--- a/mob_recon.xml	Wed Sep 25 13:56:15 2019 -0400
+++ b/mob_recon.xml	Wed Oct 30 23:38:12 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="mob_recon" name="MOB-Recon" version="2.0.0">
+<tool id="mob_recon" name="MOB-Recon" version="2.0.0_galaxy0">
   <description>Type contigs and extract plasmid sequences</description>
   <requirements>
      <requirement type="package" version="2.0.0">mob_suite</requirement>
@@ -11,29 +11,30 @@
     #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta")
     ln -s "$input" $named_input && 
     
-    mob_recon  --num_threads \${GALAXY_SLOTS:-4}  --infile "${named_input}" 
+    mob_recon  
+      --num_threads \${GALAXY_SLOTS:-4}  
+      --infile "${named_input}" 
     #if str($adv_param.unicycler_contigs) == "True":
       --unicycler_contigs 
-    #end if   
+    #end if
     #if str($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 ${adv_param.min_length_condition.min_length_value}
     #end if 
-    --min_rep_evalue '${adv_param.min_rep_evalue}'
+    --run_typer --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}'
     --min_rep_ident '${adv_param.min_rep_ident}'
     --min_mob_ident '${adv_param.min_mob_ident}'
-    --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)    
+    --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) &&
+    tar -czf plasmids.tgz plasmids
   ]]>  
   </command>
   <inputs>
@@ -47,10 +48,6 @@
         <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>
@@ -73,12 +70,9 @@
   </inputs>
   <outputs>
     <data name="contig_report" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> 
-    <data name="repetitive_element_report" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${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 ${on_string}: Chromosome" />
-    <collection name="plasmids_collection" type="list" label="${tool.name} on ${on_string}: Plasmids">
-        <discover_datasets pattern="__name_and_ext__" directory="plasmids" />
-    </collection>    
+    <data name="repetitive_blast_report" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
+    <data name="chromosome" type="data" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name} on ${on_string}: plasmids (zipped)"/>
+    <data name="plasmids_zipped" type="data" format="zip" from_work_dir="plasmids.tgz" label="${tool.name} on ${on_string}: plasmids (zipped)"/>
   </outputs>
   <tests>
     <test>
@@ -87,7 +81,7 @@
          <param name="unicycler_contigs" value="True"/>
          <param name="run_circlator"  value="True"/>
         </section>
-        <output name="contig_report">
+        <output name="outfile1">
           <assert_contents>
             <has_text text="NC_019097"/>
           </assert_contents>