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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 19:44:04 +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 shannon-entropy" id="qiime2__diversity_lib__shannon_entropy" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Shannon's Entropy</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 shannon_entropy '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required] The feature table containing the samples for which Shannon's Entropy should be computed.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
28 </options>
29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
30 </param>
31 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
32 <param name="drop_undefined_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="drop_undefined_samples: Bool" help="[default: No] Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector."/>
33 </section>
34 </inputs>
35 <outputs>
36 <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
37 </outputs>
38 <tests>
39 <test>
40 <param name="table" value="shannon_entropy.test0.feature-table.qza" ftype="qza"/>
41 <output name="vector" ftype="qza">
42 <assert_contents>
43 <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">
44 <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
45 </has_archive_member>
46 </assert_contents>
47 </output>
48 </test>
49 <test>
50 <param name="table" value="shannon_entropy.test1.feature-table.qza" ftype="qza"/>
51 <param name="drop_undefined_samples" value="__q2galaxy__::literal::True"/>
52 <output name="vector" ftype="qza">
53 <assert_contents>
54 <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">
55 <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
56 </has_archive_member>
57 </assert_contents>
58 </output>
59 </test>
60 </tests>
61 <help>
62 QIIME 2: diversity-lib shannon-entropy
63 ======================================
64 Shannon's Entropy
65
66
67 Outputs:
68 --------
69 :vector.qza: Vector containing per-sample values for Shannon's Entropy.
70
71 |
72
73 Description:
74 ------------
75 Compute Shannon's Entropy for each sample in a feature table
76
77 Examples:
78 ---------
79
80 basic
81 *****
82 Using the ``qiime2 diversity-lib shannon-entropy`` tool:
83 #. Set *"table"* to ``#: feature-table.qza``
84 #. Press the ``Execute`` button.
85
86 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
87 (Renaming is optional, but it will make any subsequent steps easier to complete.)
88
89 .. list-table::
90 :align: left
91 :header-rows: 1
92
93 * - History Name
94 - *"Name"* to set (be sure to press ``Save``)
95 * - ``#: qiime2 diversity-lib shannon-entropy [...] : vector.qza``
96 - ``shannon-vector.qza``
97
98 dropping undefined samples
99 **************************
100 Using the ``qiime2 diversity-lib shannon-entropy`` tool:
101 #. Set *"table"* to ``#: feature-table.qza``
102 #. Expand the ``additional options`` section
103
104 - Set *"drop_undefined_samples"* to ``Yes``
105
106 #. Press the ``Execute`` button.
107
108 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
109 (Renaming is optional, but it will make any subsequent steps easier to complete.)
110
111 .. list-table::
112 :align: left
113 :header-rows: 1
114
115 * - History Name
116 - *"Name"* to set (be sure to press ``Save``)
117 * - ``#: qiime2 diversity-lib shannon-entropy [...] : vector.qza``
118 - ``shannon-vector.qza``
119
120
121 |
122
123 </help>
124 <citations>
125 <citation type="doi">10.1002/j.1538-7305.1948.tb01338.x</citation>
126 <citation type="doi">10.1038/s41587-019-0209-9</citation>
127 </citations>
128 </tool>