# HG changeset patch
# User greg
# Date 1516645119 18000
# Node ID 283dc861c75c4d5c5c6c478e6b460b03f862df30
# Parent  c6ed6c138b14421e06e4a6a856572a306fdb1c2b
Uploaded

diff -r c6ed6c138b14 -r 283dc861c75c kaks_analysis.xml
--- a/kaks_analysis.xml	Wed Dec 13 14:10:46 2017 -0500
+++ b/kaks_analysis.xml	Mon Jan 22 13:18:39 2018 -0500
@@ -79,24 +79,24 @@
     #end if
     cp kaks_analysis_log.txt '$output_kaks';
     #if str($fit_components) == 'yes':
-        cp kaks_analysis_log.txt '$output_components'
+        cp kaks_analysis_log.txt '$output_components';
     #end if
 else
-    && mv $output_dir/species1.fna '$output_species1_fna'
-    && mv $output_dir/species1.faa '$output_species1_faa'
+    mv $output_dir/species1.fna '$output_species1_fna';
+    mv $output_dir/species1.faa '$output_species1_faa';
     #if str($comparison) == 'paralogs':
-        && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
-        && mv $output_dir/*.rbhb '$output_rbhb_paralog'
+        mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog';
+        mv $output_dir/*.rbhb '$output_rbhb_paralog';
     #else:
-        && mv $output_dir/species2.faa '$output_species2_faa'
-        && mv $output_dir/species2.fna '$output_species2_fna'
-        && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
-        && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
-        && mv $output_dir/*.rbhb '$output_rbhb_ortholog'
+        mv $output_dir/species2.faa '$output_species2_faa';
+        mv $output_dir/species2.fna '$output_species2_fna';
+        mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog';
+        mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog';
+        mv $output_dir/*.rbhb '$output_rbhb_ortholog';
     #end if
-    && mv $output_dir/*.kaks '$output_kaks'
+    mv $output_dir/*.kaks '$output_kaks';
     #if str($fit_components) == 'yes':
-        && mv $output_dir/*.components '$output_components'
+        mv $output_dir/*.components '$output_components';
     #end if
 fi
     ]]></command>