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comparison qiime2/qiime_phylogeny_raxml.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" name="qiime phylogeny raxml" version="2019.7"> 2 <tool id="qiime_phylogeny_raxml" name="qiime phylogeny raxml"
3 <description> - Construct a phylogenetic tree with RAxML.</description> 3 version="2020.8">
4 <requirements> 4 <description>Construct a phylogenetic tree with 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 9 qiime phylogeny raxml
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 --p-n-searches=$pnsearches
15 17
16 #if str($pnsearches): 18 --p-n-threads=$pnthreads
17 --p-n-searches=$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 19
26 #if str($praxmlversion) != 'None': 20 #if str($praxmlversion) != 'None':
27 --p-raxml-version=$praxmlversion 21 --p-raxml-version=$praxmlversion
28 #end if 22 #end if
29 23
30 #if str($psubstitutionmodel) != 'None': 24 #if str($psubstitutionmodel) != 'None':
31 --p-substitution-model=$psubstitutionmodel 25 --p-substitution-model=$psubstitutionmodel
32 #end if 26 #end if
33 27
34 --o-tree=otree 28 --o-tree=otree
29
30 #if str($examples) != 'None':
31 --examples=$examples
32 #end if
33
35 ; 34 ;
36 cp otree.qza $otree 35 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 36
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"/> 37 ]]></command>
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"/> 38 <inputs>
43 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select"> 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" />
44 <option selected="True" value="None">Selection is Optional</option> 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" />
45 <option value="Standard">Standard</option> 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" />
46 <option value="SSE3">SSE3</option> 42 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
47 <option value="AVX2">AVX2</option> 43 <option selected="True" value="None">Selection is Optional</option>
48 </param> 44 <option value="Standard">Standard</option>
49 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select"> 45 <option value="SSE3">SSE3</option>
50 <option selected="True" value="None">Selection is Optional</option> 46 <option value="AVX2">AVX2</option>
51 <option value="GTRGAMMA">GTRGAMMA</option> 47 </param>
52 <option value="GTRGAMMAI">GTRGAMMAI</option> 48 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
53 <option value="GTRCAT">GTRCAT</option> 49 <option selected="True" value="None">Selection is Optional</option>
54 <option value="GTRCATI">GTRCATI</option> 50 <option value="GTRGAMMA">GTRGAMMA</option>
55 </param> 51 <option value="GTRGAMMAI">GTRGAMMAI</option>
56 </inputs> 52 <option value="GTRCAT">GTRCAT</option>
57 <outputs> 53 <option value="GTRCATI">GTRCATI</option>
58 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/> 54 </param>
59 </outputs> 55 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60 <help><![CDATA[ 56
57 </inputs>
58
59 <outputs>
60 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
61
62 </outputs>
63
64 <help><![CDATA[
61 Construct a phylogenetic tree with RAxML. 65 Construct a phylogenetic tree with RAxML.
62 ######################################### 66 ###############################################################
63 67
64 Construct a phylogenetic tree with RAxML. See: 68 Construct a phylogenetic tree with RAxML. See:
65 https://sco.h-its.org/exelixis/web/software/raxml/ 69 https://sco.h-its.org/exelixis/web/software/raxml/
66 70
67 Parameters 71 Parameters
73 reproduce tree results. If not supplied then one will be randomly 77 reproduce tree results. If not supplied then one will be randomly
74 chosen. 78 chosen.
75 n_searches : Int % Range(1, None), optional 79 n_searches : Int % Range(1, None), optional
76 The number of independent maximum likelihood searches to perform. The 80 The number of independent maximum likelihood searches to perform. The
77 single best scoring tree is returned. 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.
78 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional 85 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
79 Select a specific CPU optimization of RAxML to use. The SSE3 versions 86 Select a specific CPU optimization of RAxML to use. The SSE3 versions
80 will run approximately 40% faster than the standard version. The AVX2 87 will run approximately 40% faster than the standard version. The AVX2
81 version will run 10-30% faster than the SSE3 version. 88 version will run 10-30% faster than the SSE3 version.
82 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional 89 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
84 91
85 Returns 92 Returns
86 ------- 93 -------
87 tree : Phylogeny[Unrooted] 94 tree : Phylogeny[Unrooted]
88 The resulting phylogenetic tree. 95 The resulting phylogenetic tree.
89 ]]></help> 96 ]]></help>
90 <macros> 97 <macros>
91 <import>qiime_citation.xml</import> 98 <import>qiime_citation.xml</import>
92 </macros> 99 </macros>
93 <expand macro="qiime_citation"/> 100 <expand macro="qiime_citation"/>
94 </tool> 101 </tool>