Mercurial > repos > crs4 > taxonomy_krona_chart

comparison taxonomy_krona_chart.xml @ 4:8e2be617b437 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit d62a0a2d4d0a8ac23014f09c1958d7ca0ea4fbb6
author iuc
date Thu, 04 May 2017 06:04:23 -0400
parents 50f204c82159
children 020b3087d0b7
comparison
equal deleted inserted replaced
3:f11a04ed443b 4:8e2be617b437
1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.0"> 1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1">
2 <description>from taxonomic profile</description> 2 <description>from taxonomic profile</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.6">krona</requirement> 4 <requirement type="package" version="2.6.1">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><![CDATA[
8 <![CDATA[ 8 #if $type_of_data.input[0].is_of_type('taxonomy'):
9
10 #if $type_of_data.input[0].is_of_type('taxonomy'):
11
12 ktImportGalaxy 9 ktImportGalaxy
13 -d "${type_of_data.max_rank}" 10 -d '${type_of_data.max_rank}'
14 -n "${root_name}" 11 -n '${root_name}'
15 -o "${output}" 12 -o '${output}'
16 ${combine_inputs} 13 ${combine_inputs}
17 #for $input_count, $input_dataset in enumerate( $type_of_data.input ): 14 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
18 "${input_dataset},${input_count}" 15 '${input_dataset},${input_count}'
19 #end for 16 #end for
20 17 #else:
21 #else:
22
23 ktImportText 18 ktImportText
24 -n "${root_name}" 19 -n '${root_name}'
25 -o "${output}" 20 -o '${output}'
26 ${combine_inputs} 21 ${combine_inputs}
27 #for $input_count, $input_dataset in enumerate( $type_of_data.input ): 22 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
28 "${input_dataset},${input_count}" 23 '${input_dataset},${input_count}'
29 #end for 24 #end for
30 25 #end if
31 #end if 26 && [ -d '${output}.files' ] && ( mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}/' )
32 27 ]]></command>
33 && [ -d "${output}.files" ] && ( mkdir "${output.extra_files_path}" && mv "${output}.files" "${output.extra_files_path}/" )
34 ]]>
35
36 </command>
37 <inputs> 28 <inputs>
38 <conditional name="type_of_data"> 29 <conditional name="type_of_data">
39 <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"> 30 <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">
40 <option value="taxonomy" selected="True">Taxonomy</option> 31 <option value="taxonomy" selected="True">Taxonomy</option>
41 <option value="text">MetaPhlAn</option> 32 <option value="text">MetaPhlAn</option>
42 </param> 33 </param>
43 <when value="taxonomy"> 34 <when value="taxonomy">
44 <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" /> 35 <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
45 <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point"> 36 <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point">
46 <option value="8">Class</option> 37 <option value="8">Class</option>
47 <option value="0">Show entire tree</option> 38 <option value="0">Show entire tree</option>
48 <option value="1">Superkingdom</option> 39 <option value="1">Superkingdom</option>
49 <option value="2">Kingdom</option> 40 <option value="2">Kingdom</option>
50 <option value="3">Subkingdom</option> 41 <option value="3">Subkingdom</option>
51 <option value="4">Superphylum</option> 42 <option value="4">Superphylum</option>
70 <when value="text"> 61 <when value="text">
71 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" /> 62 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
72 </when> 63 </when>
73 </conditional> 64 </conditional>
74 <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/> 65 <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/>
75 <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"/> 66 <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" checked="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/>
76 </inputs> 67 </inputs>
77 <outputs> 68 <outputs>
78 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/> 69 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
79 </outputs> 70 </outputs>
80 <tests> 71 <tests>
88 </test> 79 </test>
89 </tests> 80 </tests>
90 <help> 81 <help>
91 **What it does** 82 **What it does**
92 83
93 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. 84 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_.
94 85
95 86
96 .. _Krona: https://github.com/marbl/Krona/wiki 87 .. _Krona: https://github.com/marbl/Krona/wiki
97 88
98 ------ 89 ------
99 90
100 **Krona options** 91 **Krona options**
101 92
102 The Galaxy version supports the following options:: 93 The Galaxy version supports the following options::
103 94
104 -n Name of the highest level. 95 -n Name of the highest level.
105 -c Combine data from each file, rather than creating separate datasets within the chart. 96 -c Combine data from each file, rather than creating separate datasets within the chart.
106 -d Maximum depth of wedges to include in the chart. 97 -d Maximum depth of wedges to include in the chart.
107 98
108 ----- 99 -----
110 **License and citation** 101 **License and citation**
111 102
112 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. 103 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
113 104
114 .. _CRS4 Srl.: http://www.crs4.it/ 105 .. _CRS4 Srl.: http://www.crs4.it/
115 .. _MIT license: http://opensource.org/licenses/MIT 106 .. _MIT license: https://opensource.org/licenses/MIT
116 107
117 You can use this tool only if you agree to the license terms of: `Krona`_. 108 You can use this tool only if you agree to the license terms of: `Krona`_.
118 109
119 .. _Krona: http://sourceforge.net/p/krona/home/krona/ 110 .. _Krona: https://github.com/marbl/Krona/wiki
120
121
122 </help> 111 </help>
123 <citations> 112 <citations>
124 <citation type="doi">10.1186/1471-2105-12-385</citation> 113 <citation type="doi">10.1186/1471-2105-12-385</citation>
125 <citation type="doi">10.1093/bioinformatics/btu135</citation> 114 <citation type="doi">10.1093/bioinformatics/btu135</citation>
126 </citations> 115 </citations>