annotate qiime2__vsearch__fastq_stats.xml @ 2:55e1a7184edd draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 65e4952f33eb335528e8553150e9097e5ea8f556

<?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: 2023.5.0)
for:
    qiime2 (version: 2023.5.1)
-->
<tool name="qiime2 vsearch fastq-stats" id="qiime2__vsearch__fastq_stats" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Fastq stats with vsearch.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version vsearch</version_command>
    <command detect_errors="exit_code">q2galaxy run vsearch fastq_stats '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="sequences" type="data" format="qza" label="sequences: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required]  Fastq sequences">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <conditional name="__q2galaxy__GUI__conditional__threads__">
                <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of threads used for computation.">
                    <option value="auto">auto (Str)</option>
                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
                </param>
                <when value="auto">
                    <param name="threads" type="hidden" value="auto"/>
                </when>
                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
                    <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1]  The number of threads used for computation."/>
                </when>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: vsearch fastq-stats
============================
Fastq stats with vsearch.


Outputs:
--------
:visualization.qzv: &lt;no description&gt;

|  

Description:
------------
A fastq overview via vsearch's fastq_stats, fastq_eestats and fastq_eestats2 utilities. Please see https://github.com/torognes/vsearch for detailed documentation of these tools.


|  

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