annotate qiime2__deblur__denoise_16S.xml @ 4:ab9ed5ac604c draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit c7e80dcda727ce63b42aa8a946e9330310929797

<?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>