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comparison qiime2-2020.8/qiime_diversity_alpha.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_alpha" name="qiime diversity alpha"
3 version="2020.8">
4 <description>Alpha diversity</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity alpha
10
11 --i-table=$itable
12
13 --p-metric=$pmetric
14
15 --o-alpha-diversity=oalphadiversity
16
17 #if str($examples) != 'None':
18 --examples=$examples
19 #end if
20
21 ;
22 cp oalphadiversity.qza $oalphadiversity
23
24 ]]></command>
25 <inputs>
26 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples for which alpha diversity should be computed. [required]" name="itable" optional="False" type="data" />
27 <param label="--p-metric: " name="pmetric" optional="False" type="select">
28 <option value="strong">strong</option>
29 <option value="observed_features">observed_features</option>
30 <option value="heip_e">heip_e</option>
31 <option value="dominance">dominance</option>
32 <option value="goods_coverage">goods_coverage</option>
33 <option value="ace">ace</option>
34 <option value="gini_index">gini_index</option>
35 <option value="simpson_e">simpson_e</option>
36 <option value="osd">osd</option>
37 <option value="pielou_e">pielou_e</option>
38 <option value="mcintosh_e">mcintosh_e</option>
39 <option value="esty_ci">esty_ci</option>
40 <option value="berger_parker_d">berger_parker_d</option>
41 <option value="shannon">shannon</option>
42 <option value="enspie">enspie</option>
43 <option value="mcintosh_d">mcintosh_d</option>
44 <option value="chao1_ci">chao1_ci</option>
45 <option value="lladser_pe">lladser_pe</option>
46 <option value="brillouin_d">brillouin_d</option>
47 <option value="menhinick">menhinick</option>
48 <option value="simpson">simpson</option>
49 <option value="margalef">margalef</option>
50 <option value="robbins">robbins</option>
51 <option value="doubles">doubles</option>
52 <option value="chao1">chao1</option>
53 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
54 <option value="singles">singles</option>
55 <option value="kempton_taylor_q">kempton_taylor_q</option>
56 <option value="fisher_alpha">fisher_alpha</option>
57 </param>
58 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
59
60 </inputs>
61
62 <outputs>
63 <data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity" />
64
65 </outputs>
66
67 <help><![CDATA[
68 Alpha diversity
69 ###############################################################
70
71 Computes a user-specified alpha diversity metric for all samples in a
72 feature table.
73
74 Parameters
75 ----------
76 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
77 The feature table containing the samples for which alpha diversity
78 should be computed.
79 metric : Str % Choices('mcintosh_e', 'esty_ci', 'chao1', 'observed_features', 'ace', 'margalef', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'heip_e', 'michaelis_menten_fit', 'enspie', 'menhinick', 'shannon', 'pielou_e', 'singles', 'simpson', 'chao1_ci', 'strong', 'fisher_alpha', 'osd', 'dominance', 'robbins', 'lladser_pe', 'kempton_taylor_q', 'mcintosh_d', 'brillouin_d', 'goods_coverage')
80 The alpha diversity metric to be computed.
81
82 Returns
83 -------
84 alpha_diversity : SampleData[AlphaDiversity]
85 Vector containing per-sample alpha diversities.
86 ]]></help>
87 <macros>
88 <import>qiime_citation.xml</import>
89 </macros>
90 <expand macro="qiime_citation"/>
91 </tool>