Mercurial > repos > crs4 > taxonomy_krona_chart

annotate taxonomy_krona_chart.xml @ 4:8e2be617b437 draft

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author iuc
date Thu, 04 May 2017 06:04:23 -0400
parents 50f204c82159
children 020b3087d0b7
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1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1">
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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="2.6.1">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><![CDATA[
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8 #if $type_of_data.input[0].is_of_type('taxonomy'):
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9 ktImportGalaxy
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10 -d '${type_of_data.max_rank}'
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11 -n '${root_name}'
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12 -o '${output}'
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13 ${combine_inputs}
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14 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
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15 '${input_dataset},${input_count}'
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16 #end for
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17 #else:
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18 ktImportText
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19 -n '${root_name}'
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20 -o '${output}'
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21 ${combine_inputs}
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22 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
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23 '${input_dataset},${input_count}'
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24 #end for
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25 #end if
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26 && [ -d '${output}.files' ] && ( mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}/' )
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27 ]]></command>
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28 <inputs>
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29 <conditional name="type_of_data">
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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">
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31 <option value="taxonomy" selected="True">Taxonomy</option>
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32 <option value="text">MetaPhlAn</option>
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33 </param>
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34 <when value="taxonomy">
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35 <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
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36 <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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37 <option value="8">Class</option>
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38 <option value="0">Show entire tree</option>
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39 <option value="1">Superkingdom</option>
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40 <option value="2">Kingdom</option>
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41 <option value="3">Subkingdom</option>
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42 <option value="4">Superphylum</option>
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43 <option value="5">Phylum</option>
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44 <option value="6">Subphylum</option>
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45 <option value="7">Superclass</option>
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46 <option value="9">Subclass</option>
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47 <option value="10">Superorder</option>
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48 <option value="11">Order</option>
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49 <option value="12">Suborder</option>
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50 <option value="13">Superfamily</option>
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51 <option value="14">Family</option>
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52 <option value="15">Subfamily</option>
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53 <option value="16">Tribe</option>
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54 <option value="17">Subtribe</option>
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55 <option value="18">Genus</option>
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56 <option value="19">Subgenus</option>
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57 <option value="20">Species</option>
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58 <option value="21">Subspecies</option>
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59 </param>
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60 </when>
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61 <when value="text">
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62 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
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63 </when>
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64 </conditional>
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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;"/>
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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"/>
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67 </inputs>
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68 <outputs>
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69 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="type_of_data_selector" value="taxonomy"/>
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74 <param name="input" value="taxonomy_data.tax" ftype="taxonomy" />
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75 <param name="max_rank" value="Genus"/>
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76 <param name="root_name" value="Root"/>
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77 <param name="combine_inputs" value="False"/>
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78 <output name="output" file="krona_test1.html" ftype="html" lines_diff="100"/>
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79 </test>
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80 </tests>
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81 <help>
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82 **What it does**
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83
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84 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_.
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85
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86
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87 .. _Krona: https://github.com/marbl/Krona/wiki
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88
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89 ------
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90
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91 **Krona options**
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92
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93 The Galaxy version supports the following options::
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94
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95 -n Name of the highest level.
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96 -c Combine data from each file, rather than creating separate datasets within the chart.
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97 -d Maximum depth of wedges to include in the chart.
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98
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99 -----
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100
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101 **License and citation**
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102
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103 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
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104
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105 .. _CRS4 Srl.: http://www.crs4.it/
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106 .. _MIT license: https://opensource.org/licenses/MIT
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107
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108 You can use this tool only if you agree to the license terms of: `Krona`_.
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109
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110 .. _Krona: https://github.com/marbl/Krona/wiki
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111 </help>
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112 <citations>
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113 <citation type="doi">10.1186/1471-2105-12-385</citation>
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114 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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115 </citations>
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116 </tool>