# HG changeset patch
# User nml
# Date 1538420074 14400
# Node ID 05ca0dbc9f46ecfee85dee01c1352e508d4faa9e
# Parent  6eae14751768f7432e5ab6dacad5a5dfe5695b96
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 2d42861c536b44c4fe00bef20c442c6cc0e987dd-dirty

diff -r 6eae14751768 -r 05ca0dbc9f46 mykrobe_parser.xml
--- a/mykrobe_parser.xml	Fri Sep 28 16:01:47 2018 -0400
+++ b/mykrobe_parser.xml	Mon Oct 01 14:54:34 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.0">
+<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.1">
     <requirements>
         <requirement type="package" version="3.4.1">r-base</requirement>
         <requirement type="package" version="1.5.0">r-jsonlite</requirement>
@@ -14,7 +14,7 @@
         #if $input.type == 'collection'
             mkdir collection_files &&
             #for $file in $input.collection
-                cp "$file" collection_files/"$file.name".json &&
+                ln -s "$file" collection_files/"$file.element_identifier".json &&
             #end for
         #end if