Mercurial > repos > crs4 > taxonomy_krona_chart

annotate taxonomy_krona_chart.xml @ 9:1334cb4c6b68 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 0be1842634941540d5e313b1ad9cb5eb81fd7305"
author iuc
date Sat, 30 Nov 2019 13:05:03 -0500
parents c9f8fef1df74
children e9005d1f3cfd
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1334cb4c6b68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 0be1842634941540d5e313b1ad9cb5eb81fd7305"
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1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.7.1">
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2 <description>from taxonomic profile</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.1">krona</requirement>
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5 </requirements>
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6 <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
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9
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10 #if $type_of_data.input[0].is_of_type('taxonomy'):
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11 ktImportGalaxy
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12 -d '${type_of_data.max_rank}'
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13 -n '${root_name}'
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14 -o '${output}'
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15 ${combine_inputs}
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16 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
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17 '${input_dataset},${input_count}'
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18 #end for
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19 #else:
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20 ktImportText
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21 -n '${root_name}'
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22 -o '${output}'
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23 ${combine_inputs}
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24 #for $input_dataset in $type_of_data.input:
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25 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
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26 '${input_dataset},${identifier}'
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27 #end for
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28 #end if
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29 &&
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30 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
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31 ]]></command>
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32 <inputs>
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33 <conditional name="type_of_data">
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34 <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)">
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35 <option value="taxonomy" selected="True">Taxonomy</option>
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36 <option value="text">Tabular</option>
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37 </param>
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38 <when value="taxonomy">
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39 <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
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40 <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point">
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41 <option value="8">Class</option>
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42 <option value="0">Show entire tree</option>
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43 <option value="1">Superkingdom</option>
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44 <option value="2">Kingdom</option>
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45 <option value="3">Subkingdom</option>
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46 <option value="4">Superphylum</option>
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47 <option value="5">Phylum</option>
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48 <option value="6">Subphylum</option>
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49 <option value="7">Superclass</option>
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50 <option value="9">Subclass</option>
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51 <option value="10">Superorder</option>
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52 <option value="11">Order</option>
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53 <option value="12">Suborder</option>
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54 <option value="13">Superfamily</option>
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55 <option value="14">Family</option>
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56 <option value="15">Subfamily</option>
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57 <option value="16">Tribe</option>
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58 <option value="17">Subtribe</option>
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59 <option value="18">Genus</option>
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60 <option value="19">Subgenus</option>
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61 <option value="20">Species</option>
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62 <option value="21">Subspecies</option>
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63 </param>
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64 </when>
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65 <when value="text">
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66 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
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67 </when>
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68 </conditional>
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69 <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;"/>
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70 <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"/>
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71 </inputs>
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72 <outputs>
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73 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="type_of_data_selector" value="taxonomy"/>
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78 <param name="input" value="taxonomy_data.tax" ftype="taxonomy" />
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79 <param name="max_rank" value="Genus"/>
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80 <param name="root_name" value="Root"/>
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81 <param name="combine_inputs" value="False"/>
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82 <output name="output" file="krona_test1.html" ftype="html" lines_diff="102"/>
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83 </test>
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84 <test><!-- test with tabular inputs and multiple datasets -->
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85 <param name="type_of_data_selector" value="text"/>
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86 <param name="input" value="pampa-small.tsv,anguil-small.tsv" ftype="tabular" />
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87 <param name="max_rank" value="Genus"/>
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88 <param name="root_name" value="Root"/>
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89 <param name="combine_inputs" value="False"/>
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90 <output name="output" ftype="html">
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91 <assert_contents>
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92 <has_text text="KRONA"/>
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93 <has_text text="pampa-small"/>
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94 <has_text text="anguil-small"/>
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95 <has_text text="Proteobacteria"/>
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96 </assert_contents>
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97 </output>
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98 </test>
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99 </tests>
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100 <help>
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101 **What it does**
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102
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103 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_.
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104
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105
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106 ------
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107
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108 **Krona options**
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109
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110 The Galaxy version supports the following options::
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111
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112 -n Name of the highest level.
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113 -c Combine data from each file, rather than creating separate datasets within the chart.
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114 -d Maximum depth of wedges to include in the chart.
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115
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116 -----
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117
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118 **Input format**
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119
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120 *Tabular* input format should be a tab-delimited file with the first column containing a count
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121 and the remaining columns describing the hierarchy. For example::
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122
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123 2 Fats Saturated fat
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124 3 Fats Unsaturated fat Monounsaturated fat
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125 3 Fats Unsaturated fat Polyunsaturated fat
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126 13 Carbohydrates Sugars
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127 4 Carbohydrates Dietary fiber
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128 21 Carbohydrates
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129 5 Protein
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130 4
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131
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132 which would yield this `Krona plot`_.
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133
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134 .. _Krona plot: https://marbl.github.io/Krona/examples/xml.krona.html
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135
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136 -----
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137
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138 **License and citation**
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139
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140 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
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141
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142 .. _CRS4 Srl.: http://www.crs4.it/
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143 .. _MIT license: https://opensource.org/licenses/MIT
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144
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145 You can use this tool only if you agree to the license terms of: `Krona`_.
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146
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147 .. _Krona: https://github.com/marbl/Krona/wiki
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148 </help>
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149 <citations>
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150 <citation type="doi">10.1186/1471-2105-12-385</citation>
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151 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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152 </citations>
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153 </tool>