# HG changeset patch
# User greg
# Date 1486148094 18000
# Node ID 898270c680a911642cddd9ae0e25b0b3eabb6c05
# Parent  801f467f6555a3a9e235e51084c8b0a565736a9c
Uploaded

diff -r 801f467f6555 -r 898270c680a9 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Fri Feb 03 13:50:30 2017 -0500
+++ b/phylogenomics_analysis.xml	Fri Feb 03 13:54:54 2017 -0500
@@ -66,7 +66,11 @@
 
             PhylogenomicsAnalysis
             --num_threads \${GALAXY_SLOTS:-4}
-            --orthogroup_faa '$input.extra_files_path'
+            #if str($input_format) == 'ptcgf':
+                --orthogroup_faa '$input_format_cond.input_ptcgf.extra_files_path'
+            #else:
+                --orthogroup_faa '$input_format_cond.input_ptcgfcs.extra_files_path'
+            #end if
             --scaffold_dir '$scaffold_dir'
             --scaffold '$scaffold_selection'
             --method $method