# HG changeset patch
# User greg
# Date 1486495472 18000
# Node ID 4a6834056e1e687e8651878f51f4674c8059f945
# Parent  6c3fa9907d9cce2a1e20fc230c008a471456aa79
Uploaded

diff -r 6c3fa9907d9c -r 4a6834056e1e gene_family_classifier.xml
--- a/gene_family_classifier.xml	Tue Feb 07 13:53:56 2017 -0500
+++ b/gene_family_classifier.xml	Tue Feb 07 14:24:32 2017 -0500
@@ -25,7 +25,7 @@
                 #set specify_single_copy = $specify_single_copy_cond.specify_single_copy
 
                 #if str($specify_single_copy) == 'yes':
-                    #set specify_single_copy = True
+                    #set single_copy_orthogroup = True
                     #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
                     #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
                     #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
@@ -33,7 +33,7 @@
                     #set single_copy = $single_copy_cond.single_copy
                     mkdir -p $single_copy_fasta_dest_dir &&
                 #else:
-                    #set specify_single_copy = False
+                    #set single_copy_orthogroup = False
                 #end if
 
                 #if str($create_orthogroup) == 'yes':
@@ -54,7 +54,7 @@
                     #set create_corresponding_coding_sequences = False
                 #end if
             #else:
-                #set specify_single_copy = False
+                #set single_copy_orthogroup = False
                 #set create_ortho_sequences = False
                 #set create_corresponding_coding_sequences = False
             #end if
@@ -69,7 +69,7 @@
 
             #if str($options_type.options_type_selector) == 'advanced':
                 --super_orthogroups $options_type.super_orthogroups
-                #if $specify_single_copy:
+                #if $single_copy_orthogroup:
                     --single_copy_taxa $single_copy_cond.single_copy_taxa
                     --taxa_present $single_copy_cond.taxa_present
                 #end if
@@ -99,7 +99,7 @@
                 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
             #end if
 
-            #if $specify_single_copy:
+            #if $single_copy_orthogroup:
                 && 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 || true
             #end if