--- a/gene_family_classifier.xml	Thu Feb 09 11:29:23 2017 -0500
+++ b/gene_family_classifier.xml	Thu Feb 09 12:42:10 2017 -0500
@@ -14,7 +14,6 @@
     <command>
         <![CDATA[
             #import os
-            #import time
             #set scaffold_path = $scaffold.fields.path
             #set scaffold_dir = $os.path.split($scaffold_path)[0]
             #set scaffold_selection = $os.path.split($scaffold_path)[1]
@@ -118,8 +117,6 @@
                 #if $create_ortho_sequences:
                     && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
                     && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
-                #else:
-                    && mv geneFamilyClassification_dir/*.singleCopy $output_single_copy
                 #end if
             #end if
         ]]>
@@ -240,9 +237,6 @@
                 <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="yes" format="ptorthocs" />
             </change_format>
         </data>
-        <data name="output_single_copy" format="tabular" label="Single copy orthogroups on ${on_string}">
-            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'no' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
-        </data>
         <collection name="orthos" type="list">
             <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
         </collection>