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comparison qiime2__diversity_lib__beta_passthrough.xml @ 3:0969c54eddc6 draft

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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 21:03:38 +0000
parents 38a55b074008
children da6fdc7618c7
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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 beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 diversity-lib beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Beta Passthrough (non-phylogenetic)</description> 14 <description>Beta Passthrough (non-phylogenetic)</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 beta_passthrough '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run diversity_lib beta_passthrough '$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]" help="[required] The feature table containing the samples over which beta diversity should be computed."> 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples over which beta diversity 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[Frequency]"/> 26 <filter type="add_value" value="FeatureTable[Frequency]"/>
52 <option value="yule">yule</option> 52 <option value="yule">yule</option>
53 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> 53 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
54 </param> 54 </param>
55 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 55 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
56 <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1] A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics."/> 56 <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1] A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics."/>
57 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
58 <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.">
59 <option value="auto">auto (Str)</option>
60 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
61 </param>
62 <when value="auto">
63 <param name="n_jobs" type="hidden" value="auto"/>
64 </when>
65 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
66 <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."/>
67 </when>
68 </conditional>
69 </section> 57 </section>
70 </inputs> 58 </inputs>
71 <outputs> 59 <outputs>
72 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> 60 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
73 </outputs> 61 </outputs>
84 </output> 72 </output>
85 </test> 73 </test>
86 <test> 74 <test>
87 <param name="table" value="beta_passthrough.test1.feature-table.qza" ftype="qza"/> 75 <param name="table" value="beta_passthrough.test1.feature-table.qza" ftype="qza"/>
88 <param name="metric" value="kulsinski"/> 76 <param name="metric" value="kulsinski"/>
89 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
90 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
91 <param name="n_jobs" value="1"/>
92 </conditional>
93 <output name="distance_matrix" ftype="qza"> 77 <output name="distance_matrix" ftype="qza">
94 <assert_contents> 78 <assert_contents>
95 <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_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">
96 <has_line_matching expression="type: DistanceMatrix"/> 80 <has_line_matching expression="type: DistanceMatrix"/>
97 </has_archive_member> 81 </has_archive_member>
99 </output> 83 </output>
100 </test> 84 </test>
101 <test> 85 <test>
102 <param name="table" value="beta_passthrough.test2.feature-table.qza" ftype="qza"/> 86 <param name="table" value="beta_passthrough.test2.feature-table.qza" ftype="qza"/>
103 <param name="metric" value="aitchison"/> 87 <param name="metric" value="aitchison"/>
104 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
105 <param name="__q2galaxy__GUI__select__" value="auto"/>
106 <param name="n_jobs" value="auto"/>
107 </conditional>
108 <output name="distance_matrix" ftype="qza"> 88 <output name="distance_matrix" ftype="qza">
109 <assert_contents> 89 <assert_contents>
110 <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"> 90 <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">
111 <has_line_matching expression="type: DistanceMatrix"/> 91 <has_line_matching expression="type: DistanceMatrix"/>
112 </has_archive_member> 92 </has_archive_member>
115 </test> 95 </test>
116 <test> 96 <test>
117 <param name="table" value="beta_passthrough.test3.feature-table.qza" ftype="qza"/> 97 <param name="table" value="beta_passthrough.test3.feature-table.qza" ftype="qza"/>
118 <param name="metric" value="aitchison"/> 98 <param name="metric" value="aitchison"/>
119 <param name="pseudocount" value="5"/> 99 <param name="pseudocount" value="5"/>
120 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
121 <param name="__q2galaxy__GUI__select__" value="auto"/>
122 <param name="n_jobs" value="auto"/>
123 </conditional>
124 <output name="distance_matrix" ftype="qza"> 100 <output name="distance_matrix" ftype="qza">
125 <assert_contents> 101 <assert_contents>
126 <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"> 102 <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">
127 <has_line_matching expression="type: DistanceMatrix"/> 103 <has_line_matching expression="type: DistanceMatrix"/>
128 </has_archive_member> 104 </has_archive_member>
171 to run on n cores, replace 1 here with your preferred integer 147 to run on n cores, replace 1 here with your preferred integer
172 ************************************************************* 148 *************************************************************
173 Using the ``qiime2 diversity-lib beta-passthrough`` tool: 149 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
174 #. Set *"table"* to ``#: feature-table.qza`` 150 #. Set *"table"* to ``#: feature-table.qza``
175 #. Set *"metric"* to ``kulsinski`` 151 #. Set *"metric"* to ``kulsinski``
176 #. Expand the ``additional options`` section
177
178 - Leave *"n_jobs"* as its default value of ``1``
179
180 #. Press the ``Execute`` button. 152 #. Press the ``Execute`` button.
181 153
182 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 154 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
183 (Renaming is optional, but it will make any subsequent steps easier to complete.) 155 (Renaming is optional, but it will make any subsequent steps easier to complete.)
184 156
195 ************************************************************* 167 *************************************************************
196 | A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics. 168 | A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
197 Using the ``qiime2 diversity-lib beta-passthrough`` tool: 169 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
198 #. Set *"table"* to ``#: feature-table.qza`` 170 #. Set *"table"* to ``#: feature-table.qza``
199 #. Set *"metric"* to ``aitchison`` 171 #. Set *"metric"* to ``aitchison``
200 #. Expand the ``additional options`` section
201
202 - Set *"n_jobs"* to ``auto``
203
204 #. Press the ``Execute`` button. 172 #. Press the ``Execute`` button.
205 173
206 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 174 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
207 (Renaming is optional, but it will make any subsequent steps easier to complete.) 175 (Renaming is optional, but it will make any subsequent steps easier to complete.)
208 176
220 Using the ``qiime2 diversity-lib beta-passthrough`` tool: 188 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
221 #. Set *"table"* to ``#: feature-table.qza`` 189 #. Set *"table"* to ``#: feature-table.qza``
222 #. Set *"metric"* to ``aitchison`` 190 #. Set *"metric"* to ``aitchison``
223 #. Expand the ``additional options`` section 191 #. Expand the ``additional options`` section
224 192
225 #. Set *"pseudocount"* to ``5`` 193 - Set *"pseudocount"* to ``5``
226 #. Set *"n_jobs"* to ``auto``
227 194
228 #. Press the ``Execute`` button. 195 #. Press the ``Execute`` button.
229 196
230 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 197 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
231 (Renaming is optional, but it will make any subsequent steps easier to complete.) 198 (Renaming is optional, but it will make any subsequent steps easier to complete.)