Mercurial > repos > crs4 > taxonomy_krona_chart

annotate taxonomy_krona_chart.xml @ 9:dec61cdd7db2 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 46ae76d42d29ce02cf05b6ab735e0c305a86f9cd"
author iuc
date Fri, 18 Dec 2020 16:15:48 +0000
parents 0f65ba9069cf
children
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dec61cdd7db2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 46ae76d42d29ce02cf05b6ab735e0c305a86f9cd"
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1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.7.1+galaxy0">
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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 #else:
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14 ktImportText
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15 #end if
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17 -n '${root_name}'
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18 -o '${output}'
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19 ${combine_inputs}
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20 #for $input_dataset in $type_of_data.input:
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21 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
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22 '${input_dataset},${identifier}'
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23 #end for
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24 &&
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25 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
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26 ]]></command>
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27 <inputs>
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28 <conditional name="type_of_data">
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29 <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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30 <option value="taxonomy" selected="True">Taxonomy</option>
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31 <option value="text">Tabular</option>
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32 </param>
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33 <when value="taxonomy">
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34 <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
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35 <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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36 <option value="8">Class</option>
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37 <option value="0">Show entire tree</option>
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38 <option value="1">Superkingdom</option>
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39 <option value="2">Kingdom</option>
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40 <option value="3">Subkingdom</option>
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41 <option value="4">Superphylum</option>
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42 <option value="5">Phylum</option>
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43 <option value="6">Subphylum</option>
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44 <option value="7">Superclass</option>
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45 <option value="9">Subclass</option>
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46 <option value="10">Superorder</option>
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47 <option value="11">Order</option>
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48 <option value="12">Suborder</option>
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49 <option value="13">Superfamily</option>
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50 <option value="14">Family</option>
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51 <option value="15">Subfamily</option>
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52 <option value="16">Tribe</option>
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53 <option value="17">Subtribe</option>
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54 <option value="18">Genus</option>
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55 <option value="19">Subgenus</option>
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56 <option value="20">Species</option>
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57 <option value="21">Subspecies</option>
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58 </param>
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59 </when>
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60 <when value="text">
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61 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
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62 </when>
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63 </conditional>
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64 <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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65 <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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66 </inputs>
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67 <outputs>
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68 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="type_of_data_selector" value="taxonomy"/>
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73 <param name="input" value="taxonomy_data.tax" ftype="taxonomy" />
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74 <param name="max_rank" value="Genus"/>
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75 <param name="root_name" value="Root"/>
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76 <param name="combine_inputs" value="False"/>
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77 <output name="output" ftype="html">
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78 <assert_contents>
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79 <has_text text="KRONA"/>
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80 <has_text text="taxonomy_data"/>
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81 <has_text text="Eukaryota"/>
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82 <has_text text="Chordata"/>
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83 <has_text text="Rodentia"/>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 <test>
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88 <param name="type_of_data_selector" value="taxonomy"/>
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89 <param name="input" value="taxonomy_data.tax,tax2.tax" ftype="taxonomy" />
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90 <param name="max_rank" value="Genus"/>
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91 <param name="root_name" value="Root"/>
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92 <param name="combine_inputs" value="False"/>
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93 <output name="output" ftype="html">
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94 <assert_contents>
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95 <has_text text="KRONA"/>
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96 <has_text text="taxonomy_data"/>
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97 <has_text text="tax2"/>
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98 <has_text text="Proteobacteria"/>
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99 </assert_contents>
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100 </output>
0
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101 </test>
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102 <test><!-- test with tabular inputs and multiple datasets -->
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103 <param name="type_of_data_selector" value="text"/>
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104 <param name="input" value="pampa-small.tsv,anguil-small.tsv" ftype="tabular" />
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105 <param name="max_rank" value="Genus"/>
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106 <param name="root_name" value="Root"/>
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107 <param name="combine_inputs" value="False"/>
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108 <output name="output" ftype="html">
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109 <assert_contents>
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110 <has_text text="KRONA"/>
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111 <has_text text="pampa-small"/>
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112 <has_text text="anguil-small"/>
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113 <has_text text="Proteobacteria"/>
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114 </assert_contents>
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115 </output>
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116 </test>
0
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117 </tests>
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118 <help>
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119 **What it does**
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120
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121 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_.
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122
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123
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124 ------
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125
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126 **Krona options**
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127
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128 The Galaxy version supports the following options::
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129
0
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130 -n Name of the highest level.
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131 -c Combine data from each file, rather than creating separate datasets within the chart.
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132 -d Maximum depth of wedges to include in the chart.
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133
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134 -----
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135
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136 **Input format**
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137
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138 *Tabular* input format should be a tab-delimited file with the first column containing a count
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139 and the remaining columns describing the hierarchy. For example::
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140
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141 2 Fats Saturated fat
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142 3 Fats Unsaturated fat Monounsaturated fat
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143 3 Fats Unsaturated fat Polyunsaturated fat
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144 13 Carbohydrates Sugars
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145 4 Carbohydrates Dietary fiber
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146 21 Carbohydrates
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147 5 Protein
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148 4
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149
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150 which would yield this `Krona plot`_.
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151
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152 .. _Krona plot: https://marbl.github.io/Krona/examples/xml.krona.html
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153
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154 -----
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155
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156 **License and citation**
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157
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158 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
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159
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160 .. _CRS4 Srl.: http://www.crs4.it/
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161 .. _MIT license: https://opensource.org/licenses/MIT
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162
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163 You can use this tool only if you agree to the license terms of: `Krona`_.
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164
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165 .. _Krona: https://github.com/marbl/Krona/wiki
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166 </help>
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167 <citations>
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168 <citation type="doi">10.1186/1471-2105-12-385</citation>
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169 <citation type="doi">10.1093/bioinformatics/btu135</citation>
1edb7c720eb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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170 </citations>
1edb7c720eb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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171 </tool>