annotate qiime2__vizard__heatmap.xml @ 0:45c348a09fa0 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard 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 vizard heatmap" id="qiime2__vizard__heatmap" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Heatmap</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 vizard</version_command>
    <command detect_errors="exit_code">q2galaxy run vizard heatmap '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <repeat name="metadata" min="1" help="[required]  Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric." 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>
        <param name="x_measure" type="text" label="x_measure: Str" help="[required]  Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.">
            <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>
        <param name="y_measure" type="text" label="y_measure: Str" help="[required]  Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.">
            <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>
        <param name="gradient_measure" type="text" label="gradient_measure: Str" help="[required]  Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.">
            <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>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <conditional name="__q2galaxy__GUI__conditional__title__" label="title: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="title: Str" help="[optional]  The title of the heatmap.">
                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                    <option value="__q2galaxy__::control::provide">Provide a value</option>
                </param>
                <when value="__q2galaxy__::control::default">
                    <param name="title" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="title" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </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>
        <test>
            <repeat name="metadata">
                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" value="tsv"/>
                    <param name="source" value="heatmap.test0.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="x_measure" value="x"/>
            <param name="y_measure" value="y"/>
            <param name="gradient_measure" value="a"/>
            <output name="visualization" ftype="qzv"/>
        </test>
    </tests>
    <help>
QIIME 2: vizard heatmap
=======================
Heatmap


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

|  

Description:
------------
Basic heatmap for visualizing three Metadata measures.

Examples:
---------

heatmap
*******
Using the ``qiime2 vizard heatmap`` tool:
 #. For *"metadata"*:

    - Perform the following steps.

      #. Leave as ``Metadata from TSV``
      #. Set *"Metadata Source"* to ``metadata.tsv``


 #. Set *"x_measure"* to ``x``
 #. Set *"y_measure"* to ``y``
 #. Set *"gradient_measure"* to ``a``
 #. Press the ``Execute`` button.

Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
 (Renaming is optional, but it will make any subsequent steps easier to complete.)

 .. list-table::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 vizard heatmap [...] : visualization.qzv``
      - ``heatmap.qzv``


|  

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