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comparison qiime2-2020.8/qiime_phylogeny_fasttree.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_fasttree" name="qiime phylogeny fasttree"
3 version="2020.8">
4 <description>Construct a phylogenetic tree with FastTree.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime phylogeny fasttree
10
11 --i-alignment=$ialignment
12
13 #if str($pnthreads) != 'None':
14 --p-n-threads=$pnthreads
15 #end if
16
17 --o-tree=otree
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp otree.qza $otree
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data" />
29 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
30 <option selected="True" value="None">Selection is Optional</option>
31 <option value="Int % Range(1">Int % Range(1</option>
32 <option value="None">None</option>
33 </param>
34 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
35
36 </inputs>
37
38 <outputs>
39 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
40
41 </outputs>
42
43 <help><![CDATA[
44 Construct a phylogenetic tree with FastTree.
45 ###############################################################
46
47 Construct a phylogenetic tree with FastTree.
48
49 Parameters
50 ----------
51 alignment : FeatureData[AlignedSequence]
52 Aligned sequences to be used for phylogenetic reconstruction.
53 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
54 The number of threads. Using more than one thread runs the non-
55 deterministic variant of `FastTree` (`FastTreeMP`), and may result in a
56 different tree than single-threading. See
57 http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto`
58 to automatically use all available cores)
59
60 Returns
61 -------
62 tree : Phylogeny[Unrooted]
63 The resulting phylogenetic tree.
64 ]]></help>
65 <macros>
66 <import>qiime_citation.xml</import>
67 </macros>
68 <expand macro="qiime_citation"/>
69 </tool>