# HG changeset patch
# User greg
# Date 1509034804 14400
# Node ID 11e85af74c7e7760963eaddcf56f6dda042b9842
# Parent  7801f23bc5d934566d546ff7809d5a098149056d
Uploaded

diff -r 7801f23bc5d9 -r 11e85af74c7e assembly_post_processor.xml
--- a/assembly_post_processor.xml	Thu Oct 26 11:41:10 2017 -0400
+++ b/assembly_post_processor.xml	Thu Oct 26 12:20:04 2017 -0400
@@ -34,17 +34,24 @@
     --min_length $options_type.min_length
 #end if
 --num_threads \${GALAXY_SLOTS:-4}
-&& cp $output_dir/transcripts.cds '$output_cds'
-&& cp $output_dir/transcripts.pep '$output_pep'
-&& cp $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
-&& cp $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
+&>proc.log
+&& 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':
-        && cp $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
+        && if [ -f $output_dir/targeted_gene_family_assemblies.stats ]; then
+            mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
+        fi
     #end if
     #if str($options_type.dereplicate) == 'yes':
-        && cp $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
-        && cp $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
+        && if [ -f $output_dir/transcripts.cleaned.nr.cds ]; then
+            mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
+        fi
+        && if [ -f $output_dir/transcripts.cleaned.nr.pep ]; then
+            mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
+        fi
     #end if
 #end if
     ]]></command>