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1 <?xml version="1.0" ?>
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2 <tool id="qiime_phylogeny_raxml" name="qiime phylogeny raxml" version="2019.4">
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3 <description> - Construct a phylogenetic tree with 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
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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="$pseed"
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14 #end if
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15
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6
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16 #if str($pnsearches):
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0
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17 --p-n-searches=$pnsearches
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18 #end if
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19
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20 #set $pnthreads = '${GALAXY_SLOTS:-4}'
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21 #if str($pnthreads):
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22 --p-n-threads="$pnthreads"
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23 #end if
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24
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25
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26 #if str($praxmlversion) != 'None':
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27 --p-raxml-version=$praxmlversion
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28 #end if
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29
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30 #if str($psubstitutionmodel) != 'None':
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31 --p-substitution-model=$psubstitutionmodel
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32 #end if
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33
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34 --o-tree=otree
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35 ;
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36 cp otree.qza $otree
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37 ]]></command>
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38 <inputs>
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39 <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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40
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41 <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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42 <param label="--p-n-searches: INTEGER The number of independent maximum likelihood Range(1, None) searches to perform. The single best scoring tree is returned. [default: 1]" name="pnsearches" optional="True" type="integer" min="1" value="1"/>
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43 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
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44 <option selected="True" value="None">Selection is Optional</option>
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45 <option value="Standard">Standard</option>
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46 <option value="SSE3">SSE3</option>
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47 <option value="AVX2">AVX2</option>
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48 </param>
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49 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
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50 <option selected="True" value="None">Selection is Optional</option>
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51 <option value="GTRGAMMA">GTRGAMMA</option>
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52 <option value="GTRGAMMAI">GTRGAMMAI</option>
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53 <option value="GTRCAT">GTRCAT</option>
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54 <option value="GTRCATI">GTRCATI</option>
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55 </param>
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56 </inputs>
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57 <outputs>
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58 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
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59 </outputs>
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60 <help><![CDATA[
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61 Construct a phylogenetic tree with RAxML.
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62 #########################################
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63
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64 Construct a phylogenetic tree with RAxML. See:
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65 https://sco.h-its.org/exelixis/web/software/raxml/
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66
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67 Parameters
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68 ----------
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69 alignment : FeatureData[AlignedSequence]
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70 Aligned sequences to be used for phylogenetic reconstruction.
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71 seed : Int, optional
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72 Random number seed for the parsimony starting tree. This allows you to
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73 reproduce tree results. If not supplied then one will be randomly
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74 chosen.
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75 n_searches : Int % Range(1, None), optional
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76 The number of independent maximum likelihood searches to perform. The
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77 single best scoring tree is returned.
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78 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
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79 Select a specific CPU optimization of RAxML to use. The SSE3 versions
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80 will run approximately 40% faster than the standard version. The AVX2
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81 version will run 10-30% faster than the SSE3 version.
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82 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
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83 Model of Nucleotide Substitution.
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84
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85 Returns
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86 -------
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87 tree : Phylogeny[Unrooted]
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88 The resulting phylogenetic tree.
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89 ]]></help>
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90 <macros>
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91 <import>qiime_citation.xml</import>
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92 </macros>
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93 <expand macro="qiime_citation"/>
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94 </tool>
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