Mercurial > repos > q2d2 > qiime2__cutadapt__demux_single
comparison qiime2__cutadapt__demux_single.xml @ 1:d244802d52d0 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author | q2d2 |
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date | Fri, 13 Jan 2023 22:41:46 +0000 |
parents | 6fd92b8872e6 |
children | d8851a5b9360 |
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0:6fd92b8872e6 | 1:d244802d52d0 |
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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-single" id="qiime2__cutadapt__demux_single" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | 13 <tool name="qiime2 cutadapt demux-single" id="qiime2__cutadapt__demux_single" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> |
14 <description>Demultiplex single-end sequence data with barcodes in-sequence.</description> | 14 <description>Demultiplex single-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_single '$inputs'</command> | 19 <command detect_errors="exit_code">q2galaxy run cutadapt demux_single '$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: MultiplexedSingleEndBarcodeInSequence" help="[required] The single-end sequences to be demultiplexed."> | 24 <param name="seqs" type="data" format="qza" label="seqs: MultiplexedSingleEndBarcodeInSequence" help="[required] The single-end sequences to be demultiplexed."> |
54 </inputs> | 54 </inputs> |
55 <outputs> | 55 <outputs> |
56 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> | 56 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> |
57 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/> | 57 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/> |
58 </outputs> | 58 </outputs> |
59 <tests/> | 59 <tests> |
60 <test> | |
61 <param name="seqs" value="demux_single.test0.seqs.qza" ftype="qza"/> | |
62 <conditional name="barcodes"> | |
63 <param name="type" value="tsv"/> | |
64 <param name="source" value="demux_single.test0.md.tsv" ftype="qiime2.tabular"/> | |
65 <param name="column" value="2"/> | |
66 </conditional> | |
67 <output name="per_sample_sequences" ftype="qza"> | |
68 <assert_contents> | |
69 <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"> | |
70 <has_line_matching expression="type: SampleData\[SequencesWithQuality\]"/> | |
71 </has_archive_member> | |
72 </assert_contents> | |
73 </output> | |
74 <output name="untrimmed_sequences" ftype="qza"> | |
75 <assert_contents> | |
76 <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"> | |
77 <has_line_matching expression="type: MultiplexedSingleEndBarcodeInSequence"/> | |
78 </has_archive_member> | |
79 </assert_contents> | |
80 </output> | |
81 </test> | |
82 </tests> | |
60 <help> | 83 <help> |
61 QIIME 2: cutadapt demux-single | 84 QIIME 2: cutadapt demux-single |
62 ============================== | 85 ============================== |
63 Demultiplex single-end sequence data with barcodes in-sequence. | 86 Demultiplex single-end sequence data with barcodes in-sequence. |
64 | 87 |
72 | 95 |
73 Description: | 96 Description: |
74 ------------ | 97 ------------ |
75 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). | 98 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). |
76 | 99 |
100 Examples: | |
101 --------- | |
102 | |
103 demux_single | |
104 ************ | |
105 Using the ``qiime2 cutadapt demux-single`` tool: | |
106 #. Set *"seqs"* to ``#: seqs.qza`` | |
107 #. For *"barcodes"*: | |
108 | |
109 #. Leave as ``Metadata from TSV`` | |
110 #. Set *"Metadata Source"* to ``md.tsv`` | |
111 #. Set *"Column Name"* to ``BarcodeSequence`` | |
112 | |
113 #. Press the ``Execute`` button. | |
114 | |
115 | |
77 | 116 |
78 | | 117 | |
79 | 118 |
80 </help> | 119 </help> |
81 <citations> | 120 <citations> |