# HG changeset patch
# User dfornika
# Date 1569288084 14400
# Node ID 8330e4f982de86df48fcd31a7952576d0fd790b4
# Parent  4b9f7624a2550e1ee628c54d84ebaf6c8fdb28eb
planemo upload for repository https://github.com/phac-nml/mob-suite commit 0dd60ac52b9d34ee1f446182eda78cb8c01de6d1-dirty

diff -r 4b9f7624a255 -r 8330e4f982de mob_recon.xml
--- a/mob_recon.xml	Mon Sep 23 20:48:29 2019 -0400
+++ b/mob_recon.xml	Mon Sep 23 21:21:24 2019 -0400
@@ -17,11 +17,14 @@
     #end if   
     #if str($adv_param.run_circlator) == "True":
       --run_circlator 
+    #end if
+    #if str($adv_param.run_typer) == "True":
+      --run_typer 
     #end if 
     #if str($adv_param.min_length_condition.min_length_param) == "True":
       --min_length ${adv_param.min_length_condition.min_length_value}
     #end if 
-    --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}'
+    --min_rep_evalue '${adv_param.min_rep_evalue}'
     --min_rep_evalue '${adv_param.min_rep_evalue}'
     --min_mob_evalue '${adv_param.min_mob_evalue}'
     --min_con_evalue '${adv_param.min_con_evalue}'
@@ -45,6 +48,10 @@
         <option value="True">Yes</option>
         <option value="False">No</option>
       </param>
+      <param name="run_typer" label="Run MOB-Typer" type="select" value="False">
+        <option value="True">Yes</option>
+        <option value="False">No</option>
+      </param>
       <conditional name="min_length_condition">
         <param name="min_length_param" label="Minimum length of contigs to process" type="select" value="False">
           <option value="False">No</option>
@@ -70,7 +77,7 @@
     <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 ${on_string}: Chromosomal contigs" />
-    <data name="plasmids" format="tar.gz" from_work_dir="plasmids.tar.gz" label="${tool.name} on ${on_string}: Plasmid contigs (tar.gz)" />
+    <data name="plasmids" format="zip" from_work_dir="plasmids.tar.gz" label="${tool.name} on ${on_string}: Plasmid contigs (tar.gz)" />
   </outputs>
   <tests>
     <test>