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comparison qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap" version="2019.7"> 2 <tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap"
3 <description> - Construct a phylogenetic tree with bootstrap supports using RAxML.</description> 3 version="2020.8">
4 <requirements> 4 <description>Construct a phylogenetic tree with bootstrap supports using RAxML.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime phylogeny raxml-rapid-bootstrap 9 qiime phylogeny raxml-rapid-bootstrap
9 10
10 --i-alignment=$ialignment 11 --i-alignment=$ialignment
11 12
12 #if str($pseed): 13 #if str($pseed):
13 --p-seed="$pseed" 14 --p-seed=$pseed
14 #end if 15 #end if
16 #if str($prapidbootstrapseed):
17 --p-rapid-bootstrap-seed=$prapidbootstrapseed
18 #end if
19 --p-bootstrap-replicates=$pbootstrapreplicates
15 20
16 #if str($prapidbootstrapseed): 21 --p-n-threads=$pnthreads
17 --p-rapid-bootstrap-seed="$prapidbootstrapseed"
18 #end if
19
20 #if str($pbootstrapreplicates):
21 --p-bootstrap-replicates=$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 22
31 #if str($praxmlversion) != 'None': 23 #if str($praxmlversion) != 'None':
32 --p-raxml-version=$praxmlversion 24 --p-raxml-version=$praxmlversion
33 #end if 25 #end if
34 26
35 #if str($psubstitutionmodel) != 'None': 27 #if str($psubstitutionmodel) != 'None':
36 --p-substitution-model=$psubstitutionmodel 28 --p-substitution-model=$psubstitutionmodel
37 #end if 29 #end if
38 30
39 --o-tree=otree 31 --o-tree=otree
32
33 #if str($examples) != 'None':
34 --examples=$examples
35 #end if
36
40 ; 37 ;
41 cp otree.qza $otree 38 cp otree.qza $otree
42 ]]></command> 39
43 <inputs> 40 ]]></command>
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"/> 41 <inputs>
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"/> 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" />
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"/> 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" />
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"/> 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" />
48 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select"> 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" />
49 <option selected="True" value="None">Selection is Optional</option> 46 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
50 <option value="Standard">Standard</option> 47 <option selected="True" value="None">Selection is Optional</option>
51 <option value="SSE3">SSE3</option> 48 <option value="Standard">Standard</option>
52 <option value="AVX2">AVX2</option> 49 <option value="SSE3">SSE3</option>
53 </param> 50 <option value="AVX2">AVX2</option>
54 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select"> 51 </param>
55 <option selected="True" value="None">Selection is Optional</option> 52 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
56 <option value="GTRGAMMA">GTRGAMMA</option> 53 <option selected="True" value="None">Selection is Optional</option>
57 <option value="GTRGAMMAI">GTRGAMMAI</option> 54 <option value="GTRGAMMA">GTRGAMMA</option>
58 <option value="GTRCAT">GTRCAT</option> 55 <option value="GTRGAMMAI">GTRGAMMAI</option>
59 <option value="GTRCATI">GTRCATI</option> 56 <option value="GTRCAT">GTRCAT</option>
60 </param> 57 <option value="GTRCATI">GTRCATI</option>
61 </inputs> 58 </param>
62 <outputs> 59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
63 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/> 60
64 </outputs> 61 </inputs>
65 <help><![CDATA[ 62
63 <outputs>
64 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
65
66 </outputs>
67
68 <help><![CDATA[
66 Construct a phylogenetic tree with bootstrap supports using RAxML. 69 Construct a phylogenetic tree with bootstrap supports using RAxML.
67 ################################################################## 70 ###############################################################
68 71
69 Construct a phylogenetic tree with RAxML with the addition of rapid 72 Construct a phylogenetic tree with RAxML with the addition of rapid
70 bootstrapping support values. See: 73 bootstrapping support values. See:
71 https://sco.h-its.org/exelixis/web/software/raxml/ 74 https://sco.h-its.org/exelixis/web/software/raxml/
72 75
77 seed : Int, optional 80 seed : Int, optional
78 Random number seed for the parsimony starting tree. This allows you to 81 Random number seed for the parsimony starting tree. This allows you to
79 reproduce tree results. If not supplied then one will be randomly 82 reproduce tree results. If not supplied then one will be randomly
80 chosen. 83 chosen.
81 rapid_bootstrap_seed : Int, optional 84 rapid_bootstrap_seed : Int, optional
82 Specify a random seed for rapid bootstrapping. This allows you to 85 Specify a random seed for rapid bootstrapping. This allows you to
83 reproduce rapid bootstrap results. If not supplied then one will be 86 reproduce rapid bootstrap results. If not supplied then one will be
84 randomly chosen. 87 randomly chosen.
85 bootstrap_replicates : Int % Range(10, None), optional 88 bootstrap_replicates : Int % Range(10, None), optional
86 The number of bootstrap searches to perform. 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.
87 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional 93 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
88 Select a specific CPU optimization of RAxML to use. The SSE3 versions 94 Select a specific CPU optimization of RAxML to use. The SSE3 versions
89 will run approximately 40% faster than the standard version. The AVX2 95 will run approximately 40% faster than the standard version. The AVX2
90 version will run 10-30% faster than the SSE3 version. 96 version will run 10-30% faster than the SSE3 version.
91 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional 97 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
93 99
94 Returns 100 Returns
95 ------- 101 -------
96 tree : Phylogeny[Unrooted] 102 tree : Phylogeny[Unrooted]
97 The resulting phylogenetic tree. 103 The resulting phylogenetic tree.
98 ]]></help> 104 ]]></help>
99 <macros> 105 <macros>
100 <import>qiime_citation.xml</import> 106 <import>qiime_citation.xml</import>
101 </macros> 107 </macros>
102 <expand macro="qiime_citation"/> 108 <expand macro="qiime_citation"/>
103 </tool> 109 </tool>