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1 <?xml version="1.0" ?>
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2 <tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap" version="2019.4">
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3 <description> - Construct a phylogenetic tree with bootstrap supports using RAxML.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime phylogeny raxml-rapid-bootstrap
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9
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10 --i-alignment=$ialignment
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11
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12 #if str($pseed):
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13 --p-seed="$pseed"
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14 #end if
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15
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16 #if str($prapidbootstrapseed):
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17 --p-rapid-bootstrap-seed="$prapidbootstrapseed"
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18 #end if
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19
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20 #if $pbootstrapreplicates:
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21 --p-bootstrap-replicates=$pbootstrapreplicates
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22 #end if
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23
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24 #set $pnthreads = '${GALAXY_SLOTS:-4}'
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25
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26 #if str($pnthreads):
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27 --p-n-threads="$pnthreads"
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28 #end if
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29
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30
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31 #if str($praxmlversion) != 'None':
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32 --p-raxml-version=$praxmlversion
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33 #end if
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34
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35 #if str($psubstitutionmodel) != 'None':
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36 --p-substitution-model=$psubstitutionmodel
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37 #end if
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38
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39 --o-tree=otree
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40 ;
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41 cp otree.qza $otree
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42 ]]></command>
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43 <inputs>
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44 <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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45 <param label="--p-seed: INTEGER Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="True" type="integer"/>
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46 <param label="--p-rapid-bootstrap-seed: INTEGER Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen. [optional]" name="prapidbootstrapseed" optional="True" type="integer"/>
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47 <param label="--p-bootstrap-replicates: INTEGER Range(10, None) The number of bootstrap searches to perform. [default: 100]" name="pbootstrapreplicates" optional="True" type="integer" value="100"/>
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48 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
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49 <option selected="True" value="None">Selection is Optional</option>
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50 <option value="Standard">Standard</option>
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51 <option value="SSE3">SSE3</option>
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52 <option value="AVX2">AVX2</option>
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53 </param>
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54 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
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55 <option selected="True" value="None">Selection is Optional</option>
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56 <option value="GTRGAMMA">GTRGAMMA</option>
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57 <option value="GTRGAMMAI">GTRGAMMAI</option>
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58 <option value="GTRCAT">GTRCAT</option>
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59 <option value="GTRCATI">GTRCATI</option>
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60 </param>
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61 </inputs>
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62 <outputs>
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63 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
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64 </outputs>
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65 <help><![CDATA[
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66 Construct a phylogenetic tree with bootstrap supports using RAxML.
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67 ##################################################################
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68
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69 Construct a phylogenetic tree with RAxML with the addition of rapid
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70 bootstrapping support values. See:
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71 https://sco.h-its.org/exelixis/web/software/raxml/
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72
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73 Parameters
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74 ----------
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75 alignment : FeatureData[AlignedSequence]
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76 Aligned sequences to be used for phylogenetic reconstruction.
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77 seed : Int, optional
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78 Random number seed for the parsimony starting tree. This allows you to
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79 reproduce tree results. If not supplied then one will be randomly
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80 chosen.
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81 rapid_bootstrap_seed : Int, optional
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82 Specify a random seed for rapid bootstrapping. This allows you to
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83 reproduce rapid bootstrap results. If not supplied then one will be
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84 randomly chosen.
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85 bootstrap_replicates : Int % Range(10, None), optional
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86 The number of bootstrap searches to perform.
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87 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
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88 Select a specific CPU optimization of RAxML to use. The SSE3 versions
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89 will run approximately 40% faster than the standard version. The AVX2
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90 version will run 10-30% faster than the SSE3 version.
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91 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
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92 Model of Nucleotide Substitution
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93
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94 Returns
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95 -------
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96 tree : Phylogeny[Unrooted]
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97 The resulting phylogenetic tree.
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98 ]]></help>
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99 <macros>
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100 <import>qiime_citation.xml</import>
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101 </macros>
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102 <expand macro="qiime_citation"/>
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103 </tool>
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