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<tool id="clonalframeMLtool" name="clonalframeML" version="1.0">
  <description>a software package that performs efficient inference of recombination in bacterial genomes</description>
<requirements>
  <requirement type="package" version="1.12">clonalframeml</requirement>
</requirements>

<command>ClonalFrameML $input $input1 $output ; mv $output'.ML_sequence.fasta' $output ; mv $output'.labelled_tree.newick' $output1 ; mv $output'.em.txt' $output2 </command>
  <inputs>
	  <param format="newick" name="input" type="data" label="Newick file : " multiple="false" display="checkboxes"/>
	  <param format="fasta" name="input1" type="data" label="Alignement fasta file : " multiple="false" display="checkboxes"/>

 </inputs>

 <outputs>
	 <data format="fasta" name="output" label="reduced Fasta Alignment" />
	 <data format="newick" name="output1" label="labelled newick tree" />
	 <data format="tabular" name="output2" label="em.txt" />
 </outputs>

 <tests>
    <test>
            <param name="input" value="tree_45ind_190kSNP.withST.nwk" />
            <param name="input" value="190ksnp_alignment_KP2.fa" />
        <output name="output" file="results.txt" />
    </test>
</tests>

  <help>
For full documentation, please go to the ClonalframeML wiki (https://github.com/xavierdidelot/ClonalFrameML)
  </help>
  <citations>
         <citation type="doi">10.1371/journal.pcbi.1004041</citation>
                </citations>
</tool>