<?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: 2024.5.0)
for:
    qiime2 (version: 2024.5.0)
-->
<tool name="qiime2 demux emp-paired" id="qiime2__demux__emp_paired" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
    <description>Demultiplex paired-end sequence data generated with the EMP protocol.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
    </requirements>
    <version_command>q2galaxy version demux</version_command>
    <command detect_errors="exit_code">q2galaxy run demux emp_paired '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="seqs" type="data" format="qza" label="seqs: EMPPairedEndSequences" help="[required]  The paired-end sequences to be demultiplexed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="EMPPairedEndSequences"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['EMPPairedEndSequences']</validator>
        </param>
        <conditional name="barcodes">
            <param name="type" type="select" label="barcodes: MetadataColumn[Categorical]" help="[required]  The sample metadata column containing the per-sample barcodes.">
                <option value="tsv" selected="true">Metadata from TSV</option>
                <option value="qza">Metadata from Artifact</option>
            </param>
            <when value="tsv">
                <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
                    <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
                </param>
            </when>
            <when value="qza">
                <param name="source" type="data" format="qza" label="Metadata Source"/>
                <param name="column" type="text" label="Column Name">
                    <validator type="empty_field"/>
                </param>
            </when>
        </conditional>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="golay_error_correction" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="golay_error_correction: Bool" help="[default: Yes]  Perform 12nt Golay error correction on the barcode reads."/>
            <param name="rev_comp_barcodes" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="rev_comp_barcodes: Bool" help="[default: No]  If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing."/>
            <param name="rev_comp_mapping_barcodes" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="rev_comp_mapping_barcodes: Bool" help="[default: No]  If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing."/>
            <param name="ignore_description_mismatch" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_description_mismatch: Bool" help="[default: No]  If enabled, ignore mismatches in sequence record description fields."/>
        </section>
    </inputs>
    <outputs>
        <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
        <data name="error_correction_details" format="qza" label="${tool.name} on ${on_string}: error_correction_details.qza" from_work_dir="error_correction_details.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: demux emp-paired
=========================
Demultiplex paired-end sequence data generated with the EMP protocol.


Outputs:
--------
:per_sample_sequences.qza: The resulting demultiplexed sequences.
:error_correction_details.qza: Detail about the barcode error corrections.

|  

Description:
------------
Demultiplex paired-end sequence data (i.e., map barcode reads to sample ids) for data generated with the Earth Microbiome Project (EMP) amplicon sequencing protocol. Details about this protocol can be found at http://www.earthmicrobiome.org/protocols-and-standards/


|  

</help>
    <citations>
        <citation type="doi">10.1038/nmeth.1184</citation>
        <citation type="doi">10.1101/gr.085464.108</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>