annotate qiime2__vsearch__merge_pairs.xml @ 7:02137c034346 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.10.0)
for:
    qiime2 (version: 2025.10.0)
-->
<tool name="qiime2 vsearch merge-pairs" id="qiime2__vsearch__merge_pairs" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Merge paired-end reads.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
    </requirements>
    <version_command>q2galaxy version vsearch</version_command>
    <command detect_errors="exit_code">q2galaxy run vsearch merge_pairs '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[PairedEndSequencesWithQuality]" help="[required]  The demultiplexed paired-end sequences to be merged.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="truncqual" type="integer" min="0" optional="true" label="truncqual: Int % Range(0, None)" help="[optional]  Truncate sequences at the first base with the specified quality score value or lower."/>
            <param name="minlen" type="integer" min="0" value="1" label="minlen: Int % Range(0, None)" help="[default: 1]  Sequences shorter than minlen after truncation are discarded."/>
            <param name="maxns" type="integer" min="0" optional="true" label="maxns: Int % Range(0, None)" help="[optional]  Sequences with more than maxns N characters are discarded."/>
            <param name="allowmergestagger" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allowmergestagger: Bool" help="[default: No]  Allow merging of staggered read pairs."/>
            <param name="minovlen" type="integer" min="5" value="10" label="minovlen: Int % Range(5, None)" help="[default: 10]  Minimum length of the area of overlap between reads during merging."/>
            <param name="maxdiffs" type="integer" min="0" value="10" label="maxdiffs: Int % Range(0, None)" help="[default: 10]  Maximum number of mismatches in the area of overlap during merging."/>
            <param name="minmergelen" type="integer" min="0" optional="true" label="minmergelen: Int % Range(0, None)" help="[optional]  Minimum length of the merged read to be retained."/>
            <param name="maxmergelen" type="integer" min="0" optional="true" label="maxmergelen: Int % Range(0, None)" help="[optional]  Maximum length of the merged read to be retained."/>
            <param name="maxee" type="float" min="0.0" optional="true" label="maxee: Float % Range(0.0, None)" help="[optional]  Maximum number of expected errors in the merged read to be retained."/>
            <param name="qmin" type="integer" min="0" value="0" label="qmin: Int % Range(0, None)" help="[default: 0]  Minimum quality score accepted when reading FASTQ files."/>
            <param name="qminout" type="integer" min="0" value="0" label="qminout: Int % Range(0, None)" help="[default: 0]  Minimum quality score used when writing FASTQ files. Only applies to overlap region."/>
            <param name="qmax" type="integer" min="0" value="41" label="qmax: Int % Range(0, None)" help="[default: 41]  Maximum quality score accepted when reading FASTQ files."/>
            <param name="qmaxout" type="integer" min="0" value="41" label="qmaxout: Int % Range(0, None)" help="[default: 41]  Maximum quality score used when writing FASTQ files. Only applies to overlap region."/>
        </section>
    </inputs>
    <outputs>
        <data name="merged_sequences" format="qza" label="${tool.name} on ${on_string}: merged_sequences.qza" from_work_dir="merged_sequences.qza"/>
        <data name="unmerged_sequences" format="qza" label="${tool.name} on ${on_string}: unmerged_sequences.qza" from_work_dir="unmerged_sequences.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: vsearch merge-pairs
============================
Merge paired-end reads.


Outputs:
--------
:merged_sequences.qza: The merged sequences.
:unmerged_sequences.qza: The unmerged paired-end reads.

|  

Description:
------------
Merge paired-end sequence reads using vsearch's merge_pairs function. See the vsearch documentation for details on how paired-end merging is performed, and for more information on the parameters to this method.


|  

</help>
    <citations>
        <citation type="doi">10.7717/peerj.2584</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>