Mercurial > repos > q2d2 > qiime2__dada2__denoise_paired

annotate qiime2__dada2__denoise_paired.xml @ 2:06bacd08bb47 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:35:27 +0000
parents bbaba1707475
children b1ec737d40f0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
2 <!--
1
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
3 Copyright (c) 2023, QIIME 2 development team.
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
4
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
6 -->
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
7 <!--
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
8 This tool was automatically generated by:
2
06bacd08bb47 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
9 q2galaxy (version: 2023.5.0)
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
10 for:
2
06bacd08bb47 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
11 qiime2 (version: 2023.5.1)
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
12 -->
2
06bacd08bb47 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
13 <tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
14 <description>Denoise and dereplicate paired-end sequences</description>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
15 <requirements>
2
06bacd08bb47 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
16 <container type="docker">quay.io/qiime2/core:2023.5</container>
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
17 </requirements>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
18 <version_command>q2galaxy version dada2</version_command>
1
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
19 <command detect_errors="exit_code">q2galaxy run dada2 denoise_paired '$inputs'</command>
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
20 <configfiles>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
21 <inputs name="inputs" data_style="paths"/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
22 </configfiles>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
23 <inputs>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
24 <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[PairedEndSequencesWithQuality]" help="[required] The paired-end demultiplexed sequences to be denoised.">
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
25 <options options_filter_attribute="metadata.semantic_type">
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
27 </options>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]']</validator>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
29 </param>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
30 <param name="trunc_len_f" type="integer" value="" label="trunc_len_f: Int" help="[required] Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed"/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
31 <param name="trunc_len_r" type="integer" value="" label="trunc_len_r: Int" help="[required] Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed"/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
32 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
33 <param name="trim_left_f" type="integer" value="0" label="trim_left_f: Int" help="[default: 0] Position at which forward read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
34 <param name="trim_left_r" type="integer" value="0" label="trim_left_r: Int" help="[default: 0] Position at which reverse read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
35 <param name="max_ee_f" type="float" value="2.0" label="max_ee_f: Float" help="[default: 2.0] Forward reads with number of expected errors higher than this value will be discarded."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
36 <param name="max_ee_r" type="float" value="2.0" label="max_ee_r: Float" help="[default: 2.0] Reverse reads with number of expected errors higher than this value will be discarded."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
37 <param name="trunc_q" type="integer" value="2" label="trunc_q: Int" help="[default: 2] Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc_len_f` or `trunc_len_r` (depending on the direction of the read) it is discarded."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
38 <param name="min_overlap" type="integer" min="4" value="12" label="min_overlap: Int % Range(4, None)" help="[default: 12] The minimum length of the overlap required for merging the forward and reverse reads."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
39 <param name="pooling_method" type="select" label="pooling_method: Str % Choices('independent', 'pseudo')" display="radio">
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
40 <option value="independent" selected="true">independent</option>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
41 <option value="pseudo">pseudo</option>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
42 </param>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
43 <param name="chimera_method" type="select" label="chimera_method: Str % Choices('consensus', 'none', 'pooled')" display="radio">
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
44 <option value="consensus" selected="true">consensus</option>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
45 <option value="none">none</option>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
46 <option value="pooled">pooled</option>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
47 </param>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
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;."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
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 TrueIf True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
50 <param name="n_threads" type="integer" value="1" label="n_threads: Int" help="[default: 1] The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
51 <param name="n_reads_learn" type="integer" value="1000000" label="n_reads_learn: Int" help="[default: 1000000] 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."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
52 <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."/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
53 </section>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
54 </inputs>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
55 <outputs>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
56 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
57 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
58 <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
59 </outputs>
1
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
60 <tests>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
61 <test>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
62 <param name="demultiplexed_seqs" value="denoise_paired.test0.demux-paired.qza" ftype="qza"/>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
63 <param name="trunc_len_f" value="150"/>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
64 <param name="trunc_len_r" value="140"/>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
65 <output name="representative_sequences" ftype="qza">
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
66 <assert_contents>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
67 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
68 <has_line_matching expression="type: FeatureData\[Sequence\]"/>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
69 </has_archive_member>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
70 </assert_contents>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
71 </output>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
72 <output name="table" ftype="qza">
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
73 <assert_contents>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
74 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
75 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
76 </has_archive_member>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
77 </assert_contents>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
78 </output>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
79 <output name="denoising_stats" ftype="qza">
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
80 <assert_contents>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
81 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
82 <has_line_matching expression="type: SampleData\[DADA2Stats\]"/>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
83 </has_archive_member>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
84 </assert_contents>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
85 </output>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
86 </test>
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
87 </tests>
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
88 <help>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
89 QIIME 2: dada2 denoise-paired
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
90 =============================
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
91 Denoise and dereplicate paired-end sequences
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
92
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
93
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
94 Outputs:
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
95 --------
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
96 :table.qza: The resulting feature table.
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
97 :representative_sequences.qza: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence, and these sequences will be the joined paired-end sequences.
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
98 :denoising_stats.qza: &lt;no description&gt;
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
99
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
100 |
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
101
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
102 Description:
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
103 ------------
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
104 This method denoises paired-end sequences, dereplicates them, and filters chimeras.
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
105
1
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
106 Examples:
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
107 ---------
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
108
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
109 denoise_paired
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
110 **************
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
111 Using the ``qiime2 dada2 denoise-paired`` tool:
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
112 #. Set *"demultiplexed_seqs"* to ``#: demux-paired.qza``
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
113 #. Set *"trunc_len_f"* to ``150``
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
114 #. Set *"trunc_len_r"* to ``140``
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
115 #. Press the ``Execute`` button.
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
116
bbaba1707475 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
117
0
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
118
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
119 |
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
120
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
121 </help>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
122 <citations>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
123 <citation type="doi">10.1038/nmeth.3869</citation>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
124 <citation type="doi">10.1038/s41587-019-0209-9</citation>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
125 </citations>
4218e3146518 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
126 </tool>