# HG changeset patch
# User greg
# Date 1491836145 14400
# Node ID 9e68bebb3d7c38d7d3a9f849447f3f14f60a2cc8
# Parent  529f4635ddb4d10eb275fa9c1b82032957ca5f6c
Uploaded

diff -r 529f4635ddb4 -r 9e68bebb3d7c gene_family_aligner.xml
--- a/gene_family_aligner.xml	Mon Apr 10 09:37:45 2017 -0400
+++ b/gene_family_aligner.xml	Mon Apr 10 10:55:45 2017 -0400
@@ -47,11 +47,20 @@
                     #if str($remove_sequences_with_gaps) == 'yes':
                         --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
                         --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
+                        --output '$output_aln_filtered'
+                        --output_dir '$output_aln_filtered.files_path'
+                    #else:
+                        --output '$output_aln_trimmed'
+                        --output_dir '$output_aln_trimmed.files_path'
                     #end if
+                #else:
+                    --output '$output_aln'
+                    --output_dir '$output_aln.files_path'
                 #end if
+            #esle:
+                --output '$output_aln'
+                --output_dir '$output_aln.files_path'
             #end if
-            --output '$output'
-            --output_dir '$output.files_path'
         ]]>
     </command>
     <inputs>
@@ -83,7 +92,15 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output" format="ptalign" label="Aligned gene family sequences on ${on_string}" />
+        <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}">
+            <filter>options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no')</filter>
+        </data>
+        <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}">
+            <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
+        </data>
+        <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}">
+            <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
+        </data>
     </outputs>
     <tests>
         <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.