# HG changeset patch
# User greg
# Date 1484233228 18000
# Node ID 01c89742cb39b2b1c05b4c919485be6b08191d5c
# Parent  8529a3c95c2b7eaecaa6ed71a6f07d1d9e5d5a01
Uploaded

diff -r 8529a3c95c2b -r 01c89742cb39 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Jan 12 09:45:01 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Jan 12 10:00:28 2017 -0500
@@ -144,19 +144,19 @@
                 #end if
             #end if
 
-            && echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | wc -l` files" > $output_fasta
-            && ls $src_fasta_dir >> $output_fasta
+            && echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | grep f | wc -l` files" > $output_fasta
+            && ls -al $src_fasta_dir | grep f >> $output_fasta
             && mv $src_fasta_dir/* $dest_fasta_dir
 
             #if $generate_output_aln:
-                && echo "Multiple sequence alignments using method '$multiple_sequence_alignments_option': `ls $src_aln_dir | wc -l` files" > $output_aln
-                && ls $src_aln_dir >> $output_aln
+                && echo "Multiple sequence alignments using method '$multiple_sequence_alignments_option': `ls $src_aln_dir | grep f | wc -l` files" > $output_aln
+                && ls -al $src_aln_dir | grep f >> $output_aln
                 && mv $src_aln_dir/* $dest_aln_dir
             #end if
 
             #if $generate_output_tree:
-                && echo "Phylogenetic trees: `ls $src_tree_dir | wc -l` files" > $output_tree
-                && ls $src_tree_dir >> $output_tree
+                && echo "Phylogenetic trees (note that some files may be empty): `ls $src_tree_dir | grep f | wc -l` files" > $output_tree
+                && ls -al $src_tree_dir | grep f >> $output_tree
                 && mv $src_tree_dir/* $dest_tree_dir
             #end if
         ]]>