# HG changeset patch
# User dfornika
# Date 1569344005 14400
# Node ID 14d499c3fe1dd6b6506e22378d6c639b09d45a42
# Parent  3851907651ad5ea197237c3a0b05c7eba9e6cfb7
planemo upload for repository https://github.com/phac-nml/mob-suite commit 0dd60ac52b9d34ee1f446182eda78cb8c01de6d1-dirty

diff -r 3851907651ad -r 14d499c3fe1d mob_recon.xml
--- a/mob_recon.xml	Mon Sep 23 21:33:51 2019 -0400
+++ b/mob_recon.xml	Tue Sep 24 12:53:25 2019 -0400
@@ -33,7 +33,8 @@
     --min_con_ident '${adv_param.min_con_ident}'
     --min_rpp_ident '${adv_param.min_rpp_ident}'
     --outdir '.' && 
-    mkdir ./plasmids && (cp plasmid*.fasta ./plasmids 2> /dev/null || true)
+    mkdir ./plasmids && (cp plasmid*.fasta ./plasmids 2> /dev/null || true) &&
+    zip -r plasmids.zip plasmids
   ]]>  
   </command>
   <inputs>
@@ -76,9 +77,11 @@
     <data name="repetitive_element_report" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
     <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
     <data name="chromosome" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name} on ${on_string}: Chromosome" />
-    <collection name="plasmids" type="list" label="${tool.name} on ${on_string}: Plasmids">
+    <data name="plasmids_zipped" format="fasta" from_work_dir="plasmids.zip" label="${tool.name} on ${on_string}: Plasmids (zipped)" />
+    <collection name="plasmids_collection" type="list" label="${tool.name} on ${on_string}: Plasmids (Collection)">
         <discover_datasets pattern="__name_and_ext__" directory="plasmids" />
     </collection>
+    
   </outputs>
   <tests>
     <test>