# HG changeset patch
# User greg
# Date 1483647217 18000
# Node ID 16861f56079fc3f08633539f2f586b0aef0a8f39
# Parent  cac8a85418c2b53add1e3be7f9f37fb9d6609414
Uploaded

diff -r cac8a85418c2 -r 16861f56079f phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Jan 05 15:08:34 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Jan 05 15:13:37 2017 -0500
@@ -20,12 +20,22 @@
                 $sys.exit(1)
             #end if
             #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
-            #set num_orthogroup_faa = len([f for f in $os.listdir($src_dir) if f.endswith('.faa')])
+            #set num_orthogroup_faa = 0
+            #for f in $os.listdir($src_dir):
+                #if $f.endswith('.faa')])
+                    set num_orthogroup_faa = $num_orthogroup_faa + 1
+                #end if
+            #end for
             #if $num_orthogroup_faa == 0:
                 print > $sys.stderr($invalid_input)
                 $sys.exit(1)
             #end if
-            #set num_orthogroup_fna = len([f for f in $os.listdir($src_dir) if f.endswith('.fna')])
+            #set num_orthogroup_fna = 0
+            #for f in $os.listdir($src_dir):
+                #if $f.endswith('.fna')])
+                    set num_orthogroup_fna = $num_orthogroup_fna + 1
+                #end if
+            #end for
             #set dest_dir = $output.extra_files_path
             mkdir -p $dest_dir &&
             PhylogenomicsAnalysis