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comparison qiime2__feature_classifier__vsearch_global.xml @ 3:b4ccd6f48728 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:06:17 +0000
parents c7bde9e4638d
children 84d83752cc49
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2:c7bde9e4638d 3:b4ccd6f48728
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2023, QIIME 2 development team. 3 Copyright (c) 2024, 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: 2023.5.0) 9 q2galaxy (version: 2024.2.1)
10 for: 10 for:
11 qiime2 (version: 2023.5.1) 11 qiime2 (version: 2024.2.0)
12 --> 12 -->
13 <tool name="qiime2 feature-classifier vsearch-global" id="qiime2__feature_classifier__vsearch_global" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 feature-classifier vsearch-global" id="qiime2__feature_classifier__vsearch_global" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>VSEARCH global alignment search</description> 14 <description>VSEARCH global alignment search</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2023.5</container> 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version feature_classifier</version_command> 18 <version_command>q2galaxy version feature_classifier</version_command>
19 <command detect_errors="exit_code">q2galaxy run feature_classifier vsearch_global '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run feature_classifier vsearch_global '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="query" type="data" format="qza" label="query: FeatureData[Sequence]" help="[required] Query Sequences."> 24 <param name="query" type="data" format="qza" label="query: FeatureData[Sequence]" help="[required] Query Sequences.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[Sequence]"/> 26 <filter type="add_value" value="FeatureData[Sequence]"/>
78 <param name="maxrejects" type="integer" min="1" value="" label="maxrejects: Int % Range(1, None)" help="[required] Maximum number of non-matching target sequences to consider before stopping the search. This option works in pair with maxaccepts (see maxaccepts description for details)."/> 78 <param name="maxrejects" type="integer" min="1" value="" label="maxrejects: Int % Range(1, None)" help="[required] Maximum number of non-matching target sequences to consider before stopping the search. This option works in pair with maxaccepts (see maxaccepts description for details)."/>
79 </when> 79 </when>
80 </conditional> 80 </conditional>
81 <param name="output_no_hits" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="output_no_hits: Bool" help="[default: Yes] Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs."/> 81 <param name="output_no_hits" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="output_no_hits: Bool" help="[default: Yes] Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs."/>
82 <param name="weak_id" type="float" min="0.0" max="1.0" value="0.0" label="weak_id: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.0] Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc_identity). As weak_id reports weak hits that are not deduced from maxaccepts, high perc_identity values can be used, hence preserving both speed and sensitivity. Logically, weak_id must be smaller than the value indicated by perc_identity, otherwise this option will be ignored."/> 82 <param name="weak_id" type="float" min="0.0" max="1.0" value="0.0" label="weak_id: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.0] Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc_identity). As weak_id reports weak hits that are not deduced from maxaccepts, high perc_identity values can be used, hence preserving both speed and sensitivity. Logically, weak_id must be smaller than the value indicated by perc_identity, otherwise this option will be ignored."/>
83 <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] Number of threads to use for job parallelization."/>
84 </section> 83 </section>
85 </inputs> 84 </inputs>
86 <outputs> 85 <outputs>
87 <data name="search_results" format="qza" label="${tool.name} on ${on_string}: search_results.qza" from_work_dir="search_results.qza"/> 86 <data name="search_results" format="qza" label="${tool.name} on ${on_string}: search_results.qza" from_work_dir="search_results.qza"/>
88 </outputs> 87 </outputs>