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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_beta" name="qiime diversity beta" version="2018.4">
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3 <description> - Beta diversity</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity beta --i-table=$itable --p-metric=$pmetric --o-distance-matrix=odistancematrix
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9
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10 #if str($cmdconfig) != 'None':
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11 --cmd-config=$cmdconfig
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12 #end if
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13
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14 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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15
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16 #if str($pnjobs):
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17 --p-n-jobs="$pnjobs"
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18 #end if
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19
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20 ;
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21 cp odistancematrix.qza $odistancematrix;
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22 ]]></command>
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23 <inputs>
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24 <param format="qza,no_unzip.zip" label="--i-table: 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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25
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26 <param label="--p-metric: The beta diversity metric to be computed.
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27 [required]" name="pmetric" optional="False" type="select" >
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28 <option value="hamming">hamming</option>
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29 <option value="sqeuclidean">sqeuclidean</option>
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30 <option value="cityblock">cityblock</option>
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31 <option value="sokalmichener">sokalmichener</option>
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32 <option value="braycurtis">braycurtis</option>
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33 <option value="cosine">cosine</option>
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34 <option value="euclidean">euclidean</option>
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35 <option value="rogerstanimoto">rogerstanimoto</option>
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36 <option value="canberra">canberra</option>
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37 <option value="seuclidean">seuclidean</option>
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38 <option value="correlation">correlation</option>
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39 <option value="sokalsneath">sokalsneath</option>
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40 <option value="chebyshev">chebyshev</option>
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41 <option value="mahalanobis">mahalanobis</option>
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42 <option value="matching">matching</option>
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43 <option value="kulsinski">kulsinski</option>
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44 <option value="yule">yule</option>
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45 <option value="dice">dice</option>
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46 <option value="russellrao">russellrao</option>
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47 <option value="wminkowski">wminkowski</option>
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48 <option value="jaccard">jaccard</option>
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49 </param>
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50
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51 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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52 </inputs>
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53 <outputs>
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54 <data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/>
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55 </outputs>
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56 <help><![CDATA[
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57 Beta diversity
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58 --------------
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59
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60 Computes a user-specified beta diversity metric for all pairs of samples in
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61 a feature table.
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62
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63 Parameters
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64 ----------
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65 table : FeatureTable[Frequency]
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66 The feature table containing the samples over which beta diversity
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67 should be computed.
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68 metric : Str % Choices({'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'wminkowski', 'yule'})
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69 The beta diversity metric to be computed.
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70
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71 Returns
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72 -------
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73 distance_matrix : DistanceMatrix
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74 The resulting distance matrix.
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75 ]]>
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76 </help>
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77 <macros>
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78 <import>qiime_citation.xml</import>
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79 </macros>
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80 <expand macro="qiime_citation" />
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81 </tool>
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