# HG changeset patch
# User dfornika
# Date 1561488377 14400
# Node ID 4f61557abe6d70534e3e70e37bc454cf58276f8d
# Parent  1ac93528c500c376f80c934d4c07d5e2d3d8bee3
planemo upload for repository https://github.com/phac-nml/mob-suite commit 4046a822176aafd34a2ae8dc24ad6d0337fafbe6-dirty

diff -r 1ac93528c500 -r 4f61557abe6d separate_chromosome_from_plasmids.xml
--- a/separate_chromosome_from_plasmids.xml	Tue Jun 25 14:34:13 2019 -0400
+++ b/separate_chromosome_from_plasmids.xml	Tue Jun 25 14:46:17 2019 -0400
@@ -7,7 +7,7 @@
     #for $input in $inputs
         cp '${input}' '${input.element_identifier}.fasta' &&
     #end for
-    true
+    mkdir plasmids && mv 'plasmid*' plasmids
   ]]>  
   </command>
   <inputs>
@@ -16,7 +16,7 @@
   <outputs>
     <data name="chromosome" format="fasta" from_work_dir="chromosome.fasta" label="Chromosome contigs"/> 
     <collection name="plasmids" type="list" label="Plasmid contigs">
-      <discover_datasets pattern="plasmid*" format="fasta" />
+      <discover_datasets pattern="__designation_and_ext__" directory="plasmids" format="fasta" />
     </collection>
   </outputs>
   <tests>