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comparison qiime2__cutadapt__demux_paired.xml @ 1:d58b93d0a723 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:41:52 +0000
parents f003ba94e4fe
children c6a8822e19f2
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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 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Demultiplex paired-end sequence data with barcodes in-sequence.</description> 14 <description>Demultiplex paired-end sequence data with barcodes in-sequence.</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 cutadapt</version_command> 18 <version_command>q2galaxy version cutadapt</version_command>
19 <command detect_errors="aggressive">q2galaxy run cutadapt demux_paired '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run cutadapt demux_paired '$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="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required] The paired-end sequences to be demultiplexed."> 24 <param name="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required] The paired-end sequences to be demultiplexed.">
75 </inputs> 75 </inputs>
76 <outputs> 76 <outputs>
77 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> 77 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
78 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/> 78 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/>
79 </outputs> 79 </outputs>
80 <tests/> 80 <tests>
81 <test>
82 <param name="seqs" value="demux_paired.test0.seqs.qza" ftype="qza"/>
83 <conditional name="forward_barcodes">
84 <param name="type" value="tsv"/>
85 <param name="source" value="demux_paired.test0.md.tsv" ftype="qiime2.tabular"/>
86 <param name="column" value="2"/>
87 </conditional>
88 <output name="per_sample_sequences" ftype="qza">
89 <assert_contents>
90 <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">
91 <has_line_matching expression="type: SampleData\[PairedEndSequencesWithQuality\]"/>
92 </has_archive_member>
93 </assert_contents>
94 </output>
95 <output name="untrimmed_sequences" ftype="qza">
96 <assert_contents>
97 <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">
98 <has_line_matching expression="type: MultiplexedPairedEndBarcodeInSequence"/>
99 </has_archive_member>
100 </assert_contents>
101 </output>
102 </test>
103 </tests>
81 <help> 104 <help>
82 QIIME 2: cutadapt demux-paired 105 QIIME 2: cutadapt demux-paired
83 ============================== 106 ==============================
84 Demultiplex paired-end sequence data with barcodes in-sequence. 107 Demultiplex paired-end sequence data with barcodes in-sequence.
85 108
93 116
94 Description: 117 Description:
95 ------------ 118 ------------
96 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes are expected to be located within the sequence data (versus the header, or a separate barcode file). 119 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes are expected to be located within the sequence data (versus the header, or a separate barcode file).
97 120
121 Examples:
122 ---------
123
124 paired
125 ******
126 Using the ``qiime2 cutadapt demux-paired`` tool:
127 #. Set *"seqs"* to ``#: seqs.qza``
128 #. For *"forward_barcodes"*:
129
130 #. Leave as ``Metadata from TSV``
131 #. Set *"Metadata Source"* to ``md.tsv``
132 #. Set *"Column Name"* to ``barcode-sequence``
133
134 #. Press the ``Execute`` button.
135
136
98 137
99 | 138 |
100 139
101 </help> 140 </help>
102 <citations> 141 <citations>