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comparison qiime2-2020.8/qiime_phylogeny_raxml.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_raxml" name="qiime phylogeny raxml"
3 version="2020.8">
4 <description>Construct a phylogenetic tree with RAxML.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime phylogeny raxml
10
11 --i-alignment=$ialignment
12
13 #if str($pseed):
14 --p-seed=$pseed
15 #end if
16 --p-n-searches=$pnsearches
17
18 --p-n-threads=$pnthreads
19
20 #if str($praxmlversion) != 'None':
21 --p-raxml-version=$praxmlversion
22 #end if
23
24 #if str($psubstitutionmodel) != 'None':
25 --p-substitution-model=$psubstitutionmodel
26 #end if
27
28 --o-tree=otree
29
30 #if str($examples) != 'None':
31 --examples=$examples
32 #end if
33
34 ;
35 cp otree.qza $otree
36
37 ]]></command>
38 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data" />
40 <param label="--p-seed: INTEGER Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
41 <param label="--p-n-searches: INTEGER The number of independent maximum likelihood Range(1, None) searches to perform. The single best scoring tree is returned. [default: 1]" min="1" name="pnsearches" optional="True" type="integer" value="1" />
42 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
43 <option selected="True" value="None">Selection is Optional</option>
44 <option value="Standard">Standard</option>
45 <option value="SSE3">SSE3</option>
46 <option value="AVX2">AVX2</option>
47 </param>
48 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
49 <option selected="True" value="None">Selection is Optional</option>
50 <option value="GTRGAMMA">GTRGAMMA</option>
51 <option value="GTRGAMMAI">GTRGAMMAI</option>
52 <option value="GTRCAT">GTRCAT</option>
53 <option value="GTRCATI">GTRCATI</option>
54 </param>
55 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
56
57 </inputs>
58
59 <outputs>
60 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
61
62 </outputs>
63
64 <help><![CDATA[
65 Construct a phylogenetic tree with RAxML.
66 ###############################################################
67
68 Construct a phylogenetic tree with RAxML. See:
69 https://sco.h-its.org/exelixis/web/software/raxml/
70
71 Parameters
72 ----------
73 alignment : FeatureData[AlignedSequence]
74 Aligned sequences to be used for phylogenetic reconstruction.
75 seed : Int, optional
76 Random number seed for the parsimony starting tree. This allows you to
77 reproduce tree results. If not supplied then one will be randomly
78 chosen.
79 n_searches : Int % Range(1, None), optional
80 The number of independent maximum likelihood searches to perform. The
81 single best scoring tree is returned.
82 n_threads : Int % Range(1, None), optional
83 The number of threads to use for multithreaded processing. Using more
84 than one thread will enable the PTHREADS version of RAxML.
85 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
86 Select a specific CPU optimization of RAxML to use. The SSE3 versions
87 will run approximately 40% faster than the standard version. The AVX2
88 version will run 10-30% faster than the SSE3 version.
89 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
90 Model of Nucleotide Substitution.
91
92 Returns
93 -------
94 tree : Phylogeny[Unrooted]
95 The resulting phylogenetic tree.
96 ]]></help>
97 <macros>
98 <import>qiime_citation.xml</import>
99 </macros>
100 <expand macro="qiime_citation"/>
101 </tool>