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comparison qiime2__diversity_lib__jaccard.xml @ 3:760b9ecc9575 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 21:02:20 +0000
parents cf5fc36069f5
children a80fde700012
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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 jaccard" id="qiime2__diversity_lib__jaccard" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 diversity-lib jaccard" id="qiime2__diversity_lib__jaccard" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Jaccard Distance</description> 14 <description>Jaccard Distance</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 jaccard '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run diversity_lib jaccard '$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 Jaccard distance 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 Jaccard distance 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]"/>
27 <filter type="add_value" value="FeatureTable[Frequency]"/> 27 <filter type="add_value" value="FeatureTable[Frequency]"/>
28 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> 28 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
29 </options> 29 </options>
30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> 30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
31 </param> 31 </param>
32 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
33 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
34 <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.">
35 <option value="auto">auto (Str)</option>
36 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
37 </param>
38 <when value="auto">
39 <param name="n_jobs" type="hidden" value="auto"/>
40 </when>
41 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
42 <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."/>
43 </when>
44 </conditional>
45 </section>
46 </inputs> 32 </inputs>
47 <outputs> 33 <outputs>
48 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> 34 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
49 </outputs> 35 </outputs>
50 <tests> 36 <tests>
58 </assert_contents> 44 </assert_contents>
59 </output> 45 </output>
60 </test> 46 </test>
61 <test> 47 <test>
62 <param name="table" value="jaccard.test1.feature-table.qza" ftype="qza"/> 48 <param name="table" value="jaccard.test1.feature-table.qza" ftype="qza"/>
63 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
64 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
65 <param name="n_jobs" value="1"/>
66 </conditional>
67 <output name="distance_matrix" ftype="qza"> 49 <output name="distance_matrix" ftype="qza">
68 <assert_contents> 50 <assert_contents>
69 <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"> 51 <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">
70 <has_line_matching expression="type: DistanceMatrix"/> 52 <has_line_matching expression="type: DistanceMatrix"/>
71 </has_archive_member> 53 </has_archive_member>
72 </assert_contents> 54 </assert_contents>
73 </output> 55 </output>
74 </test> 56 </test>
75 <test> 57 <test>
76 <param name="table" value="jaccard.test2.feature-table.qza" ftype="qza"/> 58 <param name="table" value="jaccard.test2.feature-table.qza" ftype="qza"/>
77 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
78 <param name="__q2galaxy__GUI__select__" value="auto"/>
79 <param name="n_jobs" value="auto"/>
80 </conditional>
81 <output name="distance_matrix" ftype="qza"> 59 <output name="distance_matrix" ftype="qza">
82 <assert_contents> 60 <assert_contents>
83 <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"> 61 <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">
84 <has_line_matching expression="type: DistanceMatrix"/> 62 <has_line_matching expression="type: DistanceMatrix"/>
85 </has_archive_member> 63 </has_archive_member>
126 104
127 to run on n cores, replace 1 here with your preferred integer 105 to run on n cores, replace 1 here with your preferred integer
128 ************************************************************* 106 *************************************************************
129 Using the ``qiime2 diversity-lib jaccard`` tool: 107 Using the ``qiime2 diversity-lib jaccard`` tool:
130 #. Set *"table"* to ``#: feature-table.qza`` 108 #. Set *"table"* to ``#: feature-table.qza``
131 #. Expand the ``additional options`` section
132
133 - Leave *"n_jobs"* as its default value of ``1``
134
135 #. Press the ``Execute`` button. 109 #. Press the ``Execute`` button.
136 110
137 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 111 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
138 (Renaming is optional, but it will make any subsequent steps easier to complete.) 112 (Renaming is optional, but it will make any subsequent steps easier to complete.)
139 113
148 122
149 use 'auto' to run on all of host system's available CPU cores 123 use 'auto' to run on all of host system's available CPU cores
150 ************************************************************* 124 *************************************************************
151 Using the ``qiime2 diversity-lib jaccard`` tool: 125 Using the ``qiime2 diversity-lib jaccard`` tool:
152 #. Set *"table"* to ``#: feature-table.qza`` 126 #. Set *"table"* to ``#: feature-table.qza``
153 #. Expand the ``additional options`` section
154
155 - Set *"n_jobs"* to ``auto``
156
157 #. Press the ``Execute`` button. 127 #. Press the ``Execute`` button.
158 128
159 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 129 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
160 (Renaming is optional, but it will make any subsequent steps easier to complete.) 130 (Renaming is optional, but it will make any subsequent steps easier to complete.)
161 131