changeset 25:5aa122947f26 draft

planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 15efb6caef65e6d7b307bbf5e2b6b30f968f27c7
author sanbi-uwc
date Mon, 07 May 2018 06:06:13 -0400
parents 6b5b34b321a5
children 709eb84d9927
files novo_align.xml
diffstat 1 files changed, 2 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/novo_align.xml	Wed May 02 06:52:04 2018 -0400
+++ b/novo_align.xml	Mon May 07 06:06:13 2018 -0400
@@ -7,9 +7,8 @@
         <requirement type="package" version="04.2016">novoalign-license</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-        #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
         #if $paired_end.is_paired_end
-            #if $paired_input_type == "pair_of_files"
+            #if $paired_end.paired_input_type_conditional.paired_input_type == "pair_of_files"
                 #if $paired_end.paired_input_type_conditional.fastq_r1_in.metadata.is_gzipped
                     ln -s "${$paired_end.paired_input_type_conditional.fastq_r1_in}" ./input_mate1.gz &&
                     ln -s "${$paired_end.paired_input_type_conditional.fastq_r2_in}" ./input_mate2.gz &&
@@ -51,7 +50,7 @@
               reference.nix
             #end if
             #if $paired_end.is_paired_end
-                #if $paired_input_type == "pair_of_files"
+                #if $paired_end.paired_input_type_conditional.paired_input_type == "pair_of_files"
                     #if $paired_end.paired_input_type_conditional.fastq_r1_in.metadata.is_gzipped
                         --forward_file ./input_mate1.gz
                         --reverse_file ./input_mate2.gz