<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, 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: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Add sequences to multiple sequence alignment with MAFFT.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version alignment</version_command>
    <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  The alignment to which sequences should be added.">
            <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>
        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The sequences to be added.">
            <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">
            <conditional name="__q2galaxy__GUI__conditional__n_threads__">
                <param name="__q2galaxy__GUI__select__" type="select" label="n_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of threads. (Use `auto` to automatically use all available cores)">
                    <option value="auto">auto (Str)</option>
                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
                </param>
                <when value="auto">
                    <param name="n_threads" type="hidden" value="auto"/>
                </when>
                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
                    <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  The number of threads. (Use `auto` to automatically use all available cores)"/>
                </when>
            </conditional>
            <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No]  This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/>
            <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No]  Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/>
        </section>
    </inputs>
    <outputs>
        <data name="expanded_alignment" format="qza" label="${tool.name} on ${on_string}: expanded_alignment.qza" from_work_dir="expanded_alignment.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: alignment mafft-add
============================
Add sequences to multiple sequence alignment with MAFFT.


Outputs:
--------
:expanded_alignment.qza: Alignment containing the provided aligned and unaligned sequences.

|  

Description:
------------
Add new sequences to an existing alignment with MAFFT.


|  

</help>
    <citations>
        <citation type="doi">10.1093/molbev/mst010</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>