# HG changeset patch
# User greg
# Date 1512737235 18000
# Node ID de1b2dbdd490ea148da573f90b2ac83ac949f832
# Parent  6b071ce71267274604e56787a1a0b3f770aa567b
Uploaded

diff -r 6b071ce71267 -r de1b2dbdd490 assembly_post_processor.xml
--- a/assembly_post_processor.xml	Thu Dec 07 15:25:30 2017 -0500
+++ b/assembly_post_processor.xml	Fri Dec 08 07:47:15 2017 -0500
@@ -36,22 +36,34 @@
 --num_threads \${GALAXY_SLOTS:-4}
 &>proc.log
 && if [[ $? -ne 0 ]]; then
-    exec &>/dev/tty;
-    cat proc.log;
+    cp proc.log '$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';
+        #end if
+        #if str($options_type.dereplicate) == 'yes':
+            cp proc.log '$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';
+    #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';
+        #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';
+        #end if
+    #end if
 fi
-&& 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'
-    #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'
-    #end if
-#end if
     ]]></command>
     <inputs>
         <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>