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comparison qiime2__diversity_lib__bray_curtis.xml @ 3:6e6d848f2b5b 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 21:02:45 +0000
parents a1422e558f73
children 4111b5b17fd4
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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 bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 diversity-lib bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Bray-Curtis Dissimilarity</description> 14 <description>Bray-Curtis Dissimilarity</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 bray_curtis '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run diversity_lib bray_curtis '$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 for which Bray-Curtis dissimilarity should be computed."> 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required] The feature table containing the samples for which Bray-Curtis dissimilarity 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[Frequency]"/> 27 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 </options> 28 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> 29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
29 </param> 30 </param>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
32 <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.">
33 <option value="auto">auto (Str)</option>
34 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
35 </param>
36 <when value="auto">
37 <param name="n_jobs" type="hidden" value="auto"/>
38 </when>
39 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
40 <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."/>
41 </when>
42 </conditional>
43 </section>
44 </inputs> 31 </inputs>
45 <outputs> 32 <outputs>
46 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> 33 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
47 </outputs> 34 </outputs>
48 <tests> 35 <tests>
56 </assert_contents> 43 </assert_contents>
57 </output> 44 </output>
58 </test> 45 </test>
59 <test> 46 <test>
60 <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/> 47 <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/>
61 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
62 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
63 <param name="n_jobs" value="1"/>
64 </conditional>
65 <output name="distance_matrix" ftype="qza"> 48 <output name="distance_matrix" ftype="qza">
66 <assert_contents> 49 <assert_contents>
67 <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"> 50 <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">
68 <has_line_matching expression="type: DistanceMatrix"/> 51 <has_line_matching expression="type: DistanceMatrix"/>
69 </has_archive_member> 52 </has_archive_member>
70 </assert_contents> 53 </assert_contents>
71 </output> 54 </output>
72 </test> 55 </test>
73 <test> 56 <test>
74 <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/> 57 <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/>
75 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
76 <param name="__q2galaxy__GUI__select__" value="auto"/>
77 <param name="n_jobs" value="auto"/>
78 </conditional>
79 <output name="distance_matrix" ftype="qza"> 58 <output name="distance_matrix" ftype="qza">
80 <assert_contents> 59 <assert_contents>
81 <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"> 60 <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">
82 <has_line_matching expression="type: DistanceMatrix"/> 61 <has_line_matching expression="type: DistanceMatrix"/>
83 </has_archive_member> 62 </has_archive_member>
124 103
125 to run on n cores, replace 1 here with your preferred integer 104 to run on n cores, replace 1 here with your preferred integer
126 ************************************************************* 105 *************************************************************
127 Using the ``qiime2 diversity-lib bray-curtis`` tool: 106 Using the ``qiime2 diversity-lib bray-curtis`` tool:
128 #. Set *"table"* to ``#: feature-table.qza`` 107 #. Set *"table"* to ``#: feature-table.qza``
129 #. Expand the ``additional options`` section
130
131 - Leave *"n_jobs"* as its default value of ``1``
132
133 #. Press the ``Execute`` button. 108 #. Press the ``Execute`` button.
134 109
135 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 110 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
136 (Renaming is optional, but it will make any subsequent steps easier to complete.) 111 (Renaming is optional, but it will make any subsequent steps easier to complete.)
137 112
146 121
147 use 'auto' to run on all of host system's available CPU cores 122 use 'auto' to run on all of host system's available CPU cores
148 ************************************************************* 123 *************************************************************
149 Using the ``qiime2 diversity-lib bray-curtis`` tool: 124 Using the ``qiime2 diversity-lib bray-curtis`` tool:
150 #. Set *"table"* to ``#: feature-table.qza`` 125 #. Set *"table"* to ``#: feature-table.qza``
151 #. Expand the ``additional options`` section
152
153 - Set *"n_jobs"* to ``auto``
154
155 #. Press the ``Execute`` button. 126 #. Press the ``Execute`` button.
156 127
157 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 128 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
158 (Renaming is optional, but it will make any subsequent steps easier to complete.) 129 (Renaming is optional, but it will make any subsequent steps easier to complete.)
159 130