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comparison qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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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>