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1 <tool id="mugsy" name="Mugsy" version="1.0.1">
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2 <description>multiple whole genome aligner</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.3.1">mugsy</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 mugsy.py -r $reference -c $contigs -l $logfile --ml $mugsylog --maf $maffile
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8 </command>
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9
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10 <inputs>
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11 <param name="reference" type="data" format="fasta" label="Reference" help="FASTA format" />
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12 <param name="contigs" type="data" format="fasta" label="Contigs/draft" help="FASTA format" />
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13 </inputs>
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14 <outputs>
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15 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
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16 <data name="mugsylog" format="txt" label="${tool.name} on ${on_string}: mugsy.log" />
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17 <data name="maffile" format="maf" label="${tool.name} on ${on_string}: MAF" />
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18 </outputs>
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19 <tests>
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20
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21 </tests>
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22 <help>
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23 **What it does**
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24
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25 Mugsy generates a MAF (multiple alignment format) file containing the multiple alignments from FASTA inputs.
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26
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27 This implementation runs with two files only: reference vs contigs/draft(s). For multiple alignment a single Multi-FASTA file containing all contigs should be provided.
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28
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29 **License and citation**
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30
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31 This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
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32
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33 .. _CRS4 Srl.: http://www.crs4.it/
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34 .. _MIT license: http://opensource.org/licenses/MIT
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35
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36 If you use this tool in Galaxy, please cite the website http://orione.crs4.it/
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37
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38 This tool uses `Mugsy`_, which is licensed separately. Please cite |Angiuoli2010|_.
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39
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40 .. _Mugsy: http://mugsy.sourceforge.net/
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41 .. |Angiuoli2010| replace:: Angiuoli, S. V., Salzberg S. L. (2010) Mugsy: Fast multiple alignment of closely related whole genomes. *Bioinformatics* 27(3), 334-342
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42 .. _Angiuoli2010: http://bioinformatics.oxfordjournals.org/content/27/3/334
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43 </help>
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44 </tool>
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