# HG changeset patch
# User greg
# Date 1494612859 14400
# Node ID 3d78d366dfcc906e48401d06753b9c4d4705dcce
# Parent  62fe699992a5071ef4f56f6c918db3f2e13bb816
Uploaded

diff -r 62fe699992a5 -r 3d78d366dfcc gene_family_phylogeny_builder.xml
--- a/gene_family_phylogeny_builder.xml	Fri May 12 14:13:56 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Fri May 12 14:14:19 2017 -0400
@@ -60,6 +60,11 @@
             --min_orthogroup_size $min_orthogroup_size
             --max_orthogroup_size $max_orthogroup_size
             --num_threads \${GALAXY_SLOTS:-4}
+            #set output_pttree_dir = output_pttree_dir_cond.output_pttree_dir
+            #if str($output_pttree_dir) == 'yes':
+                --output_tree '$output_tree'
+                --output_tree_dir '$output_tree.files_path'
+            #end if
         ]]>
     </command>
     <inputs>
@@ -130,14 +135,25 @@
         </conditional>
         <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
         <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
+        <conditional name="output_pttree_dir_cond">
+            <param name="output_pttree_dir" type="select" label="Output additional directory of phylogenetic tree files?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes" />
+        </conditional>
     </inputs>
     <outputs>
+        <collection name="tree" type="list" label="GeneFamilyPhylogenyBuilder phylogenetic trees (dataset collection) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
+        </collection>
+        <data name="output_tree" format="pttree" label="GeneFamilyPhylogenyBuilder phylogenetic trees (directory) on ${on_string}">
+            <filter>output_pttree_dir_cond['output_pttree_dir'] == 'yes'</filter>
+        </data>
         <data name="output_phylip" format="ptphylip" label="GeneFamilyPhylogenyBuilder orthogroup phylip multiple sequence alignments on ${on_string}">
             <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
         </data>
-        <collection name="tree" type="list" label="GeneFamilyPhylogenyBuilder phylogenetic trees on ${on_string}">
-            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
-        </collection>
     </outputs>
     <tests>
         <test>