--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpo_clustalw.xml	Thu Aug 16 19:27:05 2018 -0400
@@ -0,0 +1,67 @@
+<tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
+  <description>makes tree from alignment</description>
+  <requirements>
+     <requirement type="package" version="2.1">clustalw</requirement>
+  </requirements>   
+  <command detect_errors="exit_code">
+  <![CDATA[  
+    clustalw2 -tree -infile=$input -outputtree=nj
+  ]]>  
+  </command>
+  <inputs>
+    <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
+  </inputs>
+  <outputs>
+    <data name="phylip" format="txt" from_work_dir="*.ph"/> 
+    <data name="njtree" format="txt" from_work_dir="*.nj*"/>
+  </outputs>
+  <tests>
+    <test>
+        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
+        <section name="adv_param">
+         <param name="evalue" value="0.00001"/>
+         <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/. 
+
+-----
+
+**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>
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