annotate qiime2__diversity__tsne.xml @ 2:70d6cf1e8db0 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 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 diversity tsne" id="qiime2__diversity__tsne" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>t-distributed stochastic neighbor embedding</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity tsne '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required]  The distance matrix on which t-SNE 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="perplexity" type="float" min="1" value="25.0" label="perplexity: Float % Range(1, None)" help="[default: 25.0]  Provide the balance between local and global structure. Low values concentrate on local structure. Large values sacrifice local details for a broader global embedding. The default value is 25 to achieve better results for small microbiome datasets."/>
            <param name="n_iter" type="integer" min="1" value="1000" label="n_iter: Int % Range(1, None)" help="[default: 1000]"/>
            <param name="learning_rate" type="float" min="10.0" value="200.0" label="learning_rate: Float % Range(10.0, None)" help="[default: 200.0]  Controls how much the weights are adjusted at each update."/>
            <param name="early_exaggeration" type="float" min="0" value="12.0" label="early_exaggeration: Float % Range(0, None)" help="[default: 12.0]  Affects the tightness of the shown clusters. Larger values increase the distance between natural clusters in the embedded space."/>
            <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="tsne" format="qza" label="${tool.name} on ${on_string}: tsne.qza" from_work_dir="tsne.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: diversity tsne
=======================
t-distributed stochastic neighbor embedding


Outputs:
--------
:tsne.qza: The resulting t-SNE matrix.

|  

Description:
------------
Apply t-distributed stochastic neighbor embedding.


|  

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