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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:25:20 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2022, QIIME 2 development team.
4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 -->
7 <!--
8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1)
10 for:
11 qiime2 (version: 2022.8.1)
12 -->
13 <tool name="qiime2 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Deblur sequences using a 16S positive filter.</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version deblur</version_command>
19 <command detect_errors="aggressive">q2galaxy run deblur denoise_16S '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be denoised.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
27 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
28 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
29 </options>
30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
31 </param>
32 <param name="trim_length" type="integer" value="" label="trim_length: Int" help="[required] Sequence trim length, specify -1 to disable trimming."/>
33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
34 <param name="left_trim_len" type="integer" min="0" value="0" label="left_trim_len: Int % Range(0, None)" help="[default: 0] Sequence trimming from the 5' end. A value of 0 will disable this trim."/>
35 <param name="sample_stats" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="sample_stats: Bool" help="[default: No] If true, gather stats per sample."/>
36 <param name="mean_error" type="float" value="0.005" label="mean_error: Float" help="[default: 0.005] The mean per nucleotide error, used for original sequence estimate."/>
37 <param name="indel_prob" type="float" value="0.01" label="indel_prob: Float" help="[default: 0.01] Insertion/deletion (indel) probability (same for N indels)."/>
38 <param name="indel_max" type="integer" value="3" label="indel_max: Int" help="[default: 3] Maximum number of insertion/deletions."/>
39 <param name="min_reads" type="integer" value="10" label="min_reads: Int" help="[default: 10] Retain only features appearing at least min_reads times across all samples in the resulting feature table."/>
40 <param name="min_size" type="integer" value="2" label="min_size: Int" help="[default: 2] In each sample, discard all features with an abundance less than min_size."/>
41 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start: Int" help="[default: 1] Number of jobs to start (if to run in parallel)."/>
42 <param name="hashed_feature_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="hashed_feature_ids: Bool" help="[default: Yes] If true, hash the feature IDs."/>
43 </section>
44 </inputs>
45 <outputs>
46 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
47 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
48 <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/>
49 </outputs>
50 <tests/>
51 <help>
52 QIIME 2: deblur denoise-16S
53 ===========================
54 Deblur sequences using a 16S positive filter.
55
56
57 Outputs:
58 --------
59 :table.qza: The resulting denoised feature table.
60 :representative_sequences.qza: The resulting feature sequences.
61 :stats.qza: Per-sample stats if requested.
62
63 |
64
65 Description:
66 ------------
67 Perform sequence quality control for Illumina data using the Deblur workflow with a 16S reference as a positive filter. Only forward reads are supported at this time. The specific reference used is the 88% OTUs from Greengenes 13_8. This mode of operation should only be used when data were generated from a 16S amplicon protocol on an Illumina platform. The reference is only used to assess whether each sequence is likely to be 16S by a local alignment using SortMeRNA with a permissive e-value; the reference is not used to characterize the sequences.
68
69
70 |
71
72 </help>
73 <citations>
74 <citation type="bibtex">@article{cite1,
75 author = {Amir, Amnon and McDonald, Daniel and Navas-Molina, Jose A and Kopylova, Evguenia and Morton, James T and Xu, Zhenjiang Zech and Kightley, Eric P and Thompson, Luke R and Hyde, Embriette R and Gonzalez, Antonio and Knight, Rob},
76 journal = {MSystems},
77 number = {2},
78 pages = {e00191--16},
79 publisher = {Am Soc Microbiol},
80 title = {Deblur rapidly resolves single-nucleotide community sequence patterns},
81 volume = {2},
82 year = {2017}
83 }
84 </citation>
85 <citation type="doi">10.1038/s41587-019-0209-9</citation>
86 </citations>
87 </tool>