Mercurial > repos > q2d2 > qiime2__diversity__alpha_correlation

annotate qiime2__diversity__alpha_correlation.xml @ 1:9235f6a16926 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:44:49 +0000
parents 4a62b47071f5
children 5850f79a2b9f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
2 <!--
1
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
3 Copyright (c) 2023, QIIME 2 development team.
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
4
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
6 -->
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
7 <!--
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
8 This tool was automatically generated by:
1
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
9 q2galaxy (version: 2022.11.1)
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
10 for:
1
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
11 qiime2 (version: 2022.11.1)
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
12 -->
1
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
13 <tool name="qiime2 diversity alpha-correlation" id="qiime2__diversity__alpha_correlation" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
14 <description>Alpha diversity correlation</description>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
15 <requirements>
1
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
16 <container type="docker">quay.io/qiime2/core:2022.11</container>
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
17 </requirements>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
18 <version_command>q2galaxy version diversity</version_command>
1
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
19 <command detect_errors="exit_code">q2galaxy run diversity alpha_correlation '$inputs'</command>
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
20 <configfiles>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
21 <inputs name="inputs" data_style="paths"/>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
22 </configfiles>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
23 <inputs>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
24 <param name="alpha_diversity" type="data" format="qza" label="alpha_diversity: SampleData[AlphaDiversity]" help="[required] Vector of alpha diversity values by sample.">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
25 <options options_filter_attribute="metadata.semantic_type">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
26 <filter type="add_value" value="SampleData[AlphaDiversity]"/>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
27 </options>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]']</validator>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
29 </param>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
30 <repeat name="metadata" min="1" help="[required] The sample metadata." title="metadata: Metadata">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
31 <conditional name="__q2galaxy__GUI__conditional__metadata__">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
32 <param name="type" type="select" label="metadata: Metadata">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
33 <option value="tsv" selected="true">Metadata from TSV</option>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
34 <option value="qza">Metadata from Artifact</option>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
35 </param>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
36 <when value="tsv">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
37 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
38 </when>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
39 <when value="qza">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
40 <param name="source" type="data" format="qza" label="Metadata Source"/>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
41 </when>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
42 </conditional>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
43 </repeat>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
45 <param name="method" type="select" label="method: Str % Choices('spearman', 'pearson')" display="radio">
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
46 <option value="spearman" selected="true">spearman</option>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
47 <option value="pearson">pearson</option>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
48 </param>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
49 <param name="intersect_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="intersect_ids: Bool" help="[default: No] If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs."/>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
50 </section>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
51 </inputs>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
52 <outputs>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
53 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
54 </outputs>
1
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
55 <tests>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
56 <test>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
57 <param name="alpha_diversity" value="alpha_correlation.test0.alpha-div-faith-pd.qza" ftype="qza"/>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
58 <repeat name="metadata">
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
59 <conditional name="__q2galaxy__GUI__conditional__metadata__">
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
60 <param name="type" value="tsv"/>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
61 <param name="source" value="alpha_correlation.test0.metadata.tsv" ftype="qiime2.tabular"/>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
62 </conditional>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
63 </repeat>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
64 <output name="visualization" ftype="qzv">
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
65 <assert_contents>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
66 <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">
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
67 <has_line_matching expression="type: Visualization"/>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
68 </has_archive_member>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
69 </assert_contents>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
70 </output>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
71 </test>
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
72 </tests>
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
73 <help>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
74 QIIME 2: diversity alpha-correlation
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
75 ====================================
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
76 Alpha diversity correlation
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
77
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
78
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
79 Outputs:
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
80 --------
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
81 :visualization.qzv: &lt;no description&gt;
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
82
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
83 |
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
84
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
85 Description:
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
86 ------------
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
87 Determine whether numeric sample metadata columns are correlated with alpha diversity.
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
88
1
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
89 Examples:
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
90 ---------
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
91
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
92 alpha_correlation_faith_pd
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
93 **************************
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
94 Using the ``qiime2 diversity alpha-correlation`` tool:
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
95 #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza``
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
96 #. For *"metadata"*:
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
97
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
98 - Perform the following steps.
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
99
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
100 #. Leave as ``Metadata from TSV``
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
101 #. Set *"Metadata Source"* to ``metadata.tsv``
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
102
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
103
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
104 #. Press the ``Execute`` button.
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
105
9235f6a16926 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
106
0
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
107
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
108 |
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
109
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
110 </help>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
111 <citations>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
112 <citation type="doi">https://doi.org/10.1098/rspl.1895.0041</citation>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
113 <citation type="doi">https://doi.org/10.2307/1422689</citation>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
114 <citation type="doi">10.1038/s41587-019-0209-9</citation>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
115 </citations>
4a62b47071f5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
116 </tool>