Mercurial > repos > q2d2 > qiime2__diversity_lib__bray_curtis

annotate qiime2__diversity_lib__bray_curtis.xml @ 4:4111b5b17fd4 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_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
author q2d2
date Mon, 03 Jun 2024 23:20:24 +0000
parents 6e6d848f2b5b
children 84b38b24a50e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
2 <!--
3
6e6d848f2b5b planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
3 Copyright (c) 2024, QIIME 2 development team.
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
4
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
6 -->
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
7 <!--
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
8 This tool was automatically generated by:
4
4111b5b17fd4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
q2d2
parents: 3
diff changeset
9 q2galaxy (version: 2024.5.0)
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
10 for:
4
4111b5b17fd4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
q2d2
parents: 3
diff changeset
11 qiime2 (version: 2024.5.0)
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
12 -->
4
4111b5b17fd4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
q2d2
parents: 3
diff changeset
13 <tool name="qiime2 diversity-lib bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
14 <description>Bray-Curtis Dissimilarity</description>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
15 <requirements>
4
4111b5b17fd4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
q2d2
parents: 3
diff changeset
16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
17 </requirements>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
18 <version_command>q2galaxy version diversity_lib</version_command>
1
b007e2c3c08b planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
19 <command detect_errors="exit_code">q2galaxy run diversity_lib bray_curtis '$inputs'</command>
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
20 <configfiles>
3
6e6d848f2b5b planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
22 </configfiles>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
23 <inputs>
3
6e6d848f2b5b planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
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.">
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
25 <options options_filter_attribute="metadata.semantic_type">
3
6e6d848f2b5b planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
27 <filter type="add_value" value="FeatureTable[Frequency]"/>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
28 </options>
3
6e6d848f2b5b planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
0
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
30 </param>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
31 </inputs>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
32 <outputs>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
33 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
34 </outputs>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
35 <tests>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
36 <test>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
37 <param name="table" value="bray_curtis.test0.feature-table.qza" ftype="qza"/>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
38 <output name="distance_matrix" ftype="qza">
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
39 <assert_contents>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
40 <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">
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
41 <has_line_matching expression="type: DistanceMatrix"/>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
42 </has_archive_member>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
43 </assert_contents>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
44 </output>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
45 </test>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
46 <test>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
47 <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
48 <output name="distance_matrix" ftype="qza">
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
49 <assert_contents>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
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">
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
51 <has_line_matching expression="type: DistanceMatrix"/>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
52 </has_archive_member>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
53 </assert_contents>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
54 </output>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
55 </test>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
56 <test>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
57 <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
58 <output name="distance_matrix" ftype="qza">
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
59 <assert_contents>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
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">
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
61 <has_line_matching expression="type: DistanceMatrix"/>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
62 </has_archive_member>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
63 </assert_contents>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
64 </output>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
65 </test>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
66 </tests>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
67 <help>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
68 QIIME 2: diversity-lib bray-curtis
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
69 ==================================
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
70 Bray-Curtis Dissimilarity
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
71
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
72
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
73 Outputs:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
74 --------
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
75 :distance_matrix.qza: Distance matrix for Bray-Curtis dissimilarity
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
76
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
77 |
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
78
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
79 Description:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
80 ------------
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
81 Compute Bray-Curtis dissimilarity for each sample in a feature table. Note: Frequency and relative frequency data produce different results unless overall sample sizes are identical. Please consider the impact on your results if you use Bray-Curtis with count data that has not been adjusted (normalized).
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
82
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
83 Examples:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
84 ---------
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
85
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
86 run on one core (by default)
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
87 ****************************
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
88 Using the ``qiime2 diversity-lib bray-curtis`` tool:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
89 #. Set *"table"* to ``#: feature-table.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
90 #. Press the ``Execute`` button.
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
91
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
92 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
93 (Renaming is optional, but it will make any subsequent steps easier to complete.)
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
94
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
95 .. list-table::
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
96 :align: left
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
97 :header-rows: 1
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
98
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
99 * - History Name
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
100 - *"Name"* to set (be sure to press ``Save``)
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
101 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
102 - ``bray-curtis-dm.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
103
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
104 to run on n cores, replace 1 here with your preferred integer
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
105 *************************************************************
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
106 Using the ``qiime2 diversity-lib bray-curtis`` tool:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
107 #. Set *"table"* to ``#: feature-table.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
108 #. Press the ``Execute`` button.
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
109
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
110 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
111 (Renaming is optional, but it will make any subsequent steps easier to complete.)
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
112
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
113 .. list-table::
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
114 :align: left
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
115 :header-rows: 1
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
116
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
117 * - History Name
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
118 - *"Name"* to set (be sure to press ``Save``)
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
119 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
120 - ``bray-curtis-dm.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
121
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
122 use 'auto' to run on all of host system's available CPU cores
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
123 *************************************************************
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
124 Using the ``qiime2 diversity-lib bray-curtis`` tool:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
125 #. Set *"table"* to ``#: feature-table.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
126 #. Press the ``Execute`` button.
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
127
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
128 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
129 (Renaming is optional, but it will make any subsequent steps easier to complete.)
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
130
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
131 .. list-table::
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
132 :align: left
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
133 :header-rows: 1
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
134
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
135 * - History Name
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
136 - *"Name"* to set (be sure to press ``Save``)
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
137 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
138 - ``bray-curtis-dm.qza``
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
139
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
140
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
141 |
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
142
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
143 </help>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
144 <citations>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
145 <citation type="bibtex">@article{cite1,
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
146 author = {Sørensen, Thorvald},
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
147 journal = {Biol. Skr.},
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
148 pages = {1--34},
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
149 title = {A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons},
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
150 volume = {5},
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
151 year = {1948}
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
152 }
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
153 </citation>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
154 <citation type="doi">10.1038/s41587-019-0209-9</citation>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
155 </citations>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
156 </tool>