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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_beta" name="qiime diversity beta" version="2019.4">
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3 <description> - Beta diversity</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity beta
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9
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10 --i-table=$itable
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6
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11
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12 --p-metric=$pmetric
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13
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6
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14 #if str($ppseudocount):
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0
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15 --p-pseudocount=$ppseudocount
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16 #end if
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17
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18 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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19 #if str($pnjobs):
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20 --p-n-jobs="$pnjobs"
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21 #end if
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22
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23 --o-distance-matrix=odistancematrix
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24 ;
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25 cp odistancematrix.qza $odistancematrix
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26 ]]></command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data"/>
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29 <param label="--p-metric: " name="pmetric" optional="False" type="select">
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30 <option value="kulsinski">kulsinski</option>
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31 <option value="wminkowski">wminkowski</option>
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32 <option value="correlation">correlation</option>
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33 <option value="hamming">hamming</option>
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34 <option value="canberra">canberra</option>
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35 <option value="canberra_adkins">canberra_adkins</option>
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36 <option value="sqeuclidean">sqeuclidean</option>
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37 <option value="sokalmichener">sokalmichener</option>
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38 <option value="cityblock">cityblock</option>
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39 <option value="braycurtis">braycurtis</option>
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40 <option value="matching">matching</option>
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41 <option value="russellrao">russellrao</option>
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42 <option value="cosine">cosine</option>
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43 <option value="yule">yule</option>
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44 <option value="euclidean">euclidean</option>
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45 <option value="rogerstanimoto">rogerstanimoto</option>
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46 <option value="seuclidean">seuclidean</option>
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47 <option value="jaccard">jaccard</option>
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48 <option value="sokalsneath">sokalsneath</option>
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49 <option value="aitchison">aitchison</option>
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50 <option value="chebyshev">chebyshev</option>
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51 <option value="dice">dice</option>
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52 <option value="mahalanobis">mahalanobis</option>
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53 </param>
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54 <param label="--p-pseudocount: INTEGER Range(1, None) A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics. [default: 1]" name="ppseudocount" optional="True" type="integer" min="1" value="1"/>
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55 </inputs>
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56 <outputs>
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57 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/>
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58 </outputs>
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59 <help><![CDATA[
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60 Beta diversity
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61 ##############
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62
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63 Computes a user-specified beta diversity metric for all pairs of samples in
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64 a feature table.
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65
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66 Parameters
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67 ----------
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68 table : FeatureTable[Frequency]
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69 The feature table containing the samples over which beta diversity
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70 should be computed.
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71 metric : Str % Choices('sokalmichener', 'yule', 'russellrao', 'rogerstanimoto', 'aitchison', 'correlation', 'jaccard', 'cosine', 'euclidean', 'sqeuclidean', 'chebyshev', 'cityblock', 'matching', 'dice', 'mahalanobis', 'wminkowski', 'kulsinski', 'seuclidean', 'sokalsneath', 'canberra', 'canberra_adkins', 'hamming', 'braycurtis')
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72 The beta diversity metric to be computed.
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73 pseudocount : Int % Range(1, None), optional
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74 A pseudocount to handle zeros for compositional metrics. This is
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75 ignored for other metrics.
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76
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77 Returns
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78 -------
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79 distance_matrix : DistanceMatrix
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80 The resulting distance matrix.
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81 ]]></help>
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82 <macros>
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83 <import>qiime_citation.xml</import>
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84 </macros>
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85 <expand macro="qiime_citation"/>
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86 </tool>
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