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author | q2d2 |
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date | Mon, 03 Jun 2024 23:17:53 +0000 |
parents | d2ba73cf503d |
children | fec8b0edda39 |
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<?xml version='1.0' encoding='utf-8'?> <!-- Copyright (c) 2024, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: q2galaxy (version: 2024.5.0) for: qiime2 (version: 2024.5.0) --> <tool name="qiime2 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> <description>Deblur sequences using a 16S positive filter.</description> <requirements> <container type="docker">quay.io/qiime2/amplicon:2024.5</container> </requirements> <version_command>q2galaxy version deblur</version_command> <command detect_errors="exit_code">q2galaxy run deblur denoise_16S '$inputs'</command> <configfiles> <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be denoised."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="SampleData[SequencesWithQuality]"/> <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator> </param> <param name="trim_length" type="integer" value="" label="trim_length: Int" help="[required] Sequence trim length, specify -1 to disable trimming."/> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> <param name="left_trim_len" type="integer" min="0" value="0" label="left_trim_len: Int % Range(0, None)" help="[default: 0] Sequence trimming from the 5' end. A value of 0 will disable this trim."/> <param name="sample_stats" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="sample_stats: Bool" help="[default: No] If true, gather stats per sample."/> <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."/> <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)."/> <param name="indel_max" type="integer" value="3" label="indel_max: Int" help="[default: 3] Maximum number of insertion/deletions."/> <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."/> <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."/> <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."/> </section> </inputs> <outputs> <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/> <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/> <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/> </outputs> <tests> <test> <param name="demultiplexed_seqs" value="denoise_16S.test0.demux-filtered.qza" ftype="qza"/> <param name="trim_length" value="120"/> <param name="sample_stats" value="__q2galaxy__::literal::True"/> <output name="representative_sequences" ftype="qza"> <assert_contents> <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"> <has_line_matching expression="type: FeatureData\[Sequence\]"/> </has_archive_member> </assert_contents> </output> <output name="table" ftype="qza"> <assert_contents> <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"> <has_line_matching expression="type: FeatureTable\[Frequency\]"/> </has_archive_member> </assert_contents> </output> <output name="stats" ftype="qza"> <assert_contents> <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"> <has_line_matching expression="type: DeblurStats"/> </has_archive_member> </assert_contents> </output> </test> </tests> <help> QIIME 2: deblur denoise-16S =========================== Deblur sequences using a 16S positive filter. Outputs: -------- :table.qza: The resulting denoised feature table. :representative_sequences.qza: The resulting feature sequences. :stats.qza: Per-sample stats if requested. | Description: ------------ Perform sequence quality control for Illumina data using the Deblur workflow with a 16S reference as a positive filter. Only forward reads are supported at this time. The specific reference used is the 88% OTUs from Greengenes 13_8. This mode of operation should only be used when data were generated from a 16S amplicon protocol on an Illumina platform. The reference is only used to assess whether each sequence is likely to be 16S by a local alignment using SortMeRNA with a permissive e-value; the reference is not used to characterize the sequences. Examples: --------- denoise_16S *********** Using the ``qiime2 deblur denoise-16S`` tool: #. Set *"demultiplexed_seqs"* to ``#: demux-filtered.qza`` #. Set *"trim_length"* to ``120`` #. Expand the ``additional options`` section - Set *"sample_stats"* to ``Yes`` #. Press the ``Execute`` button. Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows: (Renaming is optional, but it will make any subsequent steps easier to complete.) .. list-table:: :align: left :header-rows: 1 * - History Name - *"Name"* to set (be sure to press ``Save``) * - ``#: qiime2 deblur denoise-16S [...] : table.qza`` - ``table.qza`` * - ``#: qiime2 deblur denoise-16S [...] : representative_sequences.qza`` - ``representative-sequences.qza`` * - ``#: qiime2 deblur denoise-16S [...] : stats.qza`` - ``denoising-stats.qza`` | </help> <citations> <citation type="bibtex">@article{cite1, author = {Amir, Amnon and McDonald, Daniel and Navas-Molina, Jose A and Kopylova, Evguenia and Morton, James T and Xu, Zhenjiang Zech and Kightley, Eric P and Thompson, Luke R and Hyde, Embriette R and Gonzalez, Antonio and Knight, Rob}, journal = {MSystems}, number = {2}, pages = {e00191--16}, publisher = {Am Soc Microbiol}, title = {Deblur rapidly resolves single-nucleotide community sequence patterns}, volume = {2}, year = {2017} } </citation> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>