Mercurial > repos > q2d2 > qiime2__composition__add_pseudocount

annotate qiime2__composition__add_pseudocount.xml @ 5:e2822b9553cb draft default tip

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__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:36:09 +0000
parents cd98e4bb92ee
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
2 <!--
3
d6677599b512 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
3 Copyright (c) 2024, QIIME 2 development team.
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
4
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
6 -->
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
7 <!--
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
8 This tool was automatically generated by:
5
e2822b9553cb planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
9 q2galaxy (version: 2024.10.0)
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
10 for:
5
e2822b9553cb planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
11 qiime2 (version: 2024.10.1)
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
12 -->
5
e2822b9553cb planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
13 <tool name="qiime2 composition add-pseudocount" id="qiime2__composition__add_pseudocount" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
2
f92a9f40c7e1 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
14 <description>Add pseudocount to table.</description>
5
e2822b9553cb planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
15 <xrefs>
e2822b9553cb planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
16 <xref type="bio.tools">qiime2</xref>
e2822b9553cb planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
17 </xrefs>
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
18 <requirements>
5
e2822b9553cb planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
20 </requirements>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
21 <version_command>q2galaxy version composition</version_command>
1
c6780899249e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
22 <command detect_errors="exit_code">q2galaxy run composition add_pseudocount '$inputs'</command>
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
23 <configfiles>
3
d6677599b512 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
25 </configfiles>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
26 <inputs>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table to which pseudocounts should be added.">
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
28 <options options_filter_attribute="metadata.semantic_type">
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
29 <filter type="add_value" value="FeatureTable[Frequency]"/>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
30 </options>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
32 </param>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
34 <param name="pseudocount" type="integer" value="1" label="pseudocount: Int" help="[default: 1] The value to add to all counts in the feature table."/>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
35 </section>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
36 </inputs>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
37 <outputs>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
38 <data name="composition_table" format="qza" label="${tool.name} on ${on_string}: composition_table.qza" from_work_dir="composition_table.qza"/>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
39 </outputs>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
40 <tests/>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
41 <help>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
42 QIIME 2: composition add-pseudocount
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
43 ====================================
2
f92a9f40c7e1 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
44 Add pseudocount to table.
0
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
45
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
46
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
47 Outputs:
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
48 --------
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
49 :composition_table.qza: The resulting feature table.
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
50
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
51 |
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
52
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
53 Description:
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
54 ------------
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
55 Increment all counts in table by pseudocount.
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
56
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
57
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
58 |
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
59
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
60 </help>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
61 <citations>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
62 <citation type="doi">10.1038/s41587-019-0209-9</citation>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
63 </citations>
1ba5ca5ccc3e planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
64 </tool>