# HG changeset patch
# User greg
# Date 1483646914 18000
# Node ID cac8a85418c2b53add1e3be7f9f37fb9d6609414
# Parent  b3712c598290821994d38061cdfc9e5770b71b87
Uploaded

diff -r b3712c598290 -r cac8a85418c2 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Jan 05 14:56:53 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Jan 05 15:08:34 2017 -0500
@@ -20,12 +20,12 @@
                 $sys.exit(1)
             #end if
             #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
-            #set num_orthogroup_faa = `ls $src_dir/*.faa | wc -l`
+            #set num_orthogroup_faa = len([f for f in $os.listdir($src_dir) if f.endswith('.faa')])
             #if $num_orthogroup_faa == 0:
                 print > $sys.stderr($invalid_input)
                 $sys.exit(1)
             #end if
-            #set num_orthogroup_fna = `ls $src_dir/*.fna | wc -l`
+            #set num_orthogroup_fna = len([f for f in $os.listdir($src_dir) if f.endswith('.fna')])
             #set dest_dir = $output.extra_files_path
             mkdir -p $dest_dir &&
             PhylogenomicsAnalysis