annotate qiime2__rescript__orient_reads.xml @ 2:4d0fbac4fc34 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.10.0)
for:
    qiime2 (version: 2025.10.0)
-->
<tool name="qiime2 rescript orient-reads" id="qiime2__rescript__orient_reads" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Orient FASTQ reads against reference.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
    </requirements>
    <version_command>q2galaxy version rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript orient_reads '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="sequences" type="data" format="qza" label="sequences: SampleData[PairedEndSequencesWithQuality¹ | JoinedSequencesWithQuality²]" help="[required]  Sequence reads to be oriented.">
            <options options_filter_attribute="metadata.semantic_type">
                <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]']</validator>
        </param>
        <param name="reference_sequences" type="data" format="qza" label="reference_sequences: FeatureData[Sequence]" help="[required]  Reference sequences to orient against.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="dbmask" type="select" label="dbmask: Str % Choices('none', 'dust', 'soft')" display="radio">
                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
                <option value="none">none</option>
                <option value="dust">dust</option>
                <option value="soft">soft</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="oriented_reads" format="qza" label="${tool.name} on ${on_string}: oriented_reads.qza" from_work_dir="oriented_reads.qza"/>
        <data name="unmatched_reads" format="qza" label="${tool.name} on ${on_string}: unmatched_reads.qza" from_work_dir="unmatched_reads.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript orient-reads
==============================
Orient FASTQ reads against reference.


Outputs:
--------
:oriented_reads.qza: Oriented reads.
:unmatched_reads.qza: Reads that fail to match at least one reference sequence in either + or - orientation.

|  

Description:
------------
Orient input reads (FASTQ) by comparison against a set of reference sequences using VSEARCH. This action is useful for orienting reads that are in mixed orientations prior to denoising or clustering.


|  

</help>
    <citations>
        <citation type="doi">10.7717/peerj.2584</citation>
        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>