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comparison qiime_diversity_alpha.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_alpha" name="qiime diversity alpha" version="2018.4">
3 <description> - Alpha diversity</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity alpha --i-table=$itable --p-metric=$pmetric
9
10 #if str($cmdconfig) != 'None':
11 --cmd-config=$cmdconfig
12 #end if
13
14 --o-alpha-diversity=oalphadiversity;
15
16 cp oalphadiversity.qza $oalphadiversity;
17 ]]></command>
18 <inputs>
19 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed. [required]" name="itable" optional="False" type="data"/>
20 <param label="--p-metric: The alpha diversity metric to be computed.
21 [required]" name="pmetric" optional="False" type="select" >
22 <option value="goods_coverage">goods_coverage</option>
23 <option value="heip_e">heip_e</option>
24 <option value="mcintosh_d">mcintosh_d</option>
25 <option value="esty_ci">esty_ci</option>
26 <option value="doubles">doubles</option>
27 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
28 <option value="observed_otus">observed_otus</option>
29 <option value="kempton_taylor_q">kempton_taylor_q</option>
30 <option value="chao1_ci">chao1_ci</option>
31 <option value="shannon">shannon</option>
32 <option value="margalef">margalef</option>
33 <option value="simpson">simpson</option>
34 <option value="lladser_ci">lladser_ci</option>
35 <option value="lladser_pe">lladser_pe</option>
36 <option value="osd">osd</option>
37 <option value="menhinick">menhinick</option>
38 <option value="singles">singles</option>
39 <option value="gini_index">gini_index</option>
40 <option value="robbins">robbins</option>
41 <option value="ace">ace</option>
42 <option value="simpson_e">simpson_e</option>
43 <option value="enspie">enspie</option>
44 <option value="berger_parker_d">berger_parker_d</option>
45 <option value="fisher_alpha">fisher_alpha</option>
46 <option value="dominance">dominance</option>
47 <option value="pielou_e">pielou_e</option>
48 <option value="chao1">chao1</option>
49 <option value="mcintosh_e">mcintosh_e</option>
50 <option value="strong">strong</option>
51 <option value="brillouin_d">brillouin_d</option>
52 </param>
53 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
54 </inputs>
55 <outputs>
56 <data format="qza" label="${tool.name} on ${on_string}: alpha-diversity.qza" name="oalphadiversity"/>
57 </outputs>
58 <help><![CDATA[
59 Alpha diversity
60 ---------------
61
62 Computes a user-specified alpha diversity metric for all samples in a
63 feature table.
64
65 Parameters
66 ----------
67 table : FeatureTable[Frequency]
68 The feature table containing the samples for which alpha diversity
69 should be computed.
70 metric : Str % Choices({'ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_ci', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_otus', 'osd', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles', 'strong'})
71 The alpha diversity metric to be computed.
72
73 Returns
74 -------
75 alpha_diversity : SampleData[AlphaDiversity]
76 Vector containing per-sample alpha diversities.
77 ]]>
78 </help>
79 </tool>