Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_diversity_alpha.xml @ 20:d93d8888f0b0 draft
Uploaded
author | florianbegusch |
---|---|
date | Fri, 04 Sep 2020 12:44:24 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
19:6c48f8d82424 | 20:d93d8888f0b0 |
---|---|
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> |