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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:42:17 +0000
parents dba6cccafa22
children e7812ca89033
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0:dba6cccafa22 1:3c8340e400df
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2022, QIIME 2 development team. 3 Copyright (c) 2023, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1) 9 q2galaxy (version: 2022.11.1)
10 for: 10 for:
11 qiime2 (version: 2022.8.1) 11 qiime2 (version: 2022.11.1)
12 --> 12 -->
13 <tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Denoise and dereplicate single-end sequences</description> 14 <description>Denoise and dereplicate single-end sequences</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container> 16 <container type="docker">quay.io/qiime2/core:2022.11</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version dada2</version_command> 18 <version_command>q2galaxy version dada2</version_command>
19 <command detect_errors="aggressive">q2galaxy run dada2 denoise_single '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run dada2 denoise_single '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="paths"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required] The single-end demultiplexed sequences to be denoised."> 24 <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required] The single-end demultiplexed sequences to be denoised.">
52 <outputs> 52 <outputs>
53 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/> 53 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
54 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/> 54 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
55 <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/> 55 <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/>
56 </outputs> 56 </outputs>
57 <tests/> 57 <tests>
58 <test>
59 <param name="demultiplexed_seqs" value="denoise_single.test0.demux-single.qza" ftype="qza"/>
60 <param name="trunc_len" value="120"/>
61 <param name="trim_left" value="0"/>
62 <output name="representative_sequences" ftype="qza">
63 <assert_contents>
64 <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">
65 <has_line_matching expression="type: FeatureData\[Sequence\]"/>
66 </has_archive_member>
67 </assert_contents>
68 </output>
69 <output name="table" ftype="qza">
70 <assert_contents>
71 <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">
72 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
73 </has_archive_member>
74 </assert_contents>
75 </output>
76 <output name="denoising_stats" ftype="qza">
77 <assert_contents>
78 <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">
79 <has_line_matching expression="type: SampleData\[DADA2Stats\]"/>
80 </has_archive_member>
81 </assert_contents>
82 </output>
83 </test>
84 </tests>
58 <help> 85 <help>
59 QIIME 2: dada2 denoise-single 86 QIIME 2: dada2 denoise-single
60 ============================= 87 =============================
61 Denoise and dereplicate single-end sequences 88 Denoise and dereplicate single-end sequences
62 89
71 98
72 Description: 99 Description:
73 ------------ 100 ------------
74 This method denoises single-end sequences, dereplicates them, and filters chimeras. 101 This method denoises single-end sequences, dereplicates them, and filters chimeras.
75 102
103 Examples:
104 ---------
105
106 denoise_single
107 **************
108 Using the ``qiime2 dada2 denoise-single`` tool:
109 #. Set *"demultiplexed_seqs"* to ``#: demux-single.qza``
110 #. Set *"trunc_len"* to ``120``
111 #. Expand the ``additional options`` section
112
113 - Leave *"trim_left"* as its default value of ``0``
114
115 #. Press the ``Execute`` button.
116
117
76 118
77 | 119 |
78 120
79 </help> 121 </help>
80 <citations> 122 <citations>