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comparison qiime2-2020.8/qiime_phylogeny_raxml-rapid-bootstrap.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap"
3 version="2020.8">
4 <description>Construct a phylogenetic tree with bootstrap supports using RAxML.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime phylogeny raxml-rapid-bootstrap
10
11 --i-alignment=$ialignment
12
13 #if str($pseed):
14 --p-seed=$pseed
15 #end if
16 #if str($prapidbootstrapseed):
17 --p-rapid-bootstrap-seed=$prapidbootstrapseed
18 #end if
19 --p-bootstrap-replicates=$pbootstrapreplicates
20
21 --p-n-threads=$pnthreads
22
23 #if str($praxmlversion) != 'None':
24 --p-raxml-version=$praxmlversion
25 #end if
26
27 #if str($psubstitutionmodel) != 'None':
28 --p-substitution-model=$psubstitutionmodel
29 #end if
30
31 --o-tree=otree
32
33 #if str($examples) != 'None':
34 --examples=$examples
35 #end if
36
37 ;
38 cp otree.qza $otree
39
40 ]]></command>
41 <inputs>
42 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data" />
43 <param label="--p-seed: INTEGER Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
44 <param label="--p-rapid-bootstrap-seed: INTEGER Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen. [optional]" name="prapidbootstrapseed" optional="False" type="text" />
45 <param label="--p-bootstrap-replicates: INTEGER Range(10, None) The number of bootstrap searches to perform. [default: 100]" min="10" name="pbootstrapreplicates" optional="True" type="integer" value="100" />
46 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
47 <option selected="True" value="None">Selection is Optional</option>
48 <option value="Standard">Standard</option>
49 <option value="SSE3">SSE3</option>
50 <option value="AVX2">AVX2</option>
51 </param>
52 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
53 <option selected="True" value="None">Selection is Optional</option>
54 <option value="GTRGAMMA">GTRGAMMA</option>
55 <option value="GTRGAMMAI">GTRGAMMAI</option>
56 <option value="GTRCAT">GTRCAT</option>
57 <option value="GTRCATI">GTRCATI</option>
58 </param>
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60
61 </inputs>
62
63 <outputs>
64 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
65
66 </outputs>
67
68 <help><![CDATA[
69 Construct a phylogenetic tree with bootstrap supports using RAxML.
70 ###############################################################
71
72 Construct a phylogenetic tree with RAxML with the addition of rapid
73 bootstrapping support values. See:
74 https://sco.h-its.org/exelixis/web/software/raxml/
75
76 Parameters
77 ----------
78 alignment : FeatureData[AlignedSequence]
79 Aligned sequences to be used for phylogenetic reconstruction.
80 seed : Int, optional
81 Random number seed for the parsimony starting tree. This allows you to
82 reproduce tree results. If not supplied then one will be randomly
83 chosen.
84 rapid_bootstrap_seed : Int, optional
85 Specify a random seed for rapid bootstrapping. This allows you to
86 reproduce rapid bootstrap results. If not supplied then one will be
87 randomly chosen.
88 bootstrap_replicates : Int % Range(10, None), optional
89 The number of bootstrap searches to perform.
90 n_threads : Int % Range(1, None), optional
91 The number of threads to use for multithreaded processing. Using more
92 than one thread will enable the PTHREADS version of RAxML.
93 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
94 Select a specific CPU optimization of RAxML to use. The SSE3 versions
95 will run approximately 40% faster than the standard version. The AVX2
96 version will run 10-30% faster than the SSE3 version.
97 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
98 Model of Nucleotide Substitution
99
100 Returns
101 -------
102 tree : Phylogeny[Unrooted]
103 The resulting phylogenetic tree.
104 ]]></help>
105 <macros>
106 <import>qiime_citation.xml</import>
107 </macros>
108 <expand macro="qiime_citation"/>
109 </tool>