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comparison qiime2__demux__emp_single.xml @ 1:335abb486193 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 22:43:21 +0000
parents 320c9af45b63
children 75b07a996ac0
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0:320c9af45b63 1:335abb486193
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 emp-single" id="qiime2__demux__emp_single" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 demux emp-single" id="qiime2__demux__emp_single" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Demultiplex sequence data generated with the EMP protocol.</description> 14 <description>Demultiplex sequence data generated with the EMP protocol.</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 emp_single '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run demux emp_single '$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="seqs" type="data" format="qza" label="seqs: RawSequences | EMPSingleEndSequences | EMPPairedEndSequences" help="[required] The single-end sequences to be demultiplexed."> 24 <param name="seqs" type="data" format="qza" label="seqs: RawSequences | EMPSingleEndSequences | EMPPairedEndSequences" help="[required] The single-end sequences to be demultiplexed.">
56 </inputs> 56 </inputs>
57 <outputs> 57 <outputs>
58 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> 58 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
59 <data name="error_correction_details" format="qza" label="${tool.name} on ${on_string}: error_correction_details.qza" from_work_dir="error_correction_details.qza"/> 59 <data name="error_correction_details" format="qza" label="${tool.name} on ${on_string}: error_correction_details.qza" from_work_dir="error_correction_details.qza"/>
60 </outputs> 60 </outputs>
61 <tests/> 61 <tests>
62 <test>
63 <param name="seqs" value="emp_single.test0.sequences.qza" ftype="qza"/>
64 <conditional name="barcodes">
65 <param name="type" value="tsv"/>
66 <param name="source" value="emp_single.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
67 <param name="column" value="2"/>
68 </conditional>
69 <output name="per_sample_sequences" 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: SampleData\[SequencesWithQuality\]"/>
73 </has_archive_member>
74 </assert_contents>
75 </output>
76 <output name="error_correction_details" 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: ErrorCorrectionDetails"/>
80 </has_archive_member>
81 </assert_contents>
82 </output>
83 </test>
84 </tests>
62 <help> 85 <help>
63 QIIME 2: demux emp-single 86 QIIME 2: demux emp-single
64 ========================= 87 =========================
65 Demultiplex sequence data generated with the EMP protocol. 88 Demultiplex sequence data generated with the EMP protocol.
66 89
74 97
75 Description: 98 Description:
76 ------------ 99 ------------
77 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data generated with the Earth Microbiome Project (EMP) amplicon sequencing protocol. Details about this protocol can be found at http://www.earthmicrobiome.org/protocols-and-standards/ 100 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data generated with the Earth Microbiome Project (EMP) amplicon sequencing protocol. Details about this protocol can be found at http://www.earthmicrobiome.org/protocols-and-standards/
78 101
102 Examples:
103 ---------
104
105 demux
106 *****
107 Using the ``qiime2 demux emp-single`` tool:
108 #. Set *"seqs"* to ``#: sequences.qza``
109 #. For *"barcodes"*:
110
111 #. Leave as ``Metadata from TSV``
112 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
113 #. Set *"Column Name"* to ``barcode-sequence``
114
115 #. Press the ``Execute`` button.
116
117 Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:
118 (Renaming is optional, but it will make any subsequent steps easier to complete.)
119
120 .. list-table::
121 :align: left
122 :header-rows: 1
123
124 * - History Name
125 - *"Name"* to set (be sure to press ``Save``)
126 * - ``#: qiime2 demux emp-single [...] : per_sample_sequences.qza``
127 - ``demux.qza``
128 * - ``#: qiime2 demux emp-single [...] : error_correction_details.qza``
129 - ``demux-details.qza``
130
79 131
80 | 132 |
81 133
82 </help> 134 </help>
83 <citations> 135 <citations>