comparison qiime2__vizard__scatterplot_2d.xml @ 0:acada7129b61 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard commit 5f71b597c9495eae67a447744fded834f56ca1f7

0:acada7129b61

<?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 scatterplot-2d" id="qiime2__vizard__scatterplot_2d" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>2D Scatterplot</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 scatterplot_2d '$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 with at least two numeric measures for visualizing." 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">
            <conditional name="__q2galaxy__GUI__conditional__x_measure__" label="x_measure: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="x_measure: Str" help="[optional]  Numeric measure from the input Metadata that should be plotted on the x-axis.">
                    <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="x_measure" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="x_measure" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <conditional name="__q2galaxy__GUI__conditional__y_measure__" label="y_measure: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="y_measure: Str" help="[optional]  Numeric measure from the input Metadata that should be plotted on the y-axis.">
                    <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="y_measure" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="y_measure" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <conditional name="__q2galaxy__GUI__conditional__color_by__" label="color_by: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="color_by: Str" help="[optional]  Categorical measure from the input Metadata that should be used for color-coding the scatterplot.">
                    <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="color_by" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="color_by" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <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 scatterplot.">
                    <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="scatterplot_2d.test0.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <output name="visualization" ftype="qzv"/>
        </test>
        <test>
            <repeat name="metadata">
                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" value="tsv"/>
                    <param name="source" value="scatterplot_2d.test1.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="x_measure" value="x"/>
            <param name="y_measure" value="y"/>
            <param name="color_by" value="group"/>
            <output name="visualization" ftype="qzv"/>
        </test>
    </tests>
    <help>
QIIME 2: vizard scatterplot-2d
==============================
2D Scatterplot


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

|  

Description:
------------
Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Examples:
---------

scatterplot_defaults
********************
Using the ``qiime2 vizard scatterplot-2d`` tool:
 #. For *"metadata"*:

    - Perform the following steps.

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


 #. 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 scatterplot-2d [...] : visualization.qzv``
      - ``scatterplot.qzv``

scatterplot_all_measures
************************
Using the ``qiime2 vizard scatterplot-2d`` tool:
 #. For *"metadata"*:

    - Perform the following steps.

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


 #. Expand the ``additional options`` section

    #. Set *"x_measure"* to ``x``
    #. Set *"y_measure"* to ``y``
    #. Set *"color_by"* to ``group``

 #. 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 scatterplot-2d [...] : visualization.qzv``
      - ``scatterplot.qzv``


|  

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