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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:42:34 +0000
parents 0cba463cfb72
children b883cbea5623
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0:0cba463cfb72 1:2572fc0f88f2
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 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Deblur sequences using a 16S positive filter.</description> 14 <description>Deblur sequences using a 16S positive filter.</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 deblur</version_command> 18 <version_command>q2galaxy version deblur</version_command>
19 <command detect_errors="aggressive">q2galaxy run deblur denoise_16S '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run deblur denoise_16S '$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 | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be denoised."> 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"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> 27 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
27 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> 28 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
28 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
29 </options> 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> 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> 31 </param>
32 <param name="trim_length" type="integer" value="" label="trim_length: Int" help="[required] Sequence trim length, specify -1 to disable trimming."/> 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"> 33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
45 <outputs> 45 <outputs>
46 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/> 46 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
47 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/> 47 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
48 <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/> 48 <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/>
49 </outputs> 49 </outputs>
50 <tests/> 50 <tests>
51 <test>
52 <param name="demultiplexed_seqs" value="denoise_16S.test0.demux-filtered.qza" ftype="qza"/>
53 <param name="trim_length" value="120"/>
54 <param name="sample_stats" value="__q2galaxy__::literal::True"/>
55 <output name="representative_sequences" ftype="qza">
56 <assert_contents>
57 <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">
58 <has_line_matching expression="type: FeatureData\[Sequence\]"/>
59 </has_archive_member>
60 </assert_contents>
61 </output>
62 <output name="table" 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: FeatureTable\[Frequency\]"/>
66 </has_archive_member>
67 </assert_contents>
68 </output>
69 <output name="stats" 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: DeblurStats"/>
73 </has_archive_member>
74 </assert_contents>
75 </output>
76 </test>
77 </tests>
51 <help> 78 <help>
52 QIIME 2: deblur denoise-16S 79 QIIME 2: deblur denoise-16S
53 =========================== 80 ===========================
54 Deblur sequences using a 16S positive filter. 81 Deblur sequences using a 16S positive filter.
55 82
63 | 90 |
64 91
65 Description: 92 Description:
66 ------------ 93 ------------
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. 94 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.
95
96 Examples:
97 ---------
98
99 denoise_16S
100 ***********
101 Using the ``qiime2 deblur denoise-16S`` tool:
102 #. Set *"demultiplexed_seqs"* to ``#: demux-filtered.qza``
103 #. Set *"trim_length"* to ``120``
104 #. Expand the ``additional options`` section
105
106 - Set *"sample_stats"* to ``Yes``
107
108 #. Press the ``Execute`` button.
109
110 Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:
111 (Renaming is optional, but it will make any subsequent steps easier to complete.)
112
113 .. list-table::
114 :align: left
115 :header-rows: 1
116
117 * - History Name
118 - *"Name"* to set (be sure to press ``Save``)
119 * - ``#: qiime2 deblur denoise-16S [...] : table.qza``
120 - ``table.qza``
121 * - ``#: qiime2 deblur denoise-16S [...] : representative_sequences.qza``
122 - ``representative-sequences.qza``
123 * - ``#: qiime2 deblur denoise-16S [...] : stats.qza``
124 - ``denoising-stats.qza``
68 125
69 126
70 | 127 |
71 128
72 </help> 129 </help>