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comparison qiime2__vsearch__merge_pairs.xml @ 2:0eb4a44e8395 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:27:33 +0000
parents f455181d916d
children 4756c43a7181
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1:f455181d916d 2:0eb4a44e8395
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 vsearch merge-pairs" id="qiime2__vsearch__merge_pairs" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 vsearch merge-pairs" id="qiime2__vsearch__merge_pairs" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Merge paired-end reads.</description> 14 <description>Merge paired-end reads.</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 vsearch</version_command> 18 <version_command>q2galaxy version vsearch</version_command>
19 <command detect_errors="exit_code">q2galaxy run vsearch merge_pairs '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run vsearch merge_pairs '$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="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[PairedEndSequencesWithQuality]" help="[required] The demultiplexed paired-end sequences to be merged."> 24 <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[PairedEndSequencesWithQuality]" help="[required] The demultiplexed paired-end sequences to be merged.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> 26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <param name="truncqual" type="integer" min="0" optional="true" label="truncqual: Int % Range(0, None)" help="[optional] Truncate sequences at the first base with the specified quality score value or lower."/> 31 <param name="truncqual" type="integer" min="0" optional="true" label="truncqual: Int % Range(0, None)" help="[optional] Truncate sequences at the first base with the specified quality score value or lower."/>
32 <param name="minlen" type="integer" min="0" value="1" label="minlen: Int % Range(0, None)" help="[default: 1] Sequences shorter than minlen after truncation are discarded."/> 32 <param name="minlen" type="integer" min="0" value="1" label="minlen: Int % Range(0, None)" help="[default: 1] Sequences shorter than minlen after truncation are discarded."/>
33 <param name="maxns" type="integer" min="0" optional="true" label="maxns: Int % Range(0, None)" help="[optional] Sequences with more than maxns N characters are discarded."/> 33 <param name="maxns" type="integer" min="0" optional="true" label="maxns: Int % Range(0, None)" help="[optional] Sequences with more than maxns N characters are discarded."/>
34 <param name="allowmergestagger" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allowmergestagger: Bool" help="[default: No] Allow merging of staggered read pairs."/> 34 <param name="allowmergestagger" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allowmergestagger: Bool" help="[default: No] Allow merging of staggered read pairs."/>
35 <param name="minovlen" type="integer" min="0" value="10" label="minovlen: Int % Range(0, None)" help="[default: 10] Minimum length of the area of overlap between reads during merging."/> 35 <param name="minovlen" type="integer" min="5" value="10" label="minovlen: Int % Range(5, None)" help="[default: 10] Minimum length of the area of overlap between reads during merging."/>
36 <param name="maxdiffs" type="integer" min="0" value="10" label="maxdiffs: Int % Range(0, None)" help="[default: 10] Maximum number of mismatches in the area of overlap during merging."/> 36 <param name="maxdiffs" type="integer" min="0" value="10" label="maxdiffs: Int % Range(0, None)" help="[default: 10] Maximum number of mismatches in the area of overlap during merging."/>
37 <param name="minmergelen" type="integer" min="0" optional="true" label="minmergelen: Int % Range(0, None)" help="[optional] Minimum length of the merged read to be retained."/> 37 <param name="minmergelen" type="integer" min="0" optional="true" label="minmergelen: Int % Range(0, None)" help="[optional] Minimum length of the merged read to be retained."/>
38 <param name="maxmergelen" type="integer" min="0" optional="true" label="maxmergelen: Int % Range(0, None)" help="[optional] Maximum length of the merged read to be retained."/> 38 <param name="maxmergelen" type="integer" min="0" optional="true" label="maxmergelen: Int % Range(0, None)" help="[optional] Maximum length of the merged read to be retained."/>
39 <param name="maxee" type="float" min="0.0" optional="true" label="maxee: Float % Range(0.0, None)" help="[optional] Maximum number of expected errors in the merged read to be retained."/> 39 <param name="maxee" type="float" min="0.0" optional="true" label="maxee: Float % Range(0.0, None)" help="[optional] Maximum number of expected errors in the merged read to be retained."/>
40 <param name="threads" type="integer" min="0" max="8" value="1" label="threads: Int % Range(0, 8, inclusive_end=True)" help="[default: 1] The number of threads to use for computation. Does not scale much past 4 threads."/>
41 </section> 40 </section>
42 </inputs> 41 </inputs>
43 <outputs> 42 <outputs>
44 <data name="merged_sequences" format="qza" label="${tool.name} on ${on_string}: merged_sequences.qza" from_work_dir="merged_sequences.qza"/> 43 <data name="merged_sequences" format="qza" label="${tool.name} on ${on_string}: merged_sequences.qza" from_work_dir="merged_sequences.qza"/>
44 <data name="unmerged_sequences" format="qza" label="${tool.name} on ${on_string}: unmerged_sequences.qza" from_work_dir="unmerged_sequences.qza"/>
45 </outputs> 45 </outputs>
46 <tests/> 46 <tests/>
47 <help> 47 <help>
48 QIIME 2: vsearch merge-pairs 48 QIIME 2: vsearch merge-pairs
49 ============================ 49 ============================
51 51
52 52
53 Outputs: 53 Outputs:
54 -------- 54 --------
55 :merged_sequences.qza: The merged sequences. 55 :merged_sequences.qza: The merged sequences.
56 :unmerged_sequences.qza: The unmerged paired-end reads.
56 57
57 | 58 |
58 59
59 Description: 60 Description:
60 ------------ 61 ------------