<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>