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comparison qiime2-2020.8/qiime_diversity_beta.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_diversity_beta" name="qiime diversity beta"
3 version="2020.8">
4 <description>Beta diversity</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity beta
10
11 --i-table=$itable
12
13 --p-metric=$pmetric
14
15 --p-pseudocount=$ppseudocount
16
17 #if str($pnjobs) != 'None':
18 --p-n-jobs=$pnjobs
19 #end if
20
21 --o-distance-matrix=odistancematrix
22
23 #if str($examples) != 'None':
24 --examples=$examples
25 #end if
26
27 ;
28 cp odistancematrix.qza $odistancematrix
29
30 ]]></command>
31 <inputs>
32 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data" />
33 <param label="--p-metric: " name="pmetric" optional="False" type="select">
34 <option value="braycurtis">braycurtis</option>
35 <option value="euclidean">euclidean</option>
36 <option value="cityblock">cityblock</option>
37 <option value="cosine">cosine</option>
38 <option value="minkowski">minkowski</option>
39 <option value="matching">matching</option>
40 <option value="correlation">correlation</option>
41 <option value="russellrao">russellrao</option>
42 <option value="sokalsneath">sokalsneath</option>
43 <option value="seuclidean">seuclidean</option>
44 <option value="canberra">canberra</option>
45 <option value="sokalmichener">sokalmichener</option>
46 <option value="kulsinski">kulsinski</option>
47 <option value="jensenshannon">jensenshannon</option>
48 <option value="jaccard">jaccard</option>
49 <option value="hamming">hamming</option>
50 <option value="chebyshev">chebyshev</option>
51 <option value="yule">yule</option>
52 <option value="dice">dice</option>
53 <option value="sqeuclidean">sqeuclidean</option>
54 <option value="aitchison">aitchison</option>
55 <option value="canberra_adkins">canberra_adkins</option>
56 <option value="rogerstanimoto">rogerstanimoto</option>
57 </param>
58 <param label="--p-pseudocount: INTEGER Range(1, None) A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics. [default: 1]" min="1" name="ppseudocount" optional="True" type="integer" value="1" />
59 <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
60 <option selected="True" value="None">Selection is Optional</option>
61 <option value="Int % Range(1">Int % Range(1</option>
62 <option value="None">None</option>
63 </param>
64 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
65
66 </inputs>
67
68 <outputs>
69 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
70
71 </outputs>
72
73 <help><![CDATA[
74 Beta diversity
75 ###############################################################
76
77 Computes a user-specified beta diversity metric for all pairs of samples in
78 a feature table.
79
80 Parameters
81 ----------
82 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
83 The feature table containing the samples over which beta diversity
84 should be computed.
85 metric : Str % Choices('yule', 'cityblock', 'matching', 'russellrao', 'seuclidean', 'jaccard', 'braycurtis', 'minkowski', 'sokalmichener', 'aitchison', 'canberra_adkins', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'sokalsneath', 'correlation', 'hamming', 'dice', 'rogerstanimoto', 'canberra', 'chebyshev', 'jensenshannon')
86 The beta diversity metric to be computed.
87 pseudocount : Int % Range(1, None), optional
88 A pseudocount to handle zeros for compositional metrics. This is
89 ignored for other metrics.
90 n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
91 The number of concurrent jobs to use in performing this calculation.
92 May not exceed the number of available physical cores. If n_jobs =
93 'auto', one job will be launched for each identified CPU core on the
94 host.
95
96 Returns
97 -------
98 distance_matrix : DistanceMatrix
99 The resulting distance matrix.
100 ]]></help>
101 <macros>
102 <import>qiime_citation.xml</import>
103 </macros>
104 <expand macro="qiime_citation"/>
105 </tool>