--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mob_recon.xml	Wed Oct 30 23:50:10 2019 -0400
@@ -0,0 +1,127 @@
+<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>
+  </requirements>   
+  <command detect_errors="exit_code">
+  <![CDATA[  
+    #import re
+    #import os.path
+    
+    #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}" 
+    #if str($adv_param.unicycler_contigs) == "True":
+      --unicycler_contigs 
+    #end if
+    #if str($adv_param.run_circlator) == "True":
+      --run_circlator 
+    #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 '${adv_param.min_rep_evalue}'
+    --min_mob_evalue '${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) &&
+    tar -czf plasmids.tgz plasmids
+  ]]>  
+  </command>
+  <inputs>
+    <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
+    <section name="adv_param" title="Advanced parameters" expanded="False">
+      <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
+        <option value="True">Yes</option>
+        <option value="False">No</option>
+      </param>
+      <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
+        <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>
+          <option value="True">Yes</option>
+       </param>   
+        <when value="True">
+          <param name="min_length_value" type="integer" value="500" min="50"/> 
+        </when>  
+        <when value="False"/>
+      </conditional> 
+      <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float"  min="0.00001" max="1" value="0.00001"/>
+      <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float"  min="0.00001" max="1" value="0.00001"/>
+      <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float"  min="0.00001" max="1" value="0.00001"/>
+      <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float"  min="0.00001" max="1" value="0.00001"/>
+      <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer"  min="0" max="100" value="80"/>
+      <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer"  min="0" max="100" value="80"/>
+      <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer"  min="0" max="100" value="80"/>
+      <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer"  min="0" max="100" value="80"/>
+    </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)"/>
+  </outputs>
+  <tests>
+    <test>
+        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
+        <section name="adv_param">
+         <param name="unicycler_contigs" value="True"/>
+         <param name="run_circlator"  value="True"/>
+        </section>
+        <output name="outfile1">
+          <assert_contents>
+            <has_text text="NC_019097"/>
+          </assert_contents>  
+        </output> 
+    </test>
+  </tests>
+  <help>
+**Syntax**
+
+This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
+
+For more information please visit https://github.com/phac-nml/mob-suite/. 
+
+**Workflow**
+
+This preliminary \"Mobilome and Resistome Analysis Workflow\" linking mob_recon with staramr provides reports on mobilome and resistome for a given isolate given a draft genome assembly. The workflow is located in Shared Data --> Workflows --> Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR). The workflow file can also be manually downloaded from https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/workflows/AMRworkflow_STARAMR.ga.
+
+-----
+
+**Input:**
+
+A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
+
+
+**Output:**
+
+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>
+  </citations>
+</tool>