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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 19:47:51 +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 jaccard" id="qiime2__diversity_lib__jaccard" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Jaccard Distance</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 jaccard '$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 | PresenceAbsence]" help="[required] The feature table containing the samples for which Jaccard distance 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[PresenceAbsence]"/>
28 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
29 </options>
30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
31 </param>
32 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
33 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
34 <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.">
35 <option value="auto">auto (Str)</option>
36 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
37 </param>
38 <when value="auto">
39 <param name="n_jobs" type="hidden" value="auto"/>
40 </when>
41 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
42 <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."/>
43 </when>
44 </conditional>
45 </section>
46 </inputs>
47 <outputs>
48 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
49 </outputs>
50 <tests>
51 <test>
52 <param name="table" value="jaccard.test0.feature-table.qza" ftype="qza"/>
53 <output name="distance_matrix" ftype="qza">
54 <assert_contents>
55 <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">
56 <has_line_matching expression="type: DistanceMatrix"/>
57 </has_archive_member>
58 </assert_contents>
59 </output>
60 </test>
61 <test>
62 <param name="table" value="jaccard.test1.feature-table.qza" ftype="qza"/>
63 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
64 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
65 <param name="n_jobs" value="1"/>
66 </conditional>
67 <output name="distance_matrix" ftype="qza">
68 <assert_contents>
69 <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">
70 <has_line_matching expression="type: DistanceMatrix"/>
71 </has_archive_member>
72 </assert_contents>
73 </output>
74 </test>
75 <test>
76 <param name="table" value="jaccard.test2.feature-table.qza" ftype="qza"/>
77 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
78 <param name="__q2galaxy__GUI__select__" value="auto"/>
79 <param name="n_jobs" value="auto"/>
80 </conditional>
81 <output name="distance_matrix" ftype="qza">
82 <assert_contents>
83 <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">
84 <has_line_matching expression="type: DistanceMatrix"/>
85 </has_archive_member>
86 </assert_contents>
87 </output>
88 </test>
89 </tests>
90 <help>
91 QIIME 2: diversity-lib jaccard
92 ==============================
93 Jaccard Distance
94
95
96 Outputs:
97 --------
98 :distance_matrix.qza: Distance matrix for Jaccard index
99
100 |
101
102 Description:
103 ------------
104 Compute Jaccard distance for each sample in a feature table. Jaccard is calculated usingpresence/absence data. Data of type FeatureTable[Frequency | Relative Frequency] is reducedto presence/absence prior to calculation.
105
106 Examples:
107 ---------
108
109 run on one core (by default)
110 ****************************
111 Using the ``qiime2 diversity-lib jaccard`` tool:
112 #. Set *"table"* to ``#: feature-table.qza``
113 #. Press the ``Execute`` button.
114
115 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
116 (Renaming is optional, but it will make any subsequent steps easier to complete.)
117
118 .. list-table::
119 :align: left
120 :header-rows: 1
121
122 * - History Name
123 - *"Name"* to set (be sure to press ``Save``)
124 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
125 - ``jaccard-dm.qza``
126
127 to run on n cores, replace 1 here with your preferred integer
128 *************************************************************
129 Using the ``qiime2 diversity-lib jaccard`` tool:
130 #. Set *"table"* to ``#: feature-table.qza``
131 #. Expand the ``additional options`` section
132
133 - Leave *"n_jobs"* as its default value of ``1``
134
135 #. Press the ``Execute`` button.
136
137 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
138 (Renaming is optional, but it will make any subsequent steps easier to complete.)
139
140 .. list-table::
141 :align: left
142 :header-rows: 1
143
144 * - History Name
145 - *"Name"* to set (be sure to press ``Save``)
146 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
147 - ``jaccard-dm.qza``
148
149 use 'auto' to run on all of host system's available CPU cores
150 *************************************************************
151 Using the ``qiime2 diversity-lib jaccard`` tool:
152 #. Set *"table"* to ``#: feature-table.qza``
153 #. Expand the ``additional options`` section
154
155 - Set *"n_jobs"* to ``auto``
156
157 #. Press the ``Execute`` button.
158
159 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
160 (Renaming is optional, but it will make any subsequent steps easier to complete.)
161
162 .. list-table::
163 :align: left
164 :header-rows: 1
165
166 * - History Name
167 - *"Name"* to set (be sure to press ``Save``)
168 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
169 - ``jaccard-dm.qza``
170
171
172 |
173
174 </help>
175 <citations>
176 <citation type="bibtex">@article{cite1,
177 author = {Jaccard, P},
178 journal = {Bull. Soc. Vard. Sci. Nat},
179 pages = {223--270},
180 title = {Nouvelles recherches sur la distribution floral},
181 volume = {44},
182 year = {1908}
183 }
184 </citation>
185 <citation type="doi">10.1038/s41587-019-0209-9</citation>
186 </citations>
187 </tool>