Mercurial > repos > q2d2 > qiime2__deblur__denoise_16s

comparison qiime2__deblur__denoise_16S.xml @ 3:d2ba73cf503d draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 20:54:54 +0000
parents b883cbea5623
children ab9ed5ac604c
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2:b883cbea5623 3:d2ba73cf503d
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 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Deblur sequences using a 16S positive filter.</description> 14 <description>Deblur sequences using a 16S positive filter.</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 deblur</version_command> 18 <version_command>q2galaxy version deblur</version_command>
19 <command detect_errors="exit_code">q2galaxy run deblur denoise_16S '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run deblur denoise_16S '$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[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be denoised."> 24 <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be denoised.">
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]"/>
36 <param name="mean_error" type="float" value="0.005" label="mean_error: Float" help="[default: 0.005] The mean per nucleotide error, used for original sequence estimate."/> 36 <param name="mean_error" type="float" value="0.005" label="mean_error: Float" help="[default: 0.005] The mean per nucleotide error, used for original sequence estimate."/>
37 <param name="indel_prob" type="float" value="0.01" label="indel_prob: Float" help="[default: 0.01] Insertion/deletion (indel) probability (same for N indels)."/> 37 <param name="indel_prob" type="float" value="0.01" label="indel_prob: Float" help="[default: 0.01] Insertion/deletion (indel) probability (same for N indels)."/>
38 <param name="indel_max" type="integer" value="3" label="indel_max: Int" help="[default: 3] Maximum number of insertion/deletions."/> 38 <param name="indel_max" type="integer" value="3" label="indel_max: Int" help="[default: 3] Maximum number of insertion/deletions."/>
39 <param name="min_reads" type="integer" value="10" label="min_reads: Int" help="[default: 10] Retain only features appearing at least min_reads times across all samples in the resulting feature table."/> 39 <param name="min_reads" type="integer" value="10" label="min_reads: Int" help="[default: 10] Retain only features appearing at least min_reads times across all samples in the resulting feature table."/>
40 <param name="min_size" type="integer" value="2" label="min_size: Int" help="[default: 2] In each sample, discard all features with an abundance less than min_size."/> 40 <param name="min_size" type="integer" value="2" label="min_size: Int" help="[default: 2] In each sample, discard all features with an abundance less than min_size."/>
41 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start: Int" help="[default: 1] Number of jobs to start (if to run in parallel)."/>
42 <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, hash the feature IDs."/> 41 <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, hash the feature IDs."/>
43 </section> 42 </section>
44 </inputs> 43 </inputs>
45 <outputs> 44 <outputs>
46 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/> 45 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>