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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 19:40:34 +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 bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Bray-Curtis Dissimilarity</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 bray_curtis '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
29 </param>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
32 <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.">
33 <option value="auto">auto (Str)</option>
34 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
35 </param>
36 <when value="auto">
37 <param name="n_jobs" type="hidden" value="auto"/>
38 </when>
39 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
40 <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1] The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host."/>
41 </when>
42 </conditional>
43 </section>
44 </inputs>
45 <outputs>
46 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
47 </outputs>
48 <tests>
49 <test>
50 <param name="table" value="bray_curtis.test0.feature-table.qza" ftype="qza"/>
51 <output name="distance_matrix" ftype="qza">
52 <assert_contents>
53 <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">
54 <has_line_matching expression="type: DistanceMatrix"/>
55 </has_archive_member>
56 </assert_contents>
57 </output>
58 </test>
59 <test>
60 <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/>
61 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
62 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
63 <param name="n_jobs" value="1"/>
64 </conditional>
65 <output name="distance_matrix" ftype="qza">
66 <assert_contents>
67 <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">
68 <has_line_matching expression="type: DistanceMatrix"/>
69 </has_archive_member>
70 </assert_contents>
71 </output>
72 </test>
73 <test>
74 <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/>
75 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
76 <param name="__q2galaxy__GUI__select__" value="auto"/>
77 <param name="n_jobs" value="auto"/>
78 </conditional>
79 <output name="distance_matrix" ftype="qza">
80 <assert_contents>
81 <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">
82 <has_line_matching expression="type: DistanceMatrix"/>
83 </has_archive_member>
84 </assert_contents>
85 </output>
86 </test>
87 </tests>
88 <help>
89 QIIME 2: diversity-lib bray-curtis
90 ==================================
91 Bray-Curtis Dissimilarity
92
93
94 Outputs:
95 --------
96 :distance_matrix.qza: Distance matrix for Bray-Curtis dissimilarity
97
98 |
99
100 Description:
101 ------------
102 Compute Bray-Curtis dissimilarity for each sample in a feature table. Note: Frequency and relative frequency data produce different results unless overall sample sizes are identical. Please consider the impact on your results if you use Bray-Curtis with count data that has not been adjusted (normalized).
103
104 Examples:
105 ---------
106
107 run on one core (by default)
108 ****************************
109 Using the ``qiime2 diversity-lib bray-curtis`` tool:
110 #. Set *"table"* to ``#: feature-table.qza``
111 #. Press the ``Execute`` button.
112
113 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
114 (Renaming is optional, but it will make any subsequent steps easier to complete.)
115
116 .. list-table::
117 :align: left
118 :header-rows: 1
119
120 * - History Name
121 - *"Name"* to set (be sure to press ``Save``)
122 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
123 - ``bray-curtis-dm.qza``
124
125 to run on n cores, replace 1 here with your preferred integer
126 *************************************************************
127 Using the ``qiime2 diversity-lib bray-curtis`` tool:
128 #. Set *"table"* to ``#: feature-table.qza``
129 #. Expand the ``additional options`` section
130
131 - Leave *"n_jobs"* as its default value of ``1``
132
133 #. Press the ``Execute`` button.
134
135 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
136 (Renaming is optional, but it will make any subsequent steps easier to complete.)
137
138 .. list-table::
139 :align: left
140 :header-rows: 1
141
142 * - History Name
143 - *"Name"* to set (be sure to press ``Save``)
144 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
145 - ``bray-curtis-dm.qza``
146
147 use 'auto' to run on all of host system's available CPU cores
148 *************************************************************
149 Using the ``qiime2 diversity-lib bray-curtis`` tool:
150 #. Set *"table"* to ``#: feature-table.qza``
151 #. Expand the ``additional options`` section
152
153 - Set *"n_jobs"* to ``auto``
154
155 #. Press the ``Execute`` button.
156
157 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
158 (Renaming is optional, but it will make any subsequent steps easier to complete.)
159
160 .. list-table::
161 :align: left
162 :header-rows: 1
163
164 * - History Name
165 - *"Name"* to set (be sure to press ``Save``)
166 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
167 - ``bray-curtis-dm.qza``
168
169
170 |
171
172 </help>
173 <citations>
174 <citation type="bibtex">@article{cite1,
175 author = {Sørensen, Thorvald},
176 journal = {Biol. Skr.},
177 pages = {1--34},
178 title = {A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons},
179 volume = {5},
180 year = {1948}
181 }
182 </citation>
183 <citation type="doi">10.1038/s41587-019-0209-9</citation>
184 </citations>
185 </tool>