--- a/gene_family_classifier.xml	Wed Dec 21 10:13:04 2016 -0500
+++ b/gene_family_classifier.xml	Wed Jan 04 10:07:01 2017 -0500
@@ -12,11 +12,12 @@
     </stdio>
     <command>
         <![CDATA[
-            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
+        #set create_ortho_sequences = str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes'
+            #if create_ortho_sequences:
                 #import os
-                #set orthogroups_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
-                #set orthogroups_dest_dir = $options_type.create_orthogroup_cond.coding_sequences.extra_files_path
-                mkdir -p $orthogroups_dest_dir &&
+                #set src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
+                #set dest_dir = $output.extra_files_path
+                mkdir -p $dest_dir &&
             #end if
             GeneFamilyClassifier
             --proteins "$input"
@@ -36,8 +37,9 @@
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
             --num_threads \${GALAXY_SLOTS:-4}
-            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
-                && mv $orthogroups_src_dir/* $orthogroups_dest_dir
+            #if create_ortho_sequences:
+                echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output &&
+                && mv $src_dir/* $dest_dir
             #end if
         ]]>
     </command>
@@ -93,8 +95,11 @@
         </conditional>
     </inputs>
     <outputs>
+        <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}">
+            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
+        </data>
         <collection name="transcripts" type="list">
-            <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="true" ext="fasta" />
+            <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
         </collection>
     </outputs>
     <tests>
@@ -112,7 +117,7 @@
     </tests>
     <help>
 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
-complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs Gene family
+complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs gene family
 classification of the post processed de novo transcripts using either blastp (faster), HMMScan (slower but more sensitive to remote
 homologs) or both (more exhaustive).