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1 <tool id="clonalframeMLtool" name="clonalframeML" version="1.0">
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2 <description>a software package that performs efficient inference of recombination in bacterial genomes</description>
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3 <requirements>
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4 <requirement type="package" version="1.12">clonalframeml</requirement>
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5 </requirements>
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6
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7 <command>ClonalFrameML $input $input1 $output ; mv $output'.ML_sequence.fasta' $output ; mv $output'.labelled_tree.newick' $output1 ; mv $output'.em.txt' $output2 </command>
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8 <inputs>
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9 <param format="newick" name="input" type="data" label="Newick file : " multiple="false" display="checkboxes"/>
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10 <param format="fasta" name="input1" type="data" label="Alignement fasta file : " multiple="false" display="checkboxes"/>
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11
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12 </inputs>
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13
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14 <outputs>
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15 <data format="fasta" name="output" label="reduced Fasta Alignment" />
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16 <data format="newick" name="output1" label="labelled newick tree" />
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17 <data format="tabular" name="output2" label="em.txt" />
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18 </outputs>
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19
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20 <tests>
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21 <test>
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22 <param name="input" value="tree_45ind_190kSNP.withST.nwk" />
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23 <param name="input" value="190ksnp_alignment_KP2.fa" />
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24 <output name="output" file="results.txt" />
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25 </test>
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26 </tests>
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27
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28 <help>
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29 For full documentation, please go to the ClonalframeML wiki (https://github.com/katholt/Kleborate/wiki)
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30 </help>
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31 <citations>
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32 <citation type="doi">10.1371/journal.pcbi.1004041</citation>
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33 </citations>
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34 </tool>
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35
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36
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37
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