# HG changeset patch
# User greg
# Date 1482259974 18000
# Node ID 2ffac03c08fe87cc558830a949236447c2ef4c8e
# Parent  a54b3161504f58ae047b1f834c12db62a3f3ac99
Uploaded

diff -r a54b3161504f -r 2ffac03c08fe gene_family_classifier.xml
--- a/gene_family_classifier.xml	Tue Dec 20 11:22:11 2016 -0500
+++ b/gene_family_classifier.xml	Tue Dec 20 13:52:54 2016 -0500
@@ -12,6 +12,10 @@
     </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 $orthogroups_fasta_dir
+            #end if
             GeneFamilyClassifier
             --proteins "$input"
             --scaffold "$scaffold"
@@ -30,6 +34,9 @@
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
             --num_threads \${GALAXY_SLOTS:-4}
+            #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
+                && mv geneFamilyClassification_dir/orthogroups_fasta/* $orthogroups_fasta_dir
+            #end if
         ]]>
     </command>
     <inputs>