# HG changeset patch
# User greg
# Date 1513865821 18000
# Node ID 48271ee78198b1f7391a600d52babb64713be91e
# Parent  1fb0f2092177ee34d4d8999a75f2a361df13a92c
Uploaded

diff -r 1fb0f2092177 -r 48271ee78198 kaks_analysis.xml
--- a/kaks_analysis.xml	Mon Oct 30 09:54:20 2017 -0400
+++ b/kaks_analysis.xml	Thu Dec 21 09:17:01 2017 -0500
@@ -63,23 +63,42 @@
         --max_ks $set_upper_ks_limit_cond.max_ks
     #end if
 #end if
-&>proc.log
-&& 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'
-#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'
-#end if
-&& mv $output_dir/*.kaks '$output_kaks'
-#if str($fit_components) == 'yes':
-    && mv $output_dir/*.components '$output_components'
-#end if
+&>kaks_analysis_log.txt;
+if [[ $? -ne 0 ]]; then
+    cp kaks_analysis_log.txt '$output_species1_fna';
+    cp kaks_analysis_log.txt '$output_species1_faa';
+    #if str($comparison) == 'paralogs':
+        cp kaks_analysis_log.txt '$output_species1_paralog';
+        cp kaks_analysis_log.txt '$output_rbhb_paralog';
+    #else:
+        cp kaks_analysis_log.txt '$output_species2_faa';
+        cp kaks_analysis_log.txt '$output_species2_fna';
+        cp kaks_analysis_log.txt '$output_species1_ortholog';
+        cp kaks_analysis_log.txt '$output_species2_ortholog';
+        cp kaks_analysis_log.txt '$output_rbhb_ortholog';
+    #end if
+    cp kaks_analysis_log.txt '$output_kaks';
+    #if str($fit_components) == 'yes':
+        cp kaks_analysis_log.txt '$output_components'
+    #end if
+else
+    && mv $output_dir/species1.fna '$output_species1_fna'
+    && mv $output_dir/species1.faa '$output_species1_faa'
+    #if str($comparison) == 'paralogs':
+        && 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'
+    #end if
+    && mv $output_dir/*.kaks '$output_kaks'
+    #if str($fit_components) == 'yes':
+        && mv $output_dir/*.components '$output_components'
+    #end if
+fi
     ]]></command>
     <inputs>
         <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences for the first species" />