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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity-lib_faith-pd" name="qiime diversity-lib faith-pd"
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3 version="2020.8">
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4 <description>Faith\'s Phylogenetic 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-lib faith-pd
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10
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11 #if $itable:
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12 --i-table
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13 #end if
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14
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15 --i-phylogeny=$iphylogeny
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16
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17 --o-vector=ovector
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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 ovector.qza $ovector
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25
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26 ]]></command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-table: --i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples for which Faith\'s phylogenetic diversity should be computed. Table values will be converted to presence/absence. [required]" name="itable" selected="False" type="boolean" />
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29 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data" />
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30 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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31
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32 </inputs>
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33
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34 <outputs>
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35 <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
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36
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37 </outputs>
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38
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39 <help><![CDATA[
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40 Faith\'s Phylogenetic Diversity
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41 ###############################################################
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42
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43 Computes Faith's Phylogenetic Diversity for all samples in a feature table.
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44
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45 Parameters
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46 ----------
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47 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
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48 The feature table containing the samples for which Faith's phylogenetic
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49 diversity should be computed. Table values will be converted to
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50 presence/absence.
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51 phylogeny : Phylogeny[Rooted]
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52 Phylogenetic tree containing tip identifiers that correspond to the
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53 feature identifiers in the table. This tree can contain tip ids that
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54 are not present in the table, but all feature ids in the table must be
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55 present in this tree.
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56
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57 Returns
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58 -------
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59 vector : SampleData[AlphaDiversity]
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60 Vector containing per-sample values for Faith's Phylogenetic Diversity.
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61 ]]></help>
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62 <macros>
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63 <import>qiime_citation.xml</import>
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64 </macros>
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65 <expand macro="qiime_citation"/>
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66 </tool> |
