Mercurial > repos > q2d2 > qiime2__deblur__denoise_other

comparison qiime2__deblur__denoise_other.xml @ 0:574ab3a299a9 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__deblur commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:25:44 +0000
parents
children 86e36a2b44b0
comparison
equal deleted inserted replaced
-1:000000000000 0:574ab3a299a9
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-other" id="qiime2__deblur__denoise_other" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Deblur sequences using a user-specified 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_other '$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="reference_seqs" type="data" format="qza" label="reference_seqs: FeatureData[Sequence]" help="[required] Positive filtering database. Keep all sequences aligning to these sequences.">
33 <options options_filter_attribute="metadata.semantic_type">
34 <filter type="add_value" value="FeatureData[Sequence]"/>
35 </options>
36 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
37 </param>
38 <param name="trim_length" type="integer" value="" label="trim_length: Int" help="[required] Sequence trim length, specify -1 to disable trimming."/>
39 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
40 <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."/>
41 <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."/>
42 <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."/>
43 <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)."/>
44 <param name="indel_max" type="integer" value="3" label="indel_max: Int" help="[default: 3] Maximum number of insertion/deletions."/>
45 <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."/>
46 <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."/>
47 <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)."/>
48 <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."/>
49 </section>
50 </inputs>
51 <outputs>
52 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
53 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
54 <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/>
55 </outputs>
56 <tests/>
57 <help>
58 QIIME 2: deblur denoise-other
59 =============================
60 Deblur sequences using a user-specified positive filter.
61
62
63 Outputs:
64 --------
65 :table.qza: The resulting denoised feature table.
66 :representative_sequences.qza: The resulting feature sequences.
67 :stats.qza: Per-sample stats if requested.
68
69 |
70
71 Description:
72 ------------
73 Perform sequence quality control for Illumina data using the Deblur workflow, including positive alignment-based filtering. Only forward reads are supported at this time. This mode of execution is particularly useful when operating on non-16S data. For example, to apply Deblur to 18S data, you would want to specify a reference composed of 18S sequences in order to filter out sequences which do not appear to be 18S. The assessment is performed by local alignment using SortMeRNA with a permissive e-value threshold.
74
75
76 |
77
78 </help>
79 <citations>
80 <citation type="bibtex">@article{cite1,
81 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},
82 journal = {MSystems},
83 number = {2},
84 pages = {e00191--16},
85 publisher = {Am Soc Microbiol},
86 title = {Deblur rapidly resolves single-nucleotide community sequence patterns},
87 volume = {2},
88 year = {2017}
89 }
90 </citation>
91 <citation type="doi">10.1038/s41587-019-0209-9</citation>
92 </citations>
93 </tool>