# HG changeset patch
# User greg
# Date 1501611947 14400
# Node ID 95cb5d32a3b4dc4db1b99f1b1dc8f14c844d63d4
# Parent  f8603464bea77a520fde511bc350e4dac3ccb011
Uploaded

diff -r f8603464bea7 -r 95cb5d32a3b4 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Jun 08 12:48:23 2017 -0400
+++ b/gene_family_classifier.xml	Tue Aug 01 14:25:47 2017 -0400
@@ -43,7 +43,7 @@
     #set create_corresponding_coding_sequences = False
 #end if
 
-python $__tool_directory__/gene_family_classifier.py
+python '$__tool_directory__/gene_family_classifier.py'
 --input '$input'
 --scaffold '$scaffold.fields.path'
 --method $method
@@ -60,7 +60,7 @@
             #set single_copy_custom_cond = $single_copy_cond.single_copy_custom_cond
             #set single_copy_custom = $single_copy_custom_cond.single_copy_custom
             #if str($single_copy_custom) == 'no':
-                --single_copy_custom 'default'
+                --single_copy_custom default
             #else:
                 --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config'
             #end if
@@ -74,7 +74,7 @@
         #end if
     #end if
     #if $create_ortho_sequences:
-        --orthogroup_fasta "true"
+        --orthogroup_fasta true
         #if $create_corresponding_coding_sequences:
             --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences'
         #end if
@@ -82,7 +82,7 @@
 #end if
 
 #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
-    --save_hmmscan_log 'true'
+    --save_hmmscan_log true
     --hmmscan_log '$hmmscan_log'
 #end if
 #if $create_ortho_sequences: