annotate qiime2__emperor__plot.xml @ 0:e6978c621d70 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2022, 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: 2022.8.1)
for:
    qiime2 (version: 2022.8.1)
-->
<tool name="qiime2 emperor plot" id="qiime2__emperor__plot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Visualize and Interact with Principal Coordinates Analysis Plots</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version emperor</version_command>
    <command detect_errors="aggressive">q2galaxy run emperor plot '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="pcoa" type="data" format="qza" label="pcoa: PCoAResults" help="[required]  The principal coordinates matrix to be plotted.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="PCoAResults"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator>
        </param>
        <repeat name="metadata" min="1" help="[required]  The sample metadata." title="metadata: Metadata">
            <conditional name="__q2galaxy__GUI__conditional__metadata__">
                <param name="type" type="select" label="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="custom_axes" help="[optional]  Numeric sample metadata columns that should be included as axes in the Emperor plot." title="custom_axes: List[Str]">
                <param name="element" type="text" label="element: Str" help="[required]">
                    <sanitizer>
                        <valid initial="string.printable"/>
                    </sanitizer>
                    <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
                </param>
            </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="ignore_pcoa_features" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_pcoa_features: Bool" help="[default: No]  Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised."/>
        </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 plot
=====================
Visualize and Interact with Principal Coordinates Analysis Plots


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

|  

Description:
------------
Generates an interactive ordination plot where the user can visually integrate sample metadata.


|  

</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>