Mercurial > repos > q2d2 > qiime2__vsearch__dereplicate_sequences

annotate qiime2__vsearch__dereplicate_sequences.xml @ 5:d33fbe0e2c37 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__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:59:57 +0000
parents 9c9e6b7d7286
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
2 <!--
3
17d969b36de9 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
3 Copyright (c) 2024, QIIME 2 development team.
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
4
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
6 -->
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
7 <!--
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
8 This tool was automatically generated by:
5
d33fbe0e2c37 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
9 q2galaxy (version: 2024.10.0)
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
10 for:
5
d33fbe0e2c37 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
11 qiime2 (version: 2024.10.1)
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
12 -->
5
d33fbe0e2c37 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
13 <tool name="qiime2 vsearch dereplicate-sequences" id="qiime2__vsearch__dereplicate_sequences" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
14 <description>Dereplicate sequences.</description>
5
d33fbe0e2c37 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
15 <xrefs>
d33fbe0e2c37 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
16 <xref type="bio.tools">qiime2</xref>
d33fbe0e2c37 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
17 </xrefs>
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
18 <requirements>
5
d33fbe0e2c37 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 4
diff changeset
19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
20 </requirements>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
21 <version_command>q2galaxy version vsearch</version_command>
1
89cf98a14b38 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
22 <command detect_errors="exit_code">q2galaxy run vsearch dereplicate_sequences '$inputs'</command>
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
23 <configfiles>
3
17d969b36de9 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents: 2
diff changeset
24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
25 </configfiles>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
26 <inputs>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
27 <param name="sequences" type="data" format="qza" label="sequences: SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]" help="[required] The sequences to be dereplicated.">
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
28 <options options_filter_attribute="metadata.semantic_type">
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
29 <filter type="add_value" value="SampleData[Sequences]"/>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
30 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
31 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
32 </options>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
33 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality]', 'SampleData[Sequences]']</validator>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
34 </param>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
35 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
36 <param name="derep_prefix" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="derep_prefix: Bool" help="[default: No] Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant."/>
1
89cf98a14b38 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
37 <param name="min_seq_length" type="integer" min="1" value="1" label="min_seq_length: Int % Range(1, None)" help="[default: 1] Discard sequences shorter than this integer."/>
89cf98a14b38 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
38 <param name="min_unique_size" type="integer" min="1" value="1" label="min_unique_size: Int % Range(1, None)" help="[default: 1] Discard sequences with a post-dereplication abundance value smaller than integer."/>
0
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
39 </section>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
40 </inputs>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
41 <outputs>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
42 <data name="dereplicated_table" format="qza" label="${tool.name} on ${on_string}: dereplicated_table.qza" from_work_dir="dereplicated_table.qza"/>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
43 <data name="dereplicated_sequences" format="qza" label="${tool.name} on ${on_string}: dereplicated_sequences.qza" from_work_dir="dereplicated_sequences.qza"/>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
44 </outputs>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
45 <tests/>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
46 <help>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
47 QIIME 2: vsearch dereplicate-sequences
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
48 ======================================
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
49 Dereplicate sequences.
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
50
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
51
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
52 Outputs:
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
53 --------
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
54 :dereplicated_table.qza: The table of dereplicated sequences.
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
55 :dereplicated_sequences.qza: The dereplicated sequences.
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
56
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
57 |
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
58
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
59 Description:
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
60 ------------
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
61 Dereplicate sequence data and create a feature table and feature representative sequences. Feature identifiers in the resulting artifacts will be the sha1 hash of the sequence defining each feature. If clustering of features into OTUs is desired, the resulting artifacts can be passed to the cluster_features_* methods in this plugin.
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
62
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
63
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
64 |
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
65
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
66 </help>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
67 <citations>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
68 <citation type="doi">10.7717/peerj.2584</citation>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
69 <citation type="doi">10.1038/s41587-019-0209-9</citation>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
70 </citations>
29ceae287ad6 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
71 </tool>