<?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: 2024.10.0)
for:
    qiime2 (version: 2024.10.1)
-->
<tool name="qiime2 quality-control evaluate-seqs" id="qiime2__quality_control__evaluate_seqs" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Compare query (observed) vs. reference (expected) sequences.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
    </requirements>
    <version_command>q2galaxy version quality_control</version_command>
    <command detect_errors="exit_code">q2galaxy run quality_control evaluate_seqs '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="query_sequences" type="data" format="qza" label="query_sequences: FeatureData[Sequence]" help="[required]  Sequences to test for exclusion">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
        </param>
        <param name="reference_sequences" type="data" format="qza" label="reference_sequences: FeatureData[Sequence]" help="[required]  Reference sequences to align against feature sequences">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="show_alignments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="show_alignments: Bool" help="[default: No]  Option to plot pairwise alignments of query sequences and their top hits."/>
        </section>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: quality-control evaluate-seqs
======================================
Compare query (observed) vs. reference (expected) sequences.


Outputs:
--------
:visualization.qzv: &lt;no description&gt;

|  

Description:
------------
This action aligns a set of query (e.g., observed) sequences against a set of reference (e.g., expected) sequences to evaluate the quality of alignment. The intended use is to align observed sequences against expected sequences (e.g., from a mock community) to determine the frequency of mismatches between observed sequences and the most similar expected sequences, e.g., as a measure of sequencing/method error. However, any sequences may be provided as input to generate a report on pairwise alignment quality against a set of reference sequences.


|  

</help>
    <citations>
        <citation type="doi">10.1186/1471-2105-10-421</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>