--- a/gene_family_phylogeny_builder.xml	Fri May 05 10:31:06 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Wed May 10 14:29:19 2017 -0400
@@ -54,12 +54,14 @@
                     ## configuration will be used if the --rooting_order flag is missing.
                 #end if
                 --bootstrap_replicates $bootstrap_replicates
+                --output_phylip '$output_phylip'
+                --output_phylip_dir '$output_phylip.files_path'
             #end if
             --min_orthogroup_size $min_orthogroup_size
             --max_orthogroup_size $max_orthogroup_size
             --num_threads \${GALAXY_SLOTS:-4}
-            --output '$output_pttree'
-            --output_dir '$output_pttree.files_path'
+            --output_tree '$output_tree'
+            --output_tree_dir '$output_tree.files_path'
         ]]>
     </command>
     <inputs>
@@ -132,7 +134,10 @@
         <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum orthogroup size" />
     </inputs>
     <outputs>
-        <data name="output_pttree" format="pttree" label="Gene family phylogenetic trees on ${on_string}" />
+        <data name="output_phylip" format="ptphylip" label="Gene family orthogroup phylip multiple sequence alignments on ${on_string}">
+            <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
+        </data>
+        <data name="output_tree" format="pttree" label="Gene family phylogenetic trees on ${on_string}" />
     </outputs>
     <tests>
         <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.