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

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta" name="qiime diversity beta" version="2019.4">
3 <description> - Beta diversity</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity beta
9
10 --i-table=$itable
11 --p-metric=$pmetric
12
13 #if $ppseudocount:
14 --p-pseudocount=$ppseudocount
15 #end if
16
17 #set $pnjobs = '${GALAXY_SLOTS:-4}'
18 #if str($pnjobs):
19 --p-n-jobs="$pnjobs"
20 #end if
21
22 --o-distance-matrix=odistancematrix
23 ;
24 cp odistancematrix.qza $odistancematrix
25 ]]></command>
26 <inputs>
27 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data"/>
28 <param label="--p-metric: " name="pmetric" optional="False" type="select">
29 <option value="kulsinski">kulsinski</option>
30 <option value="wminkowski">wminkowski</option>
31 <option value="correlation">correlation</option>
32 <option value="hamming">hamming</option>
33 <option value="canberra">canberra</option>
34 <option value="canberra_adkins">canberra_adkins</option>
35 <option value="sqeuclidean">sqeuclidean</option>
36 <option value="sokalmichener">sokalmichener</option>
37 <option value="cityblock">cityblock</option>
38 <option value="braycurtis">braycurtis</option>
39 <option value="matching">matching</option>
40 <option value="russellrao">russellrao</option>
41 <option value="cosine">cosine</option>
42 <option value="yule">yule</option>
43 <option value="euclidean">euclidean</option>
44 <option value="rogerstanimoto">rogerstanimoto</option>
45 <option value="seuclidean">seuclidean</option>
46 <option value="jaccard">jaccard</option>
47 <option value="sokalsneath">sokalsneath</option>
48 <option value="aitchison">aitchison</option>
49 <option value="chebyshev">chebyshev</option>
50 <option value="dice">dice</option>
51 <option value="mahalanobis">mahalanobis</option>
52 </param>
53 <param label="--p-pseudocount: INTEGER Range(1, None) A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics. [default: 1]" name="ppseudocount" optional="True" type="integer" min="1" value="1"/>
54 </inputs>
55 <outputs>
56 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/>
57 </outputs>
58 <help><![CDATA[
59 Beta diversity
60 ##############
61
62 Computes a user-specified beta diversity metric for all pairs of samples in
63 a feature table.
64
65 Parameters
66 ----------
67 table : FeatureTable[Frequency]
68 The feature table containing the samples over which beta diversity
69 should be computed.
70 metric : Str % Choices('sokalmichener', 'yule', 'russellrao', 'rogerstanimoto', 'aitchison', 'correlation', 'jaccard', 'cosine', 'euclidean', 'sqeuclidean', 'chebyshev', 'cityblock', 'matching', 'dice', 'mahalanobis', 'wminkowski', 'kulsinski', 'seuclidean', 'sokalsneath', 'canberra', 'canberra_adkins', 'hamming', 'braycurtis')
71 The beta diversity metric to be computed.
72 pseudocount : Int % Range(1, None), optional
73 A pseudocount to handle zeros for compositional metrics. This is
74 ignored for other metrics.
75
76 Returns
77 -------
78 distance_matrix : DistanceMatrix
79 The resulting distance matrix.
80 ]]></help>
81 <macros>
82 <import>qiime_citation.xml</import>
83 </macros>
84 <expand macro="qiime_citation"/>
85 </tool>