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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:04:04 +0000
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1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2023, QIIME 2 development team. 3 Copyright (c) 2024, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2023.5.0) 9 q2galaxy (version: 2024.2.1)
10 for: 10 for:
11 qiime2 (version: 2023.5.1) 11 qiime2 (version: 2024.2.0)
12 --> 12 -->
13 <tool name="qiime2 diversity-lib unweighted-unifrac" id="qiime2__diversity_lib__unweighted_unifrac" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 diversity-lib unweighted-unifrac" id="qiime2__diversity_lib__unweighted_unifrac" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Unweighted Unifrac</description> 14 <description>Unweighted Unifrac</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2023.5</container> 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version diversity_lib</version_command> 18 <version_command>q2galaxy version diversity_lib</version_command>
19 <command detect_errors="exit_code">q2galaxy run diversity_lib unweighted_unifrac '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run diversity_lib unweighted_unifrac '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 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 Unweighted Unifrac should be computed."> 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples for which Unweighted Unifrac should be computed.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> 26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
34 <filter type="add_value" value="Phylogeny[Rooted]"/> 34 <filter type="add_value" value="Phylogeny[Rooted]"/>
35 </options> 35 </options>
36 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator> 36 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
37 </param> 37 </param>
38 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 38 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
39 <conditional name="__q2galaxy__GUI__conditional__threads__">
40 <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.">
41 <option value="auto">auto (Str)</option>
42 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
43 </param>
44 <when value="auto">
45 <param name="threads" type="hidden" value="auto"/>
46 </when>
47 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
48 <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."/>
49 </when>
50 </conditional>
51 <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No] In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/> 39 <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No] In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/>
52 </section> 40 </section>
53 </inputs> 41 </inputs>
54 <outputs> 42 <outputs>
55 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> 43 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
67 </output> 55 </output>
68 </test> 56 </test>
69 <test> 57 <test>
70 <param name="table" value="unweighted_unifrac.test1.feature-table.qza" ftype="qza"/> 58 <param name="table" value="unweighted_unifrac.test1.feature-table.qza" ftype="qza"/>
71 <param name="phylogeny" value="unweighted_unifrac.test1.phylogeny.qza" ftype="qza"/> 59 <param name="phylogeny" value="unweighted_unifrac.test1.phylogeny.qza" ftype="qza"/>
72 <conditional name="__q2galaxy__GUI__conditional__threads__">
73 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
74 <param name="threads" value="1"/>
75 </conditional>
76 <output name="distance_matrix" ftype="qza"> 60 <output name="distance_matrix" ftype="qza">
77 <assert_contents> 61 <assert_contents>
78 <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"> 62 <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">
79 <has_line_matching expression="type: DistanceMatrix"/> 63 <has_line_matching expression="type: DistanceMatrix"/>
80 </has_archive_member> 64 </has_archive_member>
82 </output> 66 </output>
83 </test> 67 </test>
84 <test> 68 <test>
85 <param name="table" value="unweighted_unifrac.test2.feature-table.qza" ftype="qza"/> 69 <param name="table" value="unweighted_unifrac.test2.feature-table.qza" ftype="qza"/>
86 <param name="phylogeny" value="unweighted_unifrac.test2.phylogeny.qza" ftype="qza"/> 70 <param name="phylogeny" value="unweighted_unifrac.test2.phylogeny.qza" ftype="qza"/>
87 <conditional name="__q2galaxy__GUI__conditional__threads__">
88 <param name="__q2galaxy__GUI__select__" value="auto"/>
89 <param name="threads" value="auto"/>
90 </conditional>
91 <output name="distance_matrix" ftype="qza"> 71 <output name="distance_matrix" ftype="qza">
92 <assert_contents> 72 <assert_contents>
93 <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"> 73 <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">
94 <has_line_matching expression="type: DistanceMatrix"/> 74 <has_line_matching expression="type: DistanceMatrix"/>
95 </has_archive_member> 75 </has_archive_member>
97 </output> 77 </output>
98 </test> 78 </test>
99 <test> 79 <test>
100 <param name="table" value="unweighted_unifrac.test3.feature-table.qza" ftype="qza"/> 80 <param name="table" value="unweighted_unifrac.test3.feature-table.qza" ftype="qza"/>
101 <param name="phylogeny" value="unweighted_unifrac.test3.phylogeny.qza" ftype="qza"/> 81 <param name="phylogeny" value="unweighted_unifrac.test3.phylogeny.qza" ftype="qza"/>
102 <conditional name="__q2galaxy__GUI__conditional__threads__">
103 <param name="__q2galaxy__GUI__select__" value="auto"/>
104 <param name="threads" value="auto"/>
105 </conditional>
106 <param name="bypass_tips" value="__q2galaxy__::literal::True"/> 82 <param name="bypass_tips" value="__q2galaxy__::literal::True"/>
107 <output name="distance_matrix" ftype="qza"> 83 <output name="distance_matrix" ftype="qza">
108 <assert_contents> 84 <assert_contents>
109 <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"> 85 <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">
110 <has_line_matching expression="type: DistanceMatrix"/> 86 <has_line_matching expression="type: DistanceMatrix"/>
154 to run on n cores, replace 1 here with your preferred integer 130 to run on n cores, replace 1 here with your preferred integer
155 ************************************************************* 131 *************************************************************
156 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: 132 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool:
157 #. Set *"table"* to ``#: feature-table.qza`` 133 #. Set *"table"* to ``#: feature-table.qza``
158 #. Set *"phylogeny"* to ``#: phylogeny.qza`` 134 #. Set *"phylogeny"* to ``#: phylogeny.qza``
159 #. Expand the ``additional options`` section
160
161 - Leave *"threads"* as its default value of ``1``
162
163 #. Press the ``Execute`` button. 135 #. Press the ``Execute`` button.
164 136
165 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 137 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
166 (Renaming is optional, but it will make any subsequent steps easier to complete.) 138 (Renaming is optional, but it will make any subsequent steps easier to complete.)
167 139
177 use 'auto' to run on all of host system's available CPU cores 149 use 'auto' to run on all of host system's available CPU cores
178 ************************************************************* 150 *************************************************************
179 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: 151 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool:
180 #. Set *"table"* to ``#: feature-table.qza`` 152 #. Set *"table"* to ``#: feature-table.qza``
181 #. Set *"phylogeny"* to ``#: phylogeny.qza`` 153 #. Set *"phylogeny"* to ``#: phylogeny.qza``
182 #. Expand the ``additional options`` section
183
184 - Set *"threads"* to ``auto``
185
186 #. Press the ``Execute`` button. 154 #. Press the ``Execute`` button.
187 155
188 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 156 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
189 (Renaming is optional, but it will make any subsequent steps easier to complete.) 157 (Renaming is optional, but it will make any subsequent steps easier to complete.)
190 158
203 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: 171 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool:
204 #. Set *"table"* to ``#: feature-table.qza`` 172 #. Set *"table"* to ``#: feature-table.qza``
205 #. Set *"phylogeny"* to ``#: phylogeny.qza`` 173 #. Set *"phylogeny"* to ``#: phylogeny.qza``
206 #. Expand the ``additional options`` section 174 #. Expand the ``additional options`` section
207 175
208 #. Set *"threads"* to ``auto`` 176 - Set *"bypass_tips"* to ``Yes``
209 #. Set *"bypass_tips"* to ``Yes``
210 177
211 #. Press the ``Execute`` button. 178 #. Press the ``Execute`` button.
212 179
213 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 180 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
214 (Renaming is optional, but it will make any subsequent steps easier to complete.) 181 (Renaming is optional, but it will make any subsequent steps easier to complete.)