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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity-lib_jaccard" name="qiime diversity-lib jaccard"
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3 version="2020.8">
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4 <description>Jaccard Distance</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-lib jaccard
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10
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11 --i-table=$itable
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12
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13 #if str($pnjobs) != 'None':
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14 --p-n-jobs=$pnjobs
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15 #end if
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16
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17 --o-distance-matrix=odistancematrix
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18
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19 #if str($examples) != 'None':
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20 --examples=$examples
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21 #end if
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22
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23 ;
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24 cp odistancematrix.qza $odistancematrix
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25
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26 ]]></command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples for which Jaccard distance should be computed. [required]" name="itable" optional="False" type="data" />
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29 <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
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30 <option selected="True" value="None">Selection is Optional</option>
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31 <option value="Int % Range(1">Int % Range(1</option>
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32 <option value="None">None</option>
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33 </param>
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34 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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35
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36 </inputs>
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37
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38 <outputs>
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39 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
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40
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41 </outputs>
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42
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43 <help><![CDATA[
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44 Jaccard Distance
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45 ###############################################################
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46
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47 Compute Jaccard distance for each sample in a feature table. Jaccard is
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48 calculated usingpresence/absence data. Data of type FeatureTable[Frequency
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49 | Relative Frequency] is reducedto presence/absence prior to calculation.
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50
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51 Parameters
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52 ----------
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53 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
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54 The feature table containing the samples for which Jaccard distance
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55 should be computed.
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56 n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
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57 The number of concurrent jobs to use in performing this calculation.
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58 May not exceed the number of available physical cores. If n_jobs =
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59 'auto', one job will be launched for each identified CPU core on the
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60 host.
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61
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62 Returns
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63 -------
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64 distance_matrix : DistanceMatrix
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65 Distance matrix for Jaccard index
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66 ]]></help>
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67 <macros>
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68 <import>qiime_citation.xml</import>
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69 </macros>
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70 <expand macro="qiime_citation"/>
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71 </tool> |
