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comparison qiime2__demux__summarize.xml @ 1:222b50c1cb52 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:43:10 +0000
parents 3e85de166340
children d8a9f74f1a6d
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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 demux summarize" id="qiime2__demux__summarize" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 demux summarize" id="qiime2__demux__summarize" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Summarize counts per sample.</description> 14 <description>Summarize counts per sample.</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 demux</version_command> 18 <version_command>q2galaxy version demux</version_command>
19 <command detect_errors="aggressive">q2galaxy run demux summarize '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run demux summarize '$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="data" type="data" format="qza" label="data: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be summarized."> 24 <param name="data" type="data" format="qza" label="data: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be summarized.">
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[JoinedSequencesWithQuality]"/> 27 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
27 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> 28 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
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 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 32 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
33 <param name="n" type="integer" value="10000" label="n: Int" help="[default: 10000] The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences."/> 33 <param name="n" type="integer" value="10000" label="n: Int" help="[default: 10000] The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences."/>
34 </section> 34 </section>
35 </inputs> 35 </inputs>
36 <outputs> 36 <outputs>
37 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> 37 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
38 </outputs> 38 </outputs>
39 <tests/> 39 <tests>
40 <test>
41 <param name="data" value="summarize.test0.demux.qza" ftype="qza"/>
42 <output name="visualization" ftype="qzv">
43 <assert_contents>
44 <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">
45 <has_line_matching expression="type: Visualization"/>
46 </has_archive_member>
47 </assert_contents>
48 </output>
49 </test>
50 </tests>
40 <help> 51 <help>
41 QIIME 2: demux summarize 52 QIIME 2: demux summarize
42 ======================== 53 ========================
43 Summarize counts per sample. 54 Summarize counts per sample.
44 55
51 62
52 Description: 63 Description:
53 ------------ 64 ------------
54 Summarize counts per sample for all samples, and generate interactive positional quality plots based on `n` randomly selected sequences. 65 Summarize counts per sample for all samples, and generate interactive positional quality plots based on `n` randomly selected sequences.
55 66
67 Examples:
68 ---------
69
70 demux
71 *****
72 Using the ``qiime2 demux summarize`` tool:
73 #. Set *"data"* to ``#: demux.qza``
74 #. Press the ``Execute`` button.
75
76
56 77
57 | 78 |
58 79
59 </help> 80 </help>
60 <citations> 81 <citations>