Mercurial > repos > greg > assembly_post_processor

changeset 106:d0cb6804592c draft

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Uploaded
author greg
date Fri, 08 Dec 2017 08:52:26 -0500
parents d5e4dbe5a88f
children 67420bf2013b
files assembly_post_processor.xml
diffstat 1 files changed, 16 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/assembly_post_processor.xml	Fri Dec 08 08:09:41 2017 -0500
+++ b/assembly_post_processor.xml	Fri Dec 08 08:52:26 2017 -0500
@@ -35,32 +35,33 @@
 #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>