<?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 exclude-seqs" id="qiime2__quality_control__exclude_seqs" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Exclude sequences by alignment</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 exclude_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="method" type="select" label="method: Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')²" help="[default: 'blast']  Alignment method to use for matching feature sequences against reference sequences">
                <option value="blast" selected="true">blast (Str)</option>
                <option value="blastn-short">blastn-short (Str)</option>
                <option value="vsearch">vsearch (Str)</option>
            </param>
            <param name="perc_identity" type="float" min="0.0" max="1.0" value="0.97" label="perc_identity: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.97]  Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]"/>
            <param name="evalue" type="float" optional="true" label="evalue: Float" help="[optional]  BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default."/>
            <param name="perc_query_aligned" type="float" value="0.97" label="perc_query_aligned: Float" help="[default: 0.97]  Percent of query sequence that must align to reference in order to be accepted as a hit."/>
            <param name="left_justify" type="select" label="left_justify: Bool % Choices(False)¹ | Bool²" help="[default: No]  Reject match if the pairwise alignment begins with gaps">
                <option value="__q2galaxy__::literal::False" selected="true">No (Bool)</option>
                <option value="__q2galaxy__::literal::True">Yes (Bool)</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="sequence_hits" format="qza" label="${tool.name} on ${on_string}: sequence_hits.qza" from_work_dir="sequence_hits.qza"/>
        <data name="sequence_misses" format="qza" label="${tool.name} on ${on_string}: sequence_misses.qza" from_work_dir="sequence_misses.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: quality-control exclude-seqs
=====================================
Exclude sequences by alignment


Outputs:
--------
:sequence_hits.qza: Subset of feature sequences that align to reference sequences
:sequence_misses.qza: Subset of feature sequences that do not align to reference sequences

|  

Description:
------------
This method aligns feature sequences to a set of reference sequences to identify sequences that hit/miss the reference within a specified perc_identity, evalue, and perc_query_aligned. This method could be used to define a positive filter, e.g., extract only feature sequences that align to a certain clade of bacteria; or to define a negative filter, e.g., identify sequences that align to contaminant or human DNA sequences that should be excluded from subsequent analyses. Note that filtering is performed based on the perc_identity, perc_query_aligned, and evalue thresholds (the latter only if method==BLAST and an evalue is set). Set perc_identity==0 and/or perc_query_aligned==0 to disable these filtering thresholds as necessary.


|  

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