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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:22:08 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2022, QIIME 2 development team.
4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 -->
7 <!--
8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1)
10 for:
11 qiime2 (version: 2022.8.1)
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">
14 <description>Demultiplex paired-end sequence data with barcodes in-sequence.</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version cutadapt</version_command>
19 <command detect_errors="aggressive">q2galaxy run cutadapt demux_paired '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required] The paired-end sequences to be demultiplexed.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="MultiplexedPairedEndBarcodeInSequence"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['MultiplexedPairedEndBarcodeInSequence']</validator>
29 </param>
30 <conditional name="forward_barcodes">
31 <param name="type" type="select" label="forward_barcodes: MetadataColumn[Categorical]" help="[required] The sample metadata column listing the per-sample barcodes for the forward reads.">
32 <option value="tsv" selected="true">Metadata from TSV</option>
33 <option value="qza">Metadata from Artifact</option>
34 </param>
35 <when value="tsv">
36 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
37 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
38 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
39 </param>
40 </when>
41 <when value="qza">
42 <param name="source" type="data" format="qza" label="Metadata Source"/>
43 <param name="column" type="text" label="Column Name">
44 <validator type="empty_field"/>
45 </param>
46 </when>
47 </conditional>
48 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
49 <conditional name="reverse_barcodes">
50 <param name="type" type="select" label="reverse_barcodes: MetadataColumn[Categorical]" help="[optional] The sample metadata column listing the per-sample barcodes for the reverse reads.">
51 <option value="none" selected="true">None (default)</option>
52 <option value="tsv">Metadata from TSV</option>
53 <option value="qza">Metadata from Artifact</option>
54 </param>
55 <when value="none"/>
56 <when value="tsv">
57 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
58 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
59 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
60 </param>
61 </when>
62 <when value="qza">
63 <param name="source" type="data" format="qza" label="Metadata Source"/>
64 <param name="column" type="text" label="Column Name">
65 <validator type="empty_field"/>
66 </param>
67 </when>
68 </conditional>
69 <param name="error_rate" type="float" min="0" max="1" value="0.1" label="error_rate: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.1] The level of error tolerance, specified as the maximum allowable error rate."/>
70 <param name="batch_size" type="integer" min="0" value="0" label="batch_size: Int % Range(0, None)" help="[default: 0] The number of samples cutadapt demultiplexes concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve &quot;too many files&quot; errors related to sample quantity. Set to &quot;0&quot; to process all samples at once."/>
71 <param name="minimum_length" type="integer" min="1" value="1" label="minimum_length: Int % Range(1, None)" help="[default: 1] Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records."/>
72 <param name="mixed_orientation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="mixed_orientation: Bool" help="[default: No] Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file)."/>
73 <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/>
74 </section>
75 </inputs>
76 <outputs>
77 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
78 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/>
79 </outputs>
80 <tests/>
81 <help>
82 QIIME 2: cutadapt demux-paired
83 ==============================
84 Demultiplex paired-end sequence data with barcodes in-sequence.
85
86
87 Outputs:
88 --------
89 :per_sample_sequences.qza: The resulting demultiplexed sequences.
90 :untrimmed_sequences.qza: The sequences that were unmatched to barcodes.
91
92 |
93
94 Description:
95 ------------
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).
97
98
99 |
100
101 </help>
102 <citations>
103 <citation type="doi">10.14806/ej.17.1.200</citation>
104 <citation type="doi">10.1038/s41587-019-0209-9</citation>
105 </citations>
106 </tool>