# HG changeset patch
# User greg
# Date 1482333184 18000
# Node ID d678d4c2e9e11267794fd0efee543a5ace632ea0
# Parent  4415ee99319232779823a3097c2f6e00a631ffbb
Uploaded

diff -r 4415ee993192 -r d678d4c2e9e1 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Tue Dec 20 14:37:06 2016 -0500
+++ b/gene_family_classifier.xml	Wed Dec 21 10:13:04 2016 -0500
@@ -12,9 +12,11 @@
     </stdio>
     <command>
         <![CDATA[
-            #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
-                #set orthogroups_fasta_dir = $options_type.create_orthogroup_cond.coding_sequences.extra_files_path
-                mkdir -p $orthogroups_fasta_dir &&
+            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
+                #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 $orthogroups_dest_dir &&
             #end if
             GeneFamilyClassifier
             --proteins "$input"
@@ -34,8 +36,8 @@
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
             --num_threads \${GALAXY_SLOTS:-4}
-            #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
-                && cp "./geneFamilyClassification_dir/orthogroups_fasta/*" $orthogroups_fasta_dir
+            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
+                && mv $orthogroups_src_dir/* $orthogroups_dest_dir
             #end if
         ]]>
     </command>