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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:41:15 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2022, QIIME 2 development team.
4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 -->
7 <!--
8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1)
10 for:
11 qiime2 (version: 2022.8.1)
12 -->
13 <tool name="qiime2 diversity-lib alpha-passthrough" id="qiime2__diversity_lib__alpha_passthrough" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Alpha Passthrough (non-phylogenetic)</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version diversity_lib</version_command>
19 <command detect_errors="aggressive">q2galaxy run diversity_lib alpha_passthrough '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples for which a selected metric should be computed.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
29 </param>
30 <param name="metric" type="select" label="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_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong')">
31 <option value="__q2galaxy__::literal::None">Selection required</option>
32 <option value="ace">ace</option>
33 <option value="berger_parker_d">berger_parker_d</option>
34 <option value="brillouin_d">brillouin_d</option>
35 <option value="chao1">chao1</option>
36 <option value="chao1_ci">chao1_ci</option>
37 <option value="dominance">dominance</option>
38 <option value="doubles">doubles</option>
39 <option value="enspie">enspie</option>
40 <option value="esty_ci">esty_ci</option>
41 <option value="fisher_alpha">fisher_alpha</option>
42 <option value="gini_index">gini_index</option>
43 <option value="goods_coverage">goods_coverage</option>
44 <option value="heip_e">heip_e</option>
45 <option value="kempton_taylor_q">kempton_taylor_q</option>
46 <option value="lladser_pe">lladser_pe</option>
47 <option value="margalef">margalef</option>
48 <option value="mcintosh_d">mcintosh_d</option>
49 <option value="mcintosh_e">mcintosh_e</option>
50 <option value="menhinick">menhinick</option>
51 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
52 <option value="osd">osd</option>
53 <option value="robbins">robbins</option>
54 <option value="simpson">simpson</option>
55 <option value="simpson_e">simpson_e</option>
56 <option value="singles">singles</option>
57 <option value="strong">strong</option>
58 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
59 </param>
60 </inputs>
61 <outputs>
62 <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
63 </outputs>
64 <tests>
65 <test>
66 <param name="table" value="alpha_passthrough.test0.feature-table.qza" ftype="qza"/>
67 <param name="metric" value="simpson"/>
68 <output name="vector" ftype="qza">
69 <assert_contents>
70 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
71 <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
72 </has_archive_member>
73 </assert_contents>
74 </output>
75 </test>
76 </tests>
77 <help>
78 QIIME 2: diversity-lib alpha-passthrough
79 ========================================
80 Alpha Passthrough (non-phylogenetic)
81
82
83 Outputs:
84 --------
85 :vector.qza: Vector containing per-sample values for the chosen metric.
86
87 |
88
89 Description:
90 ------------
91 Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.
92
93 Examples:
94 ---------
95
96 basic
97 *****
98 Using the ``qiime2 diversity-lib alpha-passthrough`` tool:
99 #. Set *"table"* to ``#: feature-table.qza``
100 #. Set *"metric"* to ``simpson``
101 #. Press the ``Execute`` button.
102
103 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
104 (Renaming is optional, but it will make any subsequent steps easier to complete.)
105
106 .. list-table::
107 :align: left
108 :header-rows: 1
109
110 * - History Name
111 - *"Name"* to set (be sure to press ``Save``)
112 * - ``#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza``
113 - ``simpson-vector.qza``
114
115
116 |
117
118 </help>
119 <citations>
120 <citation type="doi">10.1038/s41587-019-0209-9</citation>
121 </citations>
122 </tool>