# HG changeset patch
# User greg
# Date 1486996417 18000
# Node ID 1b256588fb0663a9d570542d4a1987dee9bf5192
# Parent  c662ff5166df0a9fac5a606bc2a92f33b24e35a3
Uploaded

diff -r c662ff5166df -r 1b256588fb06 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Fri Feb 10 14:08:42 2017 -0500
+++ b/phylogenomics_analysis.xml	Mon Feb 13 09:33:37 2017 -0500
@@ -19,9 +19,6 @@
 
             #set input_format = $input_format_cond.input_format
             #set pipeline_output_dir = 'phylogenomicsAnalysis_dir'
-            #set scaffold_path = $scaffold.fields.path
-            #set scaffold_dir = $os.path.split($scaffold_path)[0]
-            #set scaffold_selection = $os.path.split($scaffold_path)[1]
             #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln')
             #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta')
             #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree')
@@ -75,8 +72,7 @@
                 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
                 --orthogroup_fna
             #end if
-            --scaffold_dir '$scaffold_dir'
-            --scaffold '$scaffold_selection'
+            --scaffold '$scaffold.fields.path'
             --method $method
 
             #if str($options_type.options_type_selector) == 'advanced':