Mercurial > repos > crs4 > taxonomy_krona_chart

comparison taxonomy_krona_chart.xml @ 7:73486cc6170e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 40d8aaf782f1693a435ec17abe81e81fa157f724
author iuc
date Mon, 19 Feb 2018 06:29:08 -0500
parents d41b98e72c4c
children c9f8fef1df74
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6:d41b98e72c4c 7:73486cc6170e
26 && 26 &&
27 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi 27 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
28 ]]></command> 28 ]]></command>
29 <inputs> 29 <inputs>
30 <conditional name="type_of_data"> 30 <conditional name="type_of_data">
31 <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"> 31 <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Choose between Galaxy Taxonomy and generic table format (e.g. from MetaPhlAn or mothur)">
32 <option value="taxonomy" selected="True">Taxonomy</option> 32 <option value="taxonomy" selected="True">Taxonomy</option>
33 <option value="text">MetaPhlAn</option> 33 <option value="text">Tabular</option>
34 </param> 34 </param>
35 <when value="taxonomy"> 35 <when value="taxonomy">
36 <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" /> 36 <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
37 <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point"> 37 <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point">
38 <option value="8">Class</option> 38 <option value="8">Class</option>
95 -c Combine data from each file, rather than creating separate datasets within the chart. 95 -c Combine data from each file, rather than creating separate datasets within the chart.
96 -d Maximum depth of wedges to include in the chart. 96 -d Maximum depth of wedges to include in the chart.
97 97
98 ----- 98 -----
99 99
100 **Input format**
101
102 *Tabular* input format should be a tab-delimited file with the first column containing a count
103 and the remaining columns describing the hierarchy. For example::
104
105 2 Fats Saturated fat
106 3 Fats Unsaturated fat Monounsaturated fat
107 3 Fats Unsaturated fat Polyunsaturated fat
108 13 Carbohydrates Sugars
109 4 Carbohydrates Dietary fiber
110 21 Carbohydrates
111 5 Protein
112 4
113
114 which would yield this `Krona plot`_.
115
116 .. _Krona plot: https://marbl.github.io/Krona/examples/xml.krona.html
117
118 -----
119
100 **License and citation** 120 **License and citation**
101 121
102 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. 122 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
103 123
104 .. _CRS4 Srl.: http://www.crs4.it/ 124 .. _CRS4 Srl.: http://www.crs4.it/