# HG changeset patch
# User dfornika
# Date 1561483907 14400
# Node ID 1b64a4d3140874586d5cb4d7325e9ec99f76a590
# Parent  cc05569322a98dc6e9fbecdecece3fb67779a847
planemo upload for repository https://github.com/phac-nml/mob-suite commit 4046a822176aafd34a2ae8dc24ad6d0337fafbe6-dirty

diff -r cc05569322a9 -r 1b64a4d31408 separate_chromosome_from_plasmids.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/separate_chromosome_from_plasmids.xml	Tue Jun 25 13:31:47 2019 -0400
@@ -0,0 +1,27 @@
+<tool id="separate_chromosome_from_plasmids" name="Separate Chromosome from Plasmids" version="1.4.9.1">
+  <description>Separate chromosomal contigs from plasmid contigs</description>
+  <requirements>
+  </requirements>   
+  <command detect_errors="exit_code">
+  <![CDATA[
+    #for $input in $inputs
+        ln -s '${input}' '${input.element_identifier}.fasta'
+    #end for
+  ]]>  
+  </command>
+  <inputs>
+    <param name="inputs" type="data" format="fasta" multiple="true" label="Input" help="FASTA files with contig(s)"/>
+  </inputs>
+  <outputs>
+    <data name="chromosome" format="fasta" from_work_dir="chromosome.fasta" label="Chromosome contigs"/> 
+    <collection name="plasmids" type="list" label="Plasmid contigs (zipped)">
+      <discover_datasets pattern="plasmid*" format="fasta" />
+    </collection>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+  </help>
+  <citations>
+  </citations>
+</tool>