|
0
|
1 <tool id="mugsy" name="Mugsy" version="1.0.1">
|
|
|
2 <description>multiple whole genome aligner</description>
|
|
|
3 <requirements>
|
|
2
|
4 <requirement type="package" version="1.53.0">boost</requirement>
|
|
0
|
5 <requirement type="package" version="1.2.3.1">mugsy</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command interpreter="python">
|
|
|
8 mugsy.py -r $reference -c $contigs -l $logfile --ml $mugsylog --maf $maffile
|
|
|
9 </command>
|
|
|
10
|
|
|
11 <inputs>
|
|
|
12 <param name="reference" type="data" format="fasta" label="Reference" help="FASTA format" />
|
|
|
13 <param name="contigs" type="data" format="fasta" label="Contigs/draft" help="FASTA format" />
|
|
|
14 </inputs>
|
|
|
15 <outputs>
|
|
|
16 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
|
|
|
17 <data name="mugsylog" format="txt" label="${tool.name} on ${on_string}: mugsy.log" />
|
|
|
18 <data name="maffile" format="maf" label="${tool.name} on ${on_string}: MAF" />
|
|
|
19 </outputs>
|
|
|
20 <tests>
|
|
|
21
|
|
|
22 </tests>
|
|
|
23 <help>
|
|
|
24 **What it does**
|
|
|
25
|
|
|
26 Mugsy generates a MAF (multiple alignment format) file containing the multiple alignments from FASTA inputs.
|
|
|
27
|
|
|
28 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.
|
|
|
29
|
|
|
30 **License and citation**
|
|
|
31
|
|
|
32 This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
|
|
|
33
|
|
|
34 .. _CRS4 Srl.: http://www.crs4.it/
|
|
|
35 .. _MIT license: http://opensource.org/licenses/MIT
|
|
|
36
|
|
1
|
37 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
|
|
|
38
|
|
|
39 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
|
|
|
40 .. _Cuccuru2013: http://orione.crs4.it/
|
|
0
|
41
|
|
|
42 This tool uses `Mugsy`_, which is licensed separately. Please cite |Angiuoli2010|_.
|
|
|
43
|
|
|
44 .. _Mugsy: http://mugsy.sourceforge.net/
|
|
|
45 .. |Angiuoli2010| replace:: Angiuoli, S. V., Salzberg S. L. (2010) Mugsy: Fast multiple alignment of closely related whole genomes. *Bioinformatics* 27(3), 334-342
|
|
|
46 .. _Angiuoli2010: http://bioinformatics.oxfordjournals.org/content/27/3/334
|
|
|
47 </help>
|
|
|
48 </tool>
|
