# HG changeset patch
# User nml
# Date 1509122400 14400
# Node ID 09ebaa5192ab39af257acb4a394e1b0fc5340ef3
# Parent  ba271365095e1dd17ebecbf65759fcfb04cff85c
planemo upload for repository https://github.com/phac-nml/bio_hansel commit d5a37b4f48178ee8179883d0f6cf550824e975f0

diff -r ba271365095e -r 09ebaa5192ab bio_hansel.xml
--- a/bio_hansel.xml	Wed Oct 11 12:35:50 2017 -0400
+++ b/bio_hansel.xml	Fri Oct 27 12:40:00 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.2">
+<tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.3">
     <description>Genome assemblies and/or whole-genome sequencing readset</description>
     <requirements>
         <requirement type="package" version="0.1.0">bio_hansel</requirement>
@@ -13,8 +13,8 @@
 
         #elif $data_type.type == "collection":
 
-            ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.forward.name' &&
-            ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.reverse.name' &&
+            ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1 &&
+            ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2 &&
 
         #elif $data_type.type == "single":
 
@@ -70,7 +70,7 @@
             '$data_type.fastq_input1.name'
 
         #elif $data_type.type =="collection":
-            -p '$data_type.fastq_input1.forward.name'  '$data_type.fastq_input1.reverse.name'
+            -p '$data_type.fastq_input1.name'_1  '$data_type.fastq_input1.name'_2
         
         #elif $data_type.type =="paired":
             -p '$data_type.fastq_input1.name'  '$data_type.fastq_input2.name'