# HG changeset patch
# User greg
# Date 1512741661 18000
# Node ID 67420bf2013b3fab97d28fc6da8e6ecfc204225d
# Parent  d0cb6804592c6fd8b31ce9b5a81031d16e55ecfc
Uploaded

diff -r d0cb6804592c -r 67420bf2013b assembly_post_processor.xml
--- a/assembly_post_processor.xml	Fri Dec 08 08:52:26 2017 -0500
+++ b/assembly_post_processor.xml	Fri Dec 08 09:01:01 2017 -0500
@@ -35,33 +35,32 @@
 #end if
 --num_threads \${GALAXY_SLOTS:-4}
 &>proc.log
-&& if [[ $? -ne 0 ]];
-then
-    cp proc.log '$output_cds'
-    cp proc.log '$output_pep'
-    cp proc.log '$output_cleaned_cds'
-    cp proc.log '$output_cleaned_pep'
+&& if [[ $? -ne 0 ]]; then
+    cp proc.log '$output_cds';
+    cp proc.log '$output_pep';
+    cp proc.log '$output_cleaned_cds';
+    cp proc.log '$output_cleaned_pep';
     #if str($options_type.options_type_selector) == 'advanced':
         #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
-            cp proc.log '$output_targeted_gene_families_stats'
+            cp proc.log '$output_targeted_gene_families_stats';
         #end if
         #if str($options_type.dereplicate) == 'yes':
-            cp proc.log '$output_cleaned_nr_cds'
-            cp proc.log '$output_cleaned_nr_pep'
+            cp proc.log '$output_cleaned_nr_cds';
+            cp proc.log '$output_cleaned_nr_pep';
         #end if
     #end if
 else
-    mv $output_dir/transcripts.cds '$output_cds'
-    mv $output_dir/transcripts.pep '$output_pep'
-    mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
-    mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
+    mv $output_dir/transcripts.cds '$output_cds';
+    mv $output_dir/transcripts.pep '$output_pep';
+    mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds';
+    mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep';
     #if str($options_type.options_type_selector) == 'advanced':
         #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
-            mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
+            mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats';
         #end if
         #if str($options_type.dereplicate) == 'yes':
-            mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
-            mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
+            mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds';
+            mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep';
         #end if
     #end if
 fi]]></command>