Mercurial > repos > q2d2 > qiime2__diversity_lib__beta_passthrough
comparison qiime2__diversity_lib__beta_passthrough.xml @ 3:0969c54eddc6 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author | q2d2 |
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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.) |