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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:42:40 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2022, QIIME 2 development team.
4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 -->
7 <!--
8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1)
10 for:
11 qiime2 (version: 2022.8.1)
12 -->
13 <tool name="qiime2 diversity-lib observed-features" id="qiime2__diversity_lib__observed_features" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Observed Features</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version diversity_lib</version_command>
19 <command detect_errors="aggressive">q2galaxy run diversity_lib observed_features '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
28 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
29 </options>
30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
31 </param>
32 </inputs>
33 <outputs>
34 <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
35 </outputs>
36 <tests>
37 <test>
38 <param name="table" value="observed_features.test0.feature-table.qza" ftype="qza"/>
39 <output name="vector" ftype="qza">
40 <assert_contents>
41 <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">
42 <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
43 </has_archive_member>
44 <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}\/data\/alpha-diversity.tsv">
45 <has_line_matching expression="S1&#9;1"/>
46 <has_line_matching expression="S2&#9;1"/>
47 <has_line_matching expression="S3&#9;2"/>
48 <has_line_matching expression="S4&#9;2"/>
49 <has_line_matching expression="S5&#9;3"/>
50 </has_archive_member>
51 </assert_contents>
52 </output>
53 </test>
54 </tests>
55 <help>
56 QIIME 2: diversity-lib observed-features
57 ========================================
58 Observed Features
59
60
61 Outputs:
62 --------
63 :vector.qza: Vector containing per-sample counts of observed features.
64
65 |
66
67 Description:
68 ------------
69 Compute the number of observed features for each sample in a feature table
70
71 Examples:
72 ---------
73
74 basic
75 *****
76 Using the ``qiime2 diversity-lib observed-features`` tool:
77 #. Set *"table"* to ``#: feature-table.qza``
78 #. Press the ``Execute`` button.
79
80 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
81 (Renaming is optional, but it will make any subsequent steps easier to complete.)
82
83 .. list-table::
84 :align: left
85 :header-rows: 1
86
87 * - History Name
88 - *"Name"* to set (be sure to press ``Save``)
89 * - ``#: qiime2 diversity-lib observed-features [...] : vector.qza``
90 - ``obs-feat-vector.qza``
91
92
93 |
94
95 </help>
96 <citations>
97 <citation type="doi">10.1038/s41587-019-0209-9</citation>
98 </citations>
99 </tool>