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comparison qiime2__dada2__denoise_paired.xml @ 1:bbaba1707475 draft

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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 22:42:24 +0000
parents 4218e3146518
children 06bacd08bb47
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0:4218e3146518 1:bbaba1707475
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-paired" id="qiime2__dada2__denoise_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Denoise and dereplicate paired-end sequences</description> 14 <description>Denoise and dereplicate paired-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_paired '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run dada2 denoise_paired '$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[PairedEndSequencesWithQuality]" help="[required] The paired-end demultiplexed sequences to be denoised."> 24 <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[PairedEndSequencesWithQuality]" help="[required] The paired-end demultiplexed sequences to be denoised.">
55 <outputs> 55 <outputs>
56 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/> 56 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
57 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/> 57 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
58 <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/> 58 <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/>
59 </outputs> 59 </outputs>
60 <tests/> 60 <tests>
61 <test>
62 <param name="demultiplexed_seqs" value="denoise_paired.test0.demux-paired.qza" ftype="qza"/>
63 <param name="trunc_len_f" value="150"/>
64 <param name="trunc_len_r" value="140"/>
65 <output name="representative_sequences" ftype="qza">
66 <assert_contents>
67 <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">
68 <has_line_matching expression="type: FeatureData\[Sequence\]"/>
69 </has_archive_member>
70 </assert_contents>
71 </output>
72 <output name="table" ftype="qza">
73 <assert_contents>
74 <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">
75 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
76 </has_archive_member>
77 </assert_contents>
78 </output>
79 <output name="denoising_stats" ftype="qza">
80 <assert_contents>
81 <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">
82 <has_line_matching expression="type: SampleData\[DADA2Stats\]"/>
83 </has_archive_member>
84 </assert_contents>
85 </output>
86 </test>
87 </tests>
61 <help> 88 <help>
62 QIIME 2: dada2 denoise-paired 89 QIIME 2: dada2 denoise-paired
63 ============================= 90 =============================
64 Denoise and dereplicate paired-end sequences 91 Denoise and dereplicate paired-end sequences
65 92
74 101
75 Description: 102 Description:
76 ------------ 103 ------------
77 This method denoises paired-end sequences, dereplicates them, and filters chimeras. 104 This method denoises paired-end sequences, dereplicates them, and filters chimeras.
78 105
106 Examples:
107 ---------
108
109 denoise_paired
110 **************
111 Using the ``qiime2 dada2 denoise-paired`` tool:
112 #. Set *"demultiplexed_seqs"* to ``#: demux-paired.qza``
113 #. Set *"trunc_len_f"* to ``150``
114 #. Set *"trunc_len_r"* to ``140``
115 #. Press the ``Execute`` button.
116
117
79 118
80 | 119 |
81 120
82 </help> 121 </help>
83 <citations> 122 <citations>