<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2022, 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: 2022.8.1)
for:
    qiime2 (version: 2022.8.1)
-->
<tool name="qiime2 quality-control bowtie2-build" id="qiime2__quality_control__bowtie2_build" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Build bowtie2 index from reference sequences.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version quality_control</version_command>
    <command detect_errors="aggressive">q2galaxy run quality_control bowtie2_build '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  Reference sequences used to build bowtie2 index.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  Number of threads to launch"/>
        </section>
    </inputs>
    <outputs>
        <data name="database" format="qza" label="${tool.name} on ${on_string}: database.qza" from_work_dir="database.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: quality-control bowtie2-build
======================================
Build bowtie2 index from reference sequences.


Outputs:
--------
:database.qza: Bowtie2 index.

|  

Description:
------------
Build bowtie2 index from reference sequences.


|  

</help>
    <citations>
        <citation type="bibtex">@article{cite1,
 author = {Langmead, Ben and Salzberg, Steven L},
 journal = {Nature methods},
 number = {4},
 pages = {357},
 publisher = {Nature Publishing Group},
 title = {Fast gapped-read alignment with Bowtie 2},
 volume = {9},
 year = {2012}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>