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