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comparison qiime2/qiime_diversity_beta.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta" name="qiime diversity beta" version="2018.4">
3 <description> - Beta diversity</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity beta --i-table=$itable --p-metric=$pmetric --o-distance-matrix=odistancematrix
9
10 #if str($cmdconfig) != 'None':
11 --cmd-config=$cmdconfig
12 #end if
13
14 #set $pnjobs = '${GALAXY_SLOTS:-4}'
15
16 #if str($pnjobs):
17 --p-n-jobs="$pnjobs"
18 #end if
19
20 ;
21 cp odistancematrix.qza $odistancematrix;
22 ]]></command>
23 <inputs>
24 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data"/>
25
26 <param label="--p-metric: The beta diversity metric to be computed.
27 [required]" name="pmetric" optional="False" type="select" >
28 <option value="hamming">hamming</option>
29 <option value="sqeuclidean">sqeuclidean</option>
30 <option value="cityblock">cityblock</option>
31 <option value="sokalmichener">sokalmichener</option>
32 <option value="braycurtis">braycurtis</option>
33 <option value="cosine">cosine</option>
34 <option value="euclidean">euclidean</option>
35 <option value="rogerstanimoto">rogerstanimoto</option>
36 <option value="canberra">canberra</option>
37 <option value="seuclidean">seuclidean</option>
38 <option value="correlation">correlation</option>
39 <option value="sokalsneath">sokalsneath</option>
40 <option value="chebyshev">chebyshev</option>
41 <option value="mahalanobis">mahalanobis</option>
42 <option value="matching">matching</option>
43 <option value="kulsinski">kulsinski</option>
44 <option value="yule">yule</option>
45 <option value="dice">dice</option>
46 <option value="russellrao">russellrao</option>
47 <option value="wminkowski">wminkowski</option>
48 <option value="jaccard">jaccard</option>
49 </param>
50
51 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
52 </inputs>
53 <outputs>
54 <data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/>
55 </outputs>
56 <help><![CDATA[
57 Beta diversity
58 --------------
59
60 Computes a user-specified beta diversity metric for all pairs of samples in
61 a feature table.
62
63 Parameters
64 ----------
65 table : FeatureTable[Frequency]
66 The feature table containing the samples over which beta diversity
67 should be computed.
68 metric : Str % Choices({'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'wminkowski', 'yule'})
69 The beta diversity metric to be computed.
70
71 Returns
72 -------
73 distance_matrix : DistanceMatrix
74 The resulting distance matrix.
75 ]]>
76 </help>
77 <macros>
78 <import>qiime_citation.xml</import>
79 </macros>
80 <expand macro="qiime_citation" />
81 </tool>