<?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: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 emperor biplot" id="qiime2__emperor__biplot" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Visualize and Interact with Principal Coordinates Analysis Biplot</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version emperor</version_command>
    <command detect_errors="exit_code">q2galaxy run emperor biplot '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="biplot" type="data" format="qza" label="biplot: PCoAResults % Properties('biplot')" help="[required]  The principal coordinates matrix to be plotted.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="PCoAResults % Properties('biplot')"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ["PCoAResults % Properties('biplot')"]</validator>
        </param>
        <repeat name="sample_metadata" min="1" help="[required]  The sample metadata" title="sample_metadata: Metadata">
            <conditional name="__q2galaxy__GUI__conditional__sample_metadata__">
                <param name="type" type="select" label="sample_metadata: Metadata">
                    <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"/>
                </when>
                <when value="qza">
                    <param name="source" type="data" format="qza" label="Metadata Source"/>
                </when>
            </conditional>
        </repeat>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <repeat name="feature_metadata" help="[optional]  The feature metadata (useful to manipulate the arrows in the plot)." title="feature_metadata: Metadata">
                <conditional name="__q2galaxy__GUI__conditional__feature_metadata__">
                    <param name="type" type="select" label="feature_metadata: Metadata">
                        <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"/>
                    </when>
                    <when value="qza">
                        <param name="source" type="data" format="qza" label="Metadata Source"/>
                    </when>
                </conditional>
            </repeat>
            <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No]  This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: &quot;This sample has no metadata&quot;. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata."/>
            <param name="invert" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="invert: Bool" help="[default: No]  If specified, the point and arrow coordinates will be swapped."/>
            <param name="number_of_features" type="integer" min="1" value="5" label="number_of_features: Int % Range(1, None)" help="[default: 5]  The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin)."/>
        </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: emperor biplot
=======================
Visualize and Interact with Principal Coordinates Analysis Biplot


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

|  

Description:
------------
Generates an interactive ordination biplot where the user can visually integrate sample and feature metadata. Vectors representing the n most important features are then plotted in the emperor visualization (5 largest, by default).


|  

</help>
    <citations>
        <citation type="doi">10.1186/2047-217X-2-16</citation>
        <citation type="doi">10.1016/j.chom.2016.12.009</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>