Mercurial > repos > greg > assembly_post_processor

changeset 98:96e4d7bc2f2a draft

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Uploaded
author greg
date Thu, 26 Oct 2017 14:37:24 -0400
parents 9c4afc33bc87
children 01ef9d05d455
files assembly_post_processor.xml
diffstat 1 files changed, 3 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/assembly_post_processor.xml	Thu Oct 26 13:17:49 2017 -0400
+++ b/assembly_post_processor.xml	Thu Oct 26 14:37:24 2017 -0400
@@ -41,17 +41,11 @@
 && 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':
-        && if [ -f "$output_dir/targeted_gene_family_assemblies.stats" ]; then
-            mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
-        fi
+        && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
     #end if
     #if str($options_type.dereplicate) == 'yes':
-        && if [ -f "$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
+        && 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>