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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit b1fccfb38b4873cd4699743033449014a2978e7d
author q2d2
date Mon, 05 May 2025 18:42:24 +0000
parents d9e75c4f54b9
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5:d9e75c4f54b9 6:d244cbb520a0
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2024, QIIME 2 development team. 3 Copyright (c) 2025, 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: 2024.10.0) 9 q2galaxy (version: 2025.4.0)
10 for: 10 for:
11 qiime2 (version: 2024.10.1) 11 qiime2 (version: 2025.4.0)
12 --> 12 -->
13 <tool name="qiime2 dada2 denoise-pyro" id="qiime2__dada2__denoise_pyro" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 dada2 denoise-pyro" id="qiime2__dada2__denoise_pyro" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
14 <description>Denoise and dereplicate single-end pyrosequences</description> 14 <description>Denoise and dereplicate single-end pyrosequences</description>
15 <xrefs> 15 <xrefs>
16 <xref type="bio.tools">qiime2</xref> 16 <xref type="bio.tools">qiime2</xref>
17 </xrefs> 17 </xrefs>
18 <requirements> 18 <requirements>
19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container> 19 <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
20 </requirements> 20 </requirements>
21 <version_command>q2galaxy version dada2</version_command> 21 <version_command>q2galaxy version dada2</version_command>
22 <command detect_errors="exit_code">q2galaxy run dada2 denoise_pyro '$inputs'</command> 22 <command detect_errors="exit_code">q2galaxy run dada2 denoise_pyro '$inputs'</command>
23 <configfiles> 23 <configfiles>
24 <inputs name="inputs" data_style="staging_path_and_source_path"/> 24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
38 <param name="max_len" type="integer" value="0" label="max_len: Int" help="[default: 0] Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length."/> 38 <param name="max_len" type="integer" value="0" label="max_len: Int" help="[default: 0] Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length."/>
39 <param name="pooling_method" type="select" label="pooling_method: Str % Choices('independent', 'pseudo')" display="radio"> 39 <param name="pooling_method" type="select" label="pooling_method: Str % Choices('independent', 'pseudo')" display="radio">
40 <option value="independent" selected="true">independent</option> 40 <option value="independent" selected="true">independent</option>
41 <option value="pseudo">pseudo</option> 41 <option value="pseudo">pseudo</option>
42 </param> 42 </param>
43 <param name="chimera_method" type="select" label="chimera_method: Str % Choices('consensus', 'none', 'pooled')" display="radio"> 43 <param name="chimera_method" type="select" label="chimera_method: Str % Choices('consensus', 'none')" display="radio">
44 <option value="consensus" selected="true">consensus</option> 44 <option value="consensus" selected="true">consensus</option>
45 <option value="none">none</option> 45 <option value="none">none</option>
46 <option value="pooled">pooled</option>
47 </param> 46 </param>
48 <param name="min_fold_parent_over_abundance" type="float" value="1.0" label="min_fold_parent_over_abundance: Float" help="[default: 1.0] The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera_method is &quot;none&quot;."/> 47 <param name="min_fold_parent_over_abundance" type="float" value="1.0" label="min_fold_parent_over_abundance: Float" help="[default: 1.0] The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera_method is &quot;none&quot;."/>
49 <param name="allow_one_off" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allow_one_off: Bool" help="[default: No] Bimeras that are one-off from exact are also identified if the `allow_one_off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera."/> 48 <param name="allow_one_off" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allow_one_off: Bool" help="[default: No] Bimeras that are one-off from exact are also identified if the `allow_one_off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera."/>
50 <param name="n_reads_learn" type="integer" value="250000" label="n_reads_learn: Int" help="[default: 250000] The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model."/> 49 <param name="n_reads_learn" type="integer" value="250000" label="n_reads_learn: Int" help="[default: 250000] The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model."/>
51 <param name="hashed_feature_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="hashed_feature_ids: Bool" help="[default: Yes] If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run."/> 50 <param name="hashed_feature_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="hashed_feature_ids: Bool" help="[default: Yes] If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run."/>