|
0
|
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>
|
