# HG changeset patch
# User greg
# Date 1484233250 18000
# Node ID 9be4bb807c210b0d4d98e150d2f07666b1a4ea1b
# Parent  93c2ac892a19271707c9cc7dab47813d43bff84b
Uploaded

diff -r 93c2ac892a19 -r 9be4bb807c21 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Wed Jan 11 13:32:57 2017 -0500
+++ b/gene_family_classifier.xml	Thu Jan 12 10:00:50 2017 -0500
@@ -72,11 +72,11 @@
 
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    && echo "Sequences classified into pre-computed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
+                    && echo "Sequences classified into pre-computed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output
                 #else:
-                    && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
+                    && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output
                 #end if
-                && ls $orthogroups_fasta_src_dir >> $output
+                && ls -al $orthogroups_fasta_src_dir | grep f >> $output
                 && mv $orthogroups_fasta_src_dir/* $dest_dir
             #end if