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comparison taxonomy_krona_chart.xml @ 0:bd565e1e3c5f draft

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author crs4
date Fri, 11 Apr 2014 12:48:59 -0400
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1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="1.0.0">
2 <description>from taxonomic profile</description>
3 <requirements>
4 <requirement type="package" version="2.4">kronatools</requirement>
5 </requirements>
6 <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
7 <command>
8 #if $input.ext == 'taxonomy'
9 ktImportGalaxy "${input}" -o "${output}"
10 #else
11 ktImportText "${input}" -o "${output}"
12 #end if
13 </command>
14 <inputs>
15 <param name="input" type="data" format="tabular" label="Input file" help="Either a 'MetaPhlAn to Krona' result file or a taxonomy file" />
16 </inputs>
17 <outputs>
18 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
19 </outputs>
20 <help>
21 **What it does**
22
23 This tool converts the standard result file of a metagenomic profiling in a zoomable pie chart using Krona_.
24 It takes as input datasets produced by *MetaPhlAn to Krona*, *Fetch taxonomic representation*, *Find lowest diagnostic rank* and *Filter taxonomy* tools.
25
26 .. _Krona: http://sourceforge.net/p/krona/home/krona/
27
28 ------
29
30 **License and citation**
31
32 This Galaxy tool is Copyright © 2013-2014 `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
37 If you use this tool in Galaxy, please cite |Cuccuru2014|_.
38
39 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
40 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu135
41
42 This tool uses scripts from `Krona`_, which is licensed separately. Please cite |Ondov2011|_.
43
44 .. _Krona: http://sourceforge.net/p/krona/home/krona/
45 .. |Ondov2011| replace:: Ondov, B. D., Bergman, N. H., Phillippy, A. M. (2011) Interactive metagenomic visualization in a Web browser. *BMC Bioinformatics* 12, 385
46 .. _Ondov2011: http://www.biomedcentral.com/1471-2105/12/385
47 </help>
48 </tool>