_table="plant_tribes_scaffolds" />
diff -r 4d78ec10c07e -r e0fa1e2105f6 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Mon Mar 27 11:00:32 2017 -0400
+++ b/phylogenomics_analysis.xml	Mon Mar 27 11:20:26 2017 -0400
@@ -103,16 +103,8 @@
                 --output_ptorthocs '$output_ptorthocs'
                 --output_ptorthocs_dir '$output_ptorthocs.files_path'
             #end if
-
-            #if str($multiple_sequence_alignments) == 'yes'
-                --output_aln '$output_aln'
-                --output_aln_dir '$output_aln.files_path'
-            #end if
-
-            #if str($phylogenetic_trees) == 'yes':
-                --output_tree '$output_tree'
-                --output_tree_dir '$output_tree.files_path'
-            #end if
+            @OUTPUT_ALN@
+            @OUTPUT_TREE@
         ]]>
     </command>
     <inputs>