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