--- a/mob_recon.xml	Tue Nov 05 16:46:20 2019 -0500
+++ b/mob_recon.xml	Thu Nov 14 00:43:21 2019 +0000
@@ -1,7 +1,7 @@
-<tool id="mob_recon" name="MOB-Recon" version="2.0.1_galaxy0">
+<tool id="mob_recon" name="MOB-Recon" version="2.0.2+galaxy0">
   <description>Type contigs and extract plasmid sequences</description>
   <requirements>
-     <requirement type="package" version="2.0.1">mob_suite</requirement>
+     <requirement type="package" version="2.0.2">mob_suite</requirement>
   </requirements>   
   <command detect_errors="exit_code">
   <![CDATA[  
@@ -11,12 +11,10 @@
     #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 
@@ -31,10 +29,8 @@
     --min_mob_ident '${adv_param.min_mob_ident}'
     --min_con_ident  '${adv_param.min_con_ident}'
     --min_rpp_ident   '${adv_param.min_rpp_ident}'
-    --outdir '.' && 
-    mkdir ./plasmids &&
-    (cp plasmid*.fasta ./plasmids 2> /dev/null || true) &&
-    tar -czf plasmids.tgz plasmids
+    --outdir 'outdir' &&
+    mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)
   ]]>  
   </command>
   <inputs>
@@ -69,10 +65,13 @@
     </section>  
   </inputs>
   <outputs>
-    <data name="contig_report" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> 
-    <data name="repetitive_blast_report" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${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 ${on_string}: plasmids (zipped)"/>
+    <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> 
+    <data name="repetitive_blast_report" format="tabular" from_work_dir="outdir/repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
+    <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
+    <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${on_string}: Chromosome"/>
+    <collection name="plasmids" type="list" label="${tool.name} on ${on_string}: Plasmids">
+            <discover_datasets pattern="__name_and_ext__" directory="plasmids" />
+    </collection>
   </outputs>
   <tests>
     <test>
@@ -81,7 +80,7 @@
          <param name="unicycler_contigs" value="True"/>
          <param name="run_circlator"  value="True"/>
         </section>
-        <output name="outfile1">
+        <output name="contig_report">
           <assert_contents>
             <has_text text="NC_019097"/>
           </assert_contents>  
@@ -89,6 +88,7 @@
     </test>
   </tests>
   <help>
+
 **Syntax**
 
 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
@@ -111,17 +111,18 @@
 Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
 
 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
+
+
   </help>
   <citations>
     <citation type="bibtex">
-    @misc{githubmob-suite,
-      author = {Robertson J, Nash J},
-      title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
-      publisher = {GitHub},
-      journal = {GitHub repository},
-      doi = {10.1099/mgen.0.000206},
-      url = {https://github.com/phac-nml/mob-suite}
-    }
-    </citation>
+  @misc{githubmob-suite,
+  author = {Robertson J, Nash J},
+  title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  doi = {10.1099/mgen.0.000206},
+  url = {https://github.com/phac-nml/mob-suite}
+    }</citation>
   </citations>
 </tool>