# HG changeset patch
# User greg
# Date 1491505790 14400
# Node ID 9fff0561bc8ea1ae0714f2565faae94c621ceac8
# Parent  d06e3ae4eb5aad816936fe69acb4cff5a3ecd913
Uploaded

diff -r d06e3ae4eb5a -r 9fff0561bc8e gene_family_integrator.xml
--- a/gene_family_integrator.xml	Thu Apr 06 14:57:38 2017 -0400
+++ b/gene_family_integrator.xml	Thu Apr 06 15:09:50 2017 -0400
@@ -16,15 +16,20 @@
             --method $method
             #if str($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.orthogroup_fna) == 'yes':
+                #if str($input_format_cond.orthogroup_fna) == 'yes':
                     --orthogroup_fna 'true'
+                    --output '$output_ptorthocs'
+                    --output_dir '$output_ptorthocs.files_path'
+                #else:
+                    --output '$output_ptortho'
+                    --output_dir '$output_ptortho.files_path'
                 #end if
             #end if
-            --output '$output_html'
-            --output_dir '$output_html.files_path'
         ]]>
     </command>
     <inputs>
@@ -47,7 +52,12 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output_html" format="html" />
+        <data name="output_ptortho" format="ptortho" label="Integrated gene family clusters on ${on_string}">
+            <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter>
+        </data>
+        <data name="output_ptorthocs" format="ptorthocs" label="Integrated gene family clusters and corresponding coding sequences on ${on_string}">
+            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
+        </data>
     </outputs>
     <tests>
         <test>