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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_alpha" name="qiime diversity alpha" version="2018.4">
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3 <description> - Alpha 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 alpha --i-table=$itable --p-metric=$pmetric
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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 --o-alpha-diversity=oalphadiversity;
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15
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16 cp oalphadiversity.qza $oalphadiversity;
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17 ]]></command>
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18 <inputs>
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19 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed. [required]" name="itable" optional="False" type="data"/>
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20 <param label="--p-metric: The alpha diversity metric to be computed.
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21 [required]" name="pmetric" optional="False" type="select" >
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22 <option value="goods_coverage">goods_coverage</option>
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23 <option value="heip_e">heip_e</option>
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24 <option value="mcintosh_d">mcintosh_d</option>
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25 <option value="esty_ci">esty_ci</option>
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26 <option value="doubles">doubles</option>
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27 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
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28 <option value="observed_otus">observed_otus</option>
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29 <option value="kempton_taylor_q">kempton_taylor_q</option>
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30 <option value="chao1_ci">chao1_ci</option>
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31 <option value="shannon">shannon</option>
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32 <option value="margalef">margalef</option>
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33 <option value="simpson">simpson</option>
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34 <option value="lladser_ci">lladser_ci</option>
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35 <option value="lladser_pe">lladser_pe</option>
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36 <option value="osd">osd</option>
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37 <option value="menhinick">menhinick</option>
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38 <option value="singles">singles</option>
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39 <option value="gini_index">gini_index</option>
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40 <option value="robbins">robbins</option>
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41 <option value="ace">ace</option>
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42 <option value="simpson_e">simpson_e</option>
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43 <option value="enspie">enspie</option>
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44 <option value="berger_parker_d">berger_parker_d</option>
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45 <option value="fisher_alpha">fisher_alpha</option>
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46 <option value="dominance">dominance</option>
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47 <option value="pielou_e">pielou_e</option>
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48 <option value="chao1">chao1</option>
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49 <option value="mcintosh_e">mcintosh_e</option>
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50 <option value="strong">strong</option>
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51 <option value="brillouin_d">brillouin_d</option>
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52 </param>
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53 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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54 </inputs>
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55 <outputs>
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56 <data format="qza" label="${tool.name} on ${on_string}: alpha-diversity.qza" name="oalphadiversity"/>
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57 </outputs>
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58 <help><![CDATA[
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59 Alpha diversity
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60 ---------------
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61
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62 Computes a user-specified alpha diversity metric for all samples in a
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63 feature table.
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64
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65 Parameters
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66 ----------
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67 table : FeatureTable[Frequency]
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68 The feature table containing the samples for which alpha diversity
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69 should be computed.
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70 metric : Str % Choices({'ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_ci', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_otus', 'osd', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles', 'strong'})
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71 The alpha diversity metric to be computed.
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72
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73 Returns
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74 -------
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75 alpha_diversity : SampleData[AlphaDiversity]
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76 Vector containing per-sample alpha diversities.
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77 ]]>
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78 </help>
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79 </tool>
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