Mercurial > repos > q2d2 > qiime2__dada2__denoise_single
annotate qiime2__dada2__denoise_single.xml @ 1:3c8340e400df draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
| author | q2d2 |
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| date | Fri, 13 Jan 2023 22:42:17 +0000 |
| parents | dba6cccafa22 |
| children | e7812ca89033 |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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3c8340e400df
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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3 Copyright (c) 2023, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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9 q2galaxy (version: 2022.11.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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11 qiime2 (version: 2022.11.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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3c8340e400df
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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13 <tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Denoise and dereplicate single-end sequences</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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16 <container type="docker">quay.io/qiime2/core:2022.11</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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17 </requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version dada2</version_command> |
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3c8340e400df
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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19 <command detect_errors="exit_code">q2galaxy run dada2 denoise_single '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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20 <configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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21 <inputs name="inputs" data_style="paths"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required] The single-end demultiplexed sequences to be denoised."> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <options options_filter_attribute="metadata.semantic_type"> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="SampleData[SequencesWithQuality]"/> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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30 </param> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 <param name="trunc_len" type="integer" value="" label="trunc_len: Int" help="[required] Position at which 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. If 0 is provided, no truncation or length filtering will be performed"/> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 <param name="trim_left" type="integer" value="0" label="trim_left: Int" help="[default: 0] Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles."/> |
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dba6cccafa22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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34 <param name="max_ee" type="float" value="2.0" label="max_ee: Float" help="[default: 2.0] Reads with number of expected errors higher than this value will be discarded."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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35 <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`, it is discarded."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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36 <param name="pooling_method" type="select" label="pooling_method: Str % Choices('independent', 'pseudo')" display="radio"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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37 <option value="independent" selected="true">independent</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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38 <option value="pseudo">pseudo</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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39 </param> |
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40 <param name="chimera_method" type="select" label="chimera_method: Str % Choices('consensus', 'none', 'pooled')" display="radio"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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41 <option value="consensus" selected="true">consensus</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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42 <option value="none">none</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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43 <option value="pooled">pooled</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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44 </param> |
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45 <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 "none"."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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46 <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."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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47 <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."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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48 <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."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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49 <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."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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50 </section> |
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51 </inputs> |
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52 <outputs> |
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53 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/> |
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54 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/> |
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55 <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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56 </outputs> |
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57 <tests> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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58 <test> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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59 <param name="demultiplexed_seqs" value="denoise_single.test0.demux-single.qza" ftype="qza"/> |
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60 <param name="trunc_len" value="120"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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61 <param name="trim_left" value="0"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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62 <output name="representative_sequences" ftype="qza"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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63 <assert_contents> |
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64 <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"> |
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65 <has_line_matching expression="type: FeatureData\[Sequence\]"/> |
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66 </has_archive_member> |
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67 </assert_contents> |
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68 </output> |
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69 <output name="table" ftype="qza"> |
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70 <assert_contents> |
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71 <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"> |
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72 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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73 </has_archive_member> |
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74 </assert_contents> |
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75 </output> |
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76 <output name="denoising_stats" ftype="qza"> |
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77 <assert_contents> |
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78 <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"> |
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79 <has_line_matching expression="type: SampleData\[DADA2Stats\]"/> |
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80 </has_archive_member> |
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81 </assert_contents> |
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82 </output> |
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83 </test> |
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84 </tests> |
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85 <help> |
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86 QIIME 2: dada2 denoise-single |
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87 ============================= |
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88 Denoise and dereplicate single-end sequences |
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89 |
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90 |
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91 Outputs: |
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92 -------- |
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93 :table.qza: The resulting feature table. |
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94 :representative_sequences.qza: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. |
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95 :denoising_stats.qza: <no description> |
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96 |
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97 | |
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98 |
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99 Description: |
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100 ------------ |
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101 This method denoises single-end sequences, dereplicates them, and filters chimeras. |
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102 |
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1
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103 Examples: |
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104 --------- |
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105 |
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106 denoise_single |
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107 ************** |
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108 Using the ``qiime2 dada2 denoise-single`` tool: |
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109 #. Set *"demultiplexed_seqs"* to ``#: demux-single.qza`` |
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110 #. Set *"trunc_len"* to ``120`` |
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111 #. Expand the ``additional options`` section |
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112 |
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113 - Leave *"trim_left"* as its default value of ``0`` |
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114 |
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115 #. Press the ``Execute`` button. |
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116 |
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117 |
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118 |
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119 | |
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120 |
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121 </help> |
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122 <citations> |
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123 <citation type="doi">10.1038/nmeth.3869</citation> |
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124 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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125 </citations> |
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126 </tool> |