annotate qiime2__diversity__umap.xml @ 5:9c7d4870e7c2 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 5f71b597c9495eae67a447744fded834f56ca1f7

<?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: 2024.10.0)
for:
    qiime2 (version: 2024.10.1)
-->
<tool name="qiime2 diversity umap" id="qiime2__diversity__umap" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Uniform Manifold Approximation and Projection</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity umap '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required]  The distance matrix on which UMAP should be computed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="DistanceMatrix"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="number_of_dimensions" type="integer" min="2" value="2" label="number_of_dimensions: Int % Range(2, None)" help="[default: 2]  Dimensions to reduce the distance matrix to."/>
            <param name="n_neighbors" type="integer" min="1" value="15" label="n_neighbors: Int % Range(1, None)" help="[default: 15]  Provide the balance between local and global structure. Low values prioritize the preservation of local structures. Large values sacrifice local details for a broader global embedding."/>
            <param name="min_dist" type="float" min="0" value="0.4" label="min_dist: Float % Range(0, None)" help="[default: 0.4]  Controls the cluster size. Low values cause clumpier clusters. Higher values preserve a broad topological structure. To get less overlapping data points the default value is set to 0.4. For more details visit: https://umap-learn.readthedocs.io/en/latest/parameters.html"/>
            <param name="random_state" type="integer" optional="true" label="random_state: Int" help="[optional]  Seed used by random number generator."/>
        </section>
    </inputs>
    <outputs>
        <data name="umap" format="qza" label="${tool.name} on ${on_string}: umap.qza" from_work_dir="umap.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: diversity umap
=======================
Uniform Manifold Approximation and Projection


Outputs:
--------
:umap.qza: The resulting UMAP matrix.

|  

Description:
------------
Apply Uniform Manifold Approximation and Projection.


|  

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