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comparison taxonomy_krona_chart.xml @ 1:09552faff9c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit e4c2b31a732b57cc0210070afeaa2dfeca1e1eb4
author iuc
date Mon, 17 Aug 2015 11:36:09 -0400
parents bd565e1e3c5f
children 50f204c82159
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0:bd565e1e3c5f 1:09552faff9c0
1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="1.0.0"> 1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.0.0">
2 <description>from taxonomic profile</description> 2 <description>from taxonomic profile</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.4">kronatools</requirement> 4 <requirement type="package" version="2.5">krona</requirement>
5 </requirements> 5 </requirements>
6 <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command> 6 <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
7 <command> 7 <command>
8 #if $input.ext == 'taxonomy' 8 <![CDATA[
9 ktImportGalaxy "${input}" -o "${output}" 9
10 #else 10 #if $type_of_data.input[0].is_of_type('taxonomy'):
11 ktImportText "${input}" -o "${output}" 11
12 #end if 12 ktImportGalaxy
13 -a
14 -d "${type_of_data.max_rank}"
15 -n "${root_name}"
16 -o ${output}
17 ${combine_inputs}
18 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
19 "${input_dataset},${input_count}"
20 #end for
21
22 #else:
23
24 ktImportText
25 -a
26 -n "${root_name}"
27 -o ${output}
28 ${combine_inputs}
29 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
30 "${input_dataset},${input_count}"
31 #end for
32
33 #end if
34
35 ]]>
36
13 </command> 37 </command>
14 <inputs> 38 <inputs>
15 <param name="input" type="data" format="tabular" label="Input file" help="Either a 'MetaPhlAn to Krona' result file or a taxonomy file" /> 39 <conditional name="type_of_data">
40 <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Select between Galaxy Taxonomy and MetaPhlAn Text">
41 <option value="taxonomy" selected="True">Taxonomy</option>
42 <option value="text">MetaPhlAn</option>
43 </param>
44 <when value="taxonomy">
45 <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
46 <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point">
47 <option value="8">Class</option>
48 <option value="0">Show entire tree</option>
49 <option value="1">Superkingdom</option>
50 <option value="2">Kingdom</option>
51 <option value="3">Subkingdom</option>
52 <option value="4">Superphylum</option>
53 <option value="5">Phylum</option>
54 <option value="6">Subphylum</option>
55 <option value="7">Superclass</option>
56 <option value="9">Subclass</option>
57 <option value="10">Superorder</option>
58 <option value="11">Order</option>
59 <option value="12">Suborder</option>
60 <option value="13">Superfamily</option>
61 <option value="14">Family</option>
62 <option value="15">Subfamily</option>
63 <option value="16">Tribe</option>
64 <option value="17">Subtribe</option>
65 <option value="18">Genus</option>
66 <option value="19">Subgenus</option>
67 <option value="20">Species</option>
68 <option value="21">Subspecies</option>
69 </param>
70 </when>
71 <when value="text">
72 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
73 </when>
74 </conditional>
75 <param name="root_name" type="text" size="20" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/>
76 <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/>
16 </inputs> 77 </inputs>
17 <outputs> 78 <outputs>
18 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/> 79 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
19 </outputs> 80 </outputs>
81 <tests>
82 <test>
83 <param name="type_of_data_selector" value="taxonomy"/>
84 <param name="input" value="taxonomy_data.tax" ftype="taxonomy" />
85 <param name="max_rank" value="Genus"/>
86 <param name="root_name" value="Root"/>
87 <param name="combine_inputs" value="False"/>
88 <output name="output" file="krona_test1.html" ftype="html" lines_diff="100"/>
89 </test>
90 </tests>
20 <help> 91 <help>
21 **What it does** 92 **What it does**
22 93
23 This tool converts the standard result file of a metagenomic profiling in a zoomable pie chart using Krona_. 94 This tool renders results of a metagenomic profiling as 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. 95
25 96
26 .. _Krona: http://sourceforge.net/p/krona/home/krona/ 97 .. _Krona: http://sourceforge.net/p/krona/home/krona/
27 98
28 ------ 99 ------
100
101 **Krona options**
102
103 The Galaxy version supports the following options::
104
105 -n Name of the highest level.
106 -c Combine data from each file, rather than creating separate datasets within the chart.
107 -d Maximum depth of wedges to include in the chart.
108
109 -----
29 110
30 **License and citation** 111 **License and citation**
31 112
32 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. 113 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
33 114
34 .. _CRS4 Srl.: http://www.crs4.it/ 115 .. _CRS4 Srl.: http://www.crs4.it/
35 .. _MIT license: http://opensource.org/licenses/MIT 116 .. _MIT license: http://opensource.org/licenses/MIT
36 117
37 If you use this tool in Galaxy, please cite |Cuccuru2014|_. 118 You can use this tool only if you agree to the license terms of: `Krona`_.
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|_.
43 119
44 .. _Krona: http://sourceforge.net/p/krona/home/krona/ 120 .. _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, 385 121
46 .. _Ondov2011: http://www.biomedcentral.com/1471-2105/12/385 122
47 </help> 123 </help>
124 <citations>
125 <citation type="doi">10.1186/1471-2105-12-385</citation>
126 <citation type="doi">10.1093/bioinformatics/btu135</citation>
127 </citations>
48 </tool> 128 </tool>