<?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 alignment mask" id="qiime2__alignment__mask" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Positional conservation and gap filtering.</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 alignment</version_command>
    <command detect_errors="exit_code">q2galaxy run alignment mask '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  The alignment to be masked.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="max_gap_frequency" type="float" min="0" max="1" value="1.0" label="max_gap_frequency: Float % Range(0, 1, inclusive_end=True)" help="[default: 1.0]  The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency."/>
            <param name="min_conservation" type="float" min="0" max="1" value="0.4" label="min_conservation: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.4]  The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences."/>
        </section>
    </inputs>
    <outputs>
        <data name="masked_alignment" format="qza" label="${tool.name} on ${on_string}: masked_alignment.qza" from_work_dir="masked_alignment.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: alignment mask
=======================
Positional conservation and gap filtering.


Outputs:
--------
:masked_alignment.qza: The masked alignment.

|  

Description:
------------
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).


|  

</help>
    <citations>
        <citation type="bibtex">@incollection{cite1,
 address = {New York},
 author = {Lane, DJ},
 booktitle = {Nucleic Acid Techniques in Bacterial Systematics},
 editor = {Stackebrandt, E and Goodfellow, M},
 pages = {115--175},
 publisher = {John Wiley and Sons},
 title = {16S/23S rRNA sequencing},
 year = {1991}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>