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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:23:41 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2024, 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: 2024.2.1)
10 for:
11 qiime2 (version: 2024.2.0)
12 -->
13 <tool name="qiime2 rescript orient-seqs" id="qiime2__rescript__orient_seqs" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Orient input sequences by comparison against reference.</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements>
18 <version_command>q2galaxy version rescript</version_command>
19 <command detect_errors="exit_code">q2galaxy run rescript orient_seqs '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles>
23 <inputs>
24 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] Sequences to be oriented.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[Sequence]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
29 </param>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <param name="reference_sequences" type="data" format="qza" optional="true" label="reference_sequences: FeatureData[Sequence]" help="[optional] Reference sequences to orient against. If no reference is provided, all the sequences will be reverse complemented and all parameters will be ignored.">
32 <options options_filter_attribute="metadata.semantic_type">
33 <filter type="add_value" value="FeatureData[Sequence]"/>
34 </options>
35 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
36 </param>
37 <param name="threads" type="integer" min="1" max="255" value="1" label="threads: Int % Range(1, 256)" help="[default: 1] Number of computation threads to use (1 to 256). The number of threads should be lesser or equal to the number of available CPU cores."/>
38 <param name="dbmask" type="select" label="dbmask: Str % Choices('none', 'dust', 'soft')" display="radio">
39 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
40 <option value="none">none</option>
41 <option value="dust">dust</option>
42 <option value="soft">soft</option>
43 </param>
44 <conditional name="__q2galaxy__GUI__conditional__relabel__" label="relabel: Str">
45 <param name="__q2galaxy__GUI__select__" type="select" label="relabel: Str" help="[optional] Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the new headers. Use --sizeout to conserve the abundance annotations.">
46 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
47 <option value="__q2galaxy__::control::provide">Provide a value</option>
48 </param>
49 <when value="__q2galaxy__::control::default">
50 <param name="relabel" type="hidden" value="__q2galaxy__::literal::None"/>
51 </when>
52 <when value="__q2galaxy__::control::provide">
53 <param name="relabel" type="text">
54 <sanitizer>
55 <valid initial="string.printable"/>
56 </sanitizer>
57 </param>
58 </when>
59 </conditional>
60 <param name="relabel_keep" type="select" label="relabel_keep: Bool" help="[optional] When relabeling, keep the original identifier in the header after a space." display="radio">
61 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
62 <option value="__q2galaxy__::literal::True">Yes</option>
63 <option value="__q2galaxy__::literal::False">No</option>
64 </param>
65 <param name="relabel_md5" type="select" label="relabel_md5: Bool" help="[optional] When relabeling, use the MD5 digest of the sequence as the new identifier. Use --sizeout to conserve the abundance annotations." display="radio">
66 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
67 <option value="__q2galaxy__::literal::True">Yes</option>
68 <option value="__q2galaxy__::literal::False">No</option>
69 </param>
70 <param name="relabel_self" type="select" label="relabel_self: Bool" help="[optional] Relabel sequences using the sequence itself as a label." display="radio">
71 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
72 <option value="__q2galaxy__::literal::True">Yes</option>
73 <option value="__q2galaxy__::literal::False">No</option>
74 </param>
75 <param name="relabel_sha1" type="select" label="relabel_sha1: Bool" help="[optional] When relabeling, use the SHA1 digest of the sequence as the new identifier. The probability of a collision is smaller than the MD5 algorithm." display="radio">
76 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
77 <option value="__q2galaxy__::literal::True">Yes</option>
78 <option value="__q2galaxy__::literal::False">No</option>
79 </param>
80 <param name="sizein" type="select" label="sizein: Bool" help="[optional] In de novo mode, abundance annotations (pattern `[&gt;;]size=integer[;]`) present in sequence headers are taken into account." display="radio">
81 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
82 <option value="__q2galaxy__::literal::True">Yes</option>
83 <option value="__q2galaxy__::literal::False">No</option>
84 </param>
85 <param name="sizeout" type="select" label="sizeout: Bool" help="[optional] Add abundance annotations to the output FASTA files." display="radio">
86 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
87 <option value="__q2galaxy__::literal::True">Yes</option>
88 <option value="__q2galaxy__::literal::False">No</option>
89 </param>
90 </section>
91 </inputs>
92 <outputs>
93 <data name="oriented_seqs" format="qza" label="${tool.name} on ${on_string}: oriented_seqs.qza" from_work_dir="oriented_seqs.qza"/>
94 <data name="unmatched_seqs" format="qza" label="${tool.name} on ${on_string}: unmatched_seqs.qza" from_work_dir="unmatched_seqs.qza"/>
95 </outputs>
96 <tests/>
97 <help>
98 QIIME 2: rescript orient-seqs
99 =============================
100 Orient input sequences by comparison against reference.
101
102
103 Outputs:
104 --------
105 :oriented_seqs.qza: Query sequences in same orientation as top matching reference sequence.
106 :unmatched_seqs.qza: Query sequences that fail to match at least one reference sequence in either + or - orientation. This will be empty if no refrence is provided.
107
108 |
109
110 Description:
111 ------------
112 Orient input sequences by comparison against a set of reference sequences using VSEARCH. This action can also be used to quickly filter out sequences that (do not) match a set of reference sequences in either orientation. Alternatively, if no reference sequences are provided as input, all input sequences will be reverse-complemented. In this case, no alignment is performed, and all alignment parameters (`dbmask`, `relabel`, `relabel_keep`, `relabel_md5`, `relabel_self`, `relabel_sha1`, `sizein`, `sizeout` and `threads`) are ignored.
113
114
115 |
116
117 </help>
118 <citations>
119 <citation type="doi">10.7717/peerj.2584</citation>
120 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
121 <citation type="doi">10.1038/s41587-019-0209-9</citation>
122 </citations>
123 </tool>