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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_beta" name="qiime diversity beta"
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3 version="2020.8">
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4 <description>Beta diversity</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime diversity beta
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10
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11 --i-table=$itable
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12
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13 --p-metric=$pmetric
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15 --p-pseudocount=$ppseudocount
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16
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17 #if str($pnjobs) != 'None':
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18 --p-n-jobs=$pnjobs
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19 #end if
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20
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21 --o-distance-matrix=odistancematrix
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22
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23 #if str($examples) != 'None':
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24 --examples=$examples
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25 #end if
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26
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27 ;
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28 cp odistancematrix.qza $odistancematrix
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29
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30 ]]></command>
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31 <inputs>
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32 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data" />
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33 <param label="--p-metric: " name="pmetric" optional="False" type="select">
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34 <option value="braycurtis">braycurtis</option>
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35 <option value="euclidean">euclidean</option>
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36 <option value="cityblock">cityblock</option>
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37 <option value="cosine">cosine</option>
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38 <option value="minkowski">minkowski</option>
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39 <option value="matching">matching</option>
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40 <option value="correlation">correlation</option>
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41 <option value="russellrao">russellrao</option>
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42 <option value="sokalsneath">sokalsneath</option>
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43 <option value="seuclidean">seuclidean</option>
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44 <option value="canberra">canberra</option>
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45 <option value="sokalmichener">sokalmichener</option>
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46 <option value="kulsinski">kulsinski</option>
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47 <option value="jensenshannon">jensenshannon</option>
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48 <option value="jaccard">jaccard</option>
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49 <option value="hamming">hamming</option>
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50 <option value="chebyshev">chebyshev</option>
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51 <option value="yule">yule</option>
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52 <option value="dice">dice</option>
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53 <option value="sqeuclidean">sqeuclidean</option>
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54 <option value="aitchison">aitchison</option>
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55 <option value="canberra_adkins">canberra_adkins</option>
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56 <option value="rogerstanimoto">rogerstanimoto</option>
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57 </param>
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58 <param label="--p-pseudocount: INTEGER Range(1, None) A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics. [default: 1]" min="1" name="ppseudocount" optional="True" type="integer" value="1" />
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59 <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
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60 <option selected="True" value="None">Selection is Optional</option>
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61 <option value="Int % Range(1">Int % Range(1</option>
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62 <option value="None">None</option>
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63 </param>
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64 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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65
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66 </inputs>
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67
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68 <outputs>
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69 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
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70
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71 </outputs>
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72
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73 <help><![CDATA[
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74 Beta diversity
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75 ###############################################################
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76
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77 Computes a user-specified beta diversity metric for all pairs of samples in
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78 a feature table.
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79
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80 Parameters
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81 ----------
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82 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
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83 The feature table containing the samples over which beta diversity
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84 should be computed.
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85 metric : Str % Choices('yule', 'cityblock', 'matching', 'russellrao', 'seuclidean', 'jaccard', 'braycurtis', 'minkowski', 'sokalmichener', 'aitchison', 'canberra_adkins', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'sokalsneath', 'correlation', 'hamming', 'dice', 'rogerstanimoto', 'canberra', 'chebyshev', 'jensenshannon')
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86 The beta diversity metric to be computed.
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87 pseudocount : Int % Range(1, None), optional
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88 A pseudocount to handle zeros for compositional metrics. This is
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89 ignored for other metrics.
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90 n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
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91 The number of concurrent jobs to use in performing this calculation.
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92 May not exceed the number of available physical cores. If n_jobs =
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93 'auto', one job will be launched for each identified CPU core on the
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94 host.
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95
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96 Returns
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97 -------
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98 distance_matrix : DistanceMatrix
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99 The resulting distance matrix.
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100 ]]></help>
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101 <macros>
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102 <import>qiime_citation.xml</import>
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103 </macros>
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104 <expand macro="qiime_citation"/>
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105 </tool> |
