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1 <?xml version="1.0" ?>
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2 <tool id="qiime_phylogeny_fasttree" name="qiime phylogeny fasttree"
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3 version="2020.8">
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4 <description>Construct a phylogenetic tree with FastTree.</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 phylogeny fasttree
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10
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11 --i-alignment=$ialignment
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12
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13 #if str($pnthreads) != 'None':
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14 --p-n-threads=$pnthreads
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15 #end if
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16
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17 --o-tree=otree
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18
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19 #if str($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 otree.qza $otree
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25
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26 ]]></command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data" />
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29 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
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30 <option selected="True" value="None">Selection is Optional</option>
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31 <option value="Int % Range(1">Int % Range(1</option>
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32 <option value="None">None</option>
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33 </param>
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34 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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35
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36 </inputs>
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37
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38 <outputs>
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39 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
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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 Construct a phylogenetic tree with FastTree.
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45 ###############################################################
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46
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47 Construct a phylogenetic tree with FastTree.
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48
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49 Parameters
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50 ----------
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51 alignment : FeatureData[AlignedSequence]
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52 Aligned sequences to be used for phylogenetic reconstruction.
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53 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
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54 The number of threads. Using more than one thread runs the non-
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55 deterministic variant of `FastTree` (`FastTreeMP`), and may result in a
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56 different tree than single-threading. See
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57 http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto`
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58 to automatically use all available cores)
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59
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60 Returns
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61 -------
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62 tree : Phylogeny[Unrooted]
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63 The resulting phylogenetic tree.
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64 ]]></help>
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65 <macros>
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66 <import>qiime_citation.xml</import>
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67 </macros>
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68 <expand macro="qiime_citation"/>
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69 </tool> |
