Mercurial > repos > q2d2 > qiime2__diversity_lib__beta_passthrough
comparison qiime2__diversity_lib__beta_passthrough.xml @ 4:da6fdc7618c7 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
author | q2d2 |
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date | Mon, 03 Jun 2024 23:20:43 +0000 |
parents | 0969c54eddc6 |
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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: 2024.2.1) | 9 q2galaxy (version: 2024.5.0) |
10 for: | 10 for: |
11 qiime2 (version: 2024.2.0) | 11 qiime2 (version: 2024.5.0) |
12 --> | 12 --> |
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"> | 13 <tool name="qiime2 diversity-lib beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2024.5.0+q2galaxy.2024.5.0" 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/amplicon:2024.2</container> | 16 <container type="docker">quay.io/qiime2/amplicon:2024.5</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="staging_path_and_source_path"/> | 21 <inputs name="inputs" data_style="staging_path_and_source_path"/> |
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]"/> |
27 </options> | 27 </options> |
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> | 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> |
29 </param> | 29 </param> |
30 <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'kulsinski', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')"> | 30 <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')"> |
31 <option value="__q2galaxy__::literal::None">Selection required</option> | 31 <option value="__q2galaxy__::literal::None">Selection required</option> |
32 <option value="aitchison">aitchison</option> | 32 <option value="aitchison">aitchison</option> |
33 <option value="canberra">canberra</option> | 33 <option value="canberra">canberra</option> |
34 <option value="canberra_adkins">canberra_adkins</option> | 34 <option value="canberra_adkins">canberra_adkins</option> |
35 <option value="chebyshev">chebyshev</option> | 35 <option value="chebyshev">chebyshev</option> |
38 <option value="cosine">cosine</option> | 38 <option value="cosine">cosine</option> |
39 <option value="dice">dice</option> | 39 <option value="dice">dice</option> |
40 <option value="euclidean">euclidean</option> | 40 <option value="euclidean">euclidean</option> |
41 <option value="hamming">hamming</option> | 41 <option value="hamming">hamming</option> |
42 <option value="jensenshannon">jensenshannon</option> | 42 <option value="jensenshannon">jensenshannon</option> |
43 <option value="kulsinski">kulsinski</option> | |
44 <option value="matching">matching</option> | 43 <option value="matching">matching</option> |
45 <option value="minkowski">minkowski</option> | 44 <option value="minkowski">minkowski</option> |
46 <option value="rogerstanimoto">rogerstanimoto</option> | 45 <option value="rogerstanimoto">rogerstanimoto</option> |
47 <option value="russellrao">russellrao</option> | 46 <option value="russellrao">russellrao</option> |
48 <option value="seuclidean">seuclidean</option> | 47 <option value="seuclidean">seuclidean</option> |
71 </assert_contents> | 70 </assert_contents> |
72 </output> | 71 </output> |
73 </test> | 72 </test> |
74 <test> | 73 <test> |
75 <param name="table" value="beta_passthrough.test1.feature-table.qza" ftype="qza"/> | 74 <param name="table" value="beta_passthrough.test1.feature-table.qza" ftype="qza"/> |
76 <param name="metric" value="kulsinski"/> | 75 <param name="metric" value="euclidean"/> |
77 <output name="distance_matrix" ftype="qza"> | 76 <output name="distance_matrix" ftype="qza"> |
78 <assert_contents> | 77 <assert_contents> |
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"> | 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"> |
80 <has_line_matching expression="type: DistanceMatrix"/> | 79 <has_line_matching expression="type: DistanceMatrix"/> |
81 </has_archive_member> | 80 </has_archive_member> |
146 | 145 |
147 to run on n cores, replace 1 here with your preferred integer | 146 to run on n cores, replace 1 here with your preferred integer |
148 ************************************************************* | 147 ************************************************************* |
149 Using the ``qiime2 diversity-lib beta-passthrough`` tool: | 148 Using the ``qiime2 diversity-lib beta-passthrough`` tool: |
150 #. Set *"table"* to ``#: feature-table.qza`` | 149 #. Set *"table"* to ``#: feature-table.qza`` |
151 #. Set *"metric"* to ``kulsinski`` | 150 #. Set *"metric"* to ``euclidean`` |
152 #. Press the ``Execute`` button. | 151 #. Press the ``Execute`` button. |
153 | 152 |
154 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: | 153 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
155 (Renaming is optional, but it will make any subsequent steps easier to complete.) | 154 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
156 | 155 |
157 .. list-table:: | 156 .. list-table:: |
158 :align: left | 157 :align: left |
159 :header-rows: 1 | 158 :header-rows: 1 |
160 | 159 |
161 * - History Name | 160 * - History Name |
162 - *"Name"* to set (be sure to press ``Save``) | 161 - *"Name"* to set (be sure to press ``Save``) |
163 * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`` | 162 * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`` |
164 - ``kulsinski-dm.qza`` | 163 - ``euclidean-dm.qza`` |
165 | 164 |
166 use 'auto' to run on all of host system's available CPU cores | 165 use 'auto' to run on all of host system's available CPU cores |
167 ************************************************************* | 166 ************************************************************* |
168 | A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics. | 167 | A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics. |
169 Using the ``qiime2 diversity-lib beta-passthrough`` tool: | 168 Using the ``qiime2 diversity-lib beta-passthrough`` tool: |