--- a/gene_family_aligner.xml	Fri Apr 07 14:37:29 2017 -0400
+++ b/gene_family_aligner.xml	Mon Apr 10 09:36:08 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="0.8.0">
+<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.0">
     <description>aligns gene family sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -23,18 +23,11 @@
             --num_threads \${GALAXY_SLOTS:-4}
             #if str($input_format) == 'ptortho':
                 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
-                --output '$output_ptortho'
-                --output_dir '$output_ptortho.files_path'
             #else:
                 ## str($input_format) == 'ptorthocs'
                 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
                 #if str($input_format_cond.codon_alignments) == 'yes':
                     --codon_alignments 'true'
-                    --output '$output_ptorthocs'
-                    --output_dir '$output_ptorthocs.files_path'
-                #else:
-                    --output '$output_ptortho'
-                    --output_dir '$output_ptortho.files_path'
                 #end if
             #end if
             #if str($options_type_cond.options_type) == 'advanced':
@@ -57,6 +50,8 @@
                     #end if
                 #end if
             #end if
+            --output '$output'
+            --output_dir '$output.files_path'
         ]]>
     </command>
     <inputs>
@@ -88,12 +83,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output_ptortho" format="ptortho" label="Aligned gene family sequences on ${on_string}">
-            <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')</filter>
-        </data>
-        <data name="output_ptorthocs" format="ptorthocs" label="Aligned gene family sequences and corresponding coding sequences on ${on_string}">
-            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes'</filter>
-        </data>
+        <data name="output" format="ptalign" label="Aligned gene family sequences on ${on_string}" />
     </outputs>
     <tests>
         <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.