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comparison qiime2/qiime_diversity_beta.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta" name="qiime diversity beta" version="2019.7"> 2 <tool id="qiime_diversity_beta" name="qiime diversity beta"
3 <description> - Beta diversity</description> 3 version="2020.8">
4 <requirements> 4 <description>Beta diversity</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime diversity beta 9 qiime diversity beta
9 10
10 --i-table=$itable 11 --i-table=$itable
11 12
12 --p-metric=$pmetric 13 --p-metric=$pmetric
13 14
14 #if str($ppseudocount): 15 --p-pseudocount=$ppseudocount
15 --p-pseudocount=$ppseudocount
16 #end if
17 16
18 #set $pnjobs = '${GALAXY_SLOTS:-4}' 17 #if str($pnjobs) != 'None':
19 #if str($pnjobs): 18 --p-n-jobs=$pnjobs
20 --p-n-jobs="$pnjobs"
21 #end if 19 #end if
22 20
23 --o-distance-matrix=odistancematrix 21 --o-distance-matrix=odistancematrix
22
23 #if str($examples) != 'None':
24 --examples=$examples
25 #end if
26
24 ; 27 ;
25 cp odistancematrix.qza $odistancematrix 28 cp odistancematrix.qza $odistancematrix
26 ]]></command> 29
27 <inputs> 30 ]]></command>
28 <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"/> 31 <inputs>
29 <param label="--p-metric: " name="pmetric" optional="False" type="select"> 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" />
30 <option value="kulsinski">kulsinski</option> 33 <param label="--p-metric: " name="pmetric" optional="False" type="select">
31 <option value="wminkowski">wminkowski</option> 34 <option value="braycurtis">braycurtis</option>
32 <option value="correlation">correlation</option> 35 <option value="euclidean">euclidean</option>
33 <option value="hamming">hamming</option> 36 <option value="cityblock">cityblock</option>
34 <option value="canberra">canberra</option> 37 <option value="cosine">cosine</option>
35 <option value="canberra_adkins">canberra_adkins</option> 38 <option value="minkowski">minkowski</option>
36 <option value="sqeuclidean">sqeuclidean</option> 39 <option value="matching">matching</option>
37 <option value="sokalmichener">sokalmichener</option> 40 <option value="correlation">correlation</option>
38 <option value="cityblock">cityblock</option> 41 <option value="russellrao">russellrao</option>
39 <option value="braycurtis">braycurtis</option> 42 <option value="sokalsneath">sokalsneath</option>
40 <option value="matching">matching</option> 43 <option value="seuclidean">seuclidean</option>
41 <option value="russellrao">russellrao</option> 44 <option value="canberra">canberra</option>
42 <option value="cosine">cosine</option> 45 <option value="sokalmichener">sokalmichener</option>
43 <option value="yule">yule</option> 46 <option value="kulsinski">kulsinski</option>
44 <option value="euclidean">euclidean</option> 47 <option value="jensenshannon">jensenshannon</option>
45 <option value="rogerstanimoto">rogerstanimoto</option> 48 <option value="jaccard">jaccard</option>
46 <option value="seuclidean">seuclidean</option> 49 <option value="hamming">hamming</option>
47 <option value="jaccard">jaccard</option> 50 <option value="chebyshev">chebyshev</option>
48 <option value="sokalsneath">sokalsneath</option> 51 <option value="yule">yule</option>
49 <option value="aitchison">aitchison</option> 52 <option value="dice">dice</option>
50 <option value="chebyshev">chebyshev</option> 53 <option value="sqeuclidean">sqeuclidean</option>
51 <option value="dice">dice</option> 54 <option value="aitchison">aitchison</option>
52 <option value="mahalanobis">mahalanobis</option> 55 <option value="canberra_adkins">canberra_adkins</option>
53 </param> 56 <option value="rogerstanimoto">rogerstanimoto</option>
54 <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"/> 57 </param>
55 </inputs> 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" />
56 <outputs> 59 <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
57 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/> 60 <option selected="True" value="None">Selection is Optional</option>
58 </outputs> 61 <option value="Int % Range(1">Int % Range(1</option>
59 <help><![CDATA[ 62 <option value="None">None</option>
63 </param>
64 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
65
66 </inputs>
67
68 <outputs>
69 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
70
71 </outputs>
72
73 <help><![CDATA[
60 Beta diversity 74 Beta diversity
61 ############## 75 ###############################################################
62 76
63 Computes a user-specified beta diversity metric for all pairs of samples in 77 Computes a user-specified beta diversity metric for all pairs of samples in
64 a feature table. 78 a feature table.
65 79
66 Parameters 80 Parameters
67 ---------- 81 ----------
68 table : FeatureTable[Frequency] 82 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
69 The feature table containing the samples over which beta diversity 83 The feature table containing the samples over which beta diversity
70 should be computed. 84 should be computed.
71 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') 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')
72 The beta diversity metric to be computed. 86 The beta diversity metric to be computed.
73 pseudocount : Int % Range(1, None), optional 87 pseudocount : Int % Range(1, None), optional
74 A pseudocount to handle zeros for compositional metrics. This is 88 A pseudocount to handle zeros for compositional metrics. This is
75 ignored for other metrics. 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.
76 95
77 Returns 96 Returns
78 ------- 97 -------
79 distance_matrix : DistanceMatrix 98 distance_matrix : DistanceMatrix
80 The resulting distance matrix. 99 The resulting distance matrix.
81 ]]></help> 100 ]]></help>
82 <macros> 101 <macros>
83 <import>qiime_citation.xml</import> 102 <import>qiime_citation.xml</import>
84 </macros> 103 </macros>
85 <expand macro="qiime_citation"/> 104 <expand macro="qiime_citation"/>
86 </tool> 105 </tool>