Mercurial > repos > florianbegusch > qiime2_suite

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children de4c22a52df4
comparison
equal deleted inserted replaced
-1:000000000000 0:370e0b6e9826
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
16 #if $pnsearches:
17 --p-n-searches=$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>