# HG changeset patch
# User greg
# Date 1487258057 18000
# Node ID bf5cfbf2cfbc37274fa82125d2d9d88692cf252e
# Parent  29530d7a2a3df738b6e8cbede1e3541576afae1f
Uploaded

diff -r 29530d7a2a3d -r bf5cfbf2cfbc phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Feb 16 09:26:48 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Feb 16 10:14:17 2017 -0500
@@ -98,7 +98,7 @@
                         #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
                         #if str($rooting_order_file) == 'yes':
                             --rooting_order '$rooting_order_file_cond.rooting_order'
-			    # Noe else block needed here because the default rooting_order
+			    # No else block needed here because the default rooting_order
 			    # configuration will be used if the --rooting_order flag is missing.
                         #end if
                         --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
@@ -131,18 +131,24 @@
                 && echo -e "#Size\tName" > $output_fasta_ptorthocs
                 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptorthocs
             #end if
-            && mv $src_fasta_dir/* $dest_fasta_dir || true
+            #if len($os.listdir($src_fasta_dir)) > 0:
+                && mv $src_fasta_dir/* $dest_fasta_dir
+            #end if
 
             #if $generate_output_aln:
                 && echo -e "#Size\tName" > $output_aln
-                && ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln
-                && mv $src_aln_dir/* $dest_aln_dir || true
+                #if len($os.listdir($src_aln_dir)) > 0:
+                     ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln
+                    && mv $src_aln_dir/* $dest_aln_dir
+                #end if
             #end if
 
             #if $generate_output_tree:
                 && echo -e "#Size\tName" > $output_tree
-                && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree
-                && mv $src_tree_dir/* $dest_tree_dir || true
+                #if len($os.listdir($src_tree_dir)) > 0:
+                    && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree
+                    && mv $src_tree_dir/* $dest_tree_dir
+                #end if
             #end if
         ]]>
     </command>
@@ -232,7 +238,7 @@
                             </param>
                             <when value="raxml">
                                 <conditional name="rooting_order_file_cond">
-                                    <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select no for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
+                                    <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
                                         <option value="no" selected="true">No</option>
                                         <option value="yes">Yes</option>
                                     </param>