# HG changeset patch
# User dfornika
# Date 1561487026 14400
# Node ID 4ea788be628e142e7f79c8a80cb8153e4dd3dacd
# Parent  1b64a4d3140874586d5cb4d7325e9ec99f76a590
planemo upload for repository https://github.com/phac-nml/mob-suite commit 4046a822176aafd34a2ae8dc24ad6d0337fafbe6-dirty

diff -r 1b64a4d31408 -r 4ea788be628e separate_chromosome_from_plasmids.xml
--- a/separate_chromosome_from_plasmids.xml	Tue Jun 25 13:31:47 2019 -0400
+++ b/separate_chromosome_from_plasmids.xml	Tue Jun 25 14:23:46 2019 -0400
@@ -5,7 +5,7 @@
   <command detect_errors="exit_code">
   <![CDATA[
     #for $input in $inputs
-        ln -s '${input}' '${input.element_identifier}.fasta'
+        cp '${input}' '${input.element_identifier}.fasta'
     #end for
   ]]>  
   </command>
@@ -14,7 +14,7 @@
   </inputs>
   <outputs>
     <data name="chromosome" format="fasta" from_work_dir="chromosome.fasta" label="Chromosome contigs"/> 
-    <collection name="plasmids" type="list" label="Plasmid contigs (zipped)">
+    <collection name="plasmids" type="list" label="Plasmid contigs">
       <discover_datasets pattern="plasmid*" format="fasta" />
     </collection>
   </outputs>