# HG changeset patch
# User greg
# Date 1486995092 18000
# Node ID 062883e3392ceac3be3cc19c91c1080b656640b2
# Parent  7525307aa1d7d59a56608d0f0c6b1f571ffb2a65
Uploaded

diff -r 7525307aa1d7 -r 062883e3392c gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Feb 09 13:37:40 2017 -0500
+++ b/gene_family_classifier.xml	Mon Feb 13 09:11:32 2017 -0500
@@ -14,9 +14,6 @@
     <command>
         <![CDATA[
             #import os
-            #set scaffold_path = $scaffold.fields.path
-            #set scaffold_dir = $os.path.split($scaffold_path)[0]
-            #set scaffold_selection = $os.path.split($scaffold_path)[1]
 
             #if str($options_type.options_type_selector) == 'advanced':
                 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
@@ -73,8 +70,7 @@
 
             GeneFamilyClassifier
             --proteins '$input'
-            --scaffold_dir '$scaffold_dir'
-            --scaffold '$scaffold_selection'
+            --scaffold '$scaffold.fields.path'
             --method $method
             --classifier $save_hmmscan_log_cond.classifier
             --num_threads \${GALAXY_SLOTS:-4}
@@ -278,7 +274,7 @@
 
 **Options**
 
- * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
+ * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
  * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
  * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive).
  * **Super Orthogroups** - Secondary MCL clusters of orthogroups.