view qiime2__vizard__lineplot.xml @ 0:df9f1ff48c29 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 lineplot" id="qiime2__vizard__lineplot" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Lineplot</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 lineplot '$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>
        <param name="x_measure" type="text" label="x_measure: Str" help="[required]  Numeric 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 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>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="replicate_method" type="select" label="replicate_method: Str % Choices('none', 'median', 'mean')" display="radio">
                <option value="none" selected="true">none</option>
                <option value="median">median</option>
                <option value="mean">mean</option>
            </param>
            <conditional name="__q2galaxy__GUI__conditional__group_by__" label="group_by: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="group_by: Str" help="[optional]  Categorical measure from the input Metadata that should be used for grouping the lineplot.">
                    <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="group_by" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="group_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 lineplot.">
                    <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="lineplot.test0.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="x_measure" value="x"/>
            <param name="y_measure" value="y"/>
            <param name="replicate_method" value="median"/>
            <param name="group_by" value="group"/>
            <param name="title" value="Lineplot with median replicate method__comma__ grouped by `group`."/>
            <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="lineplot.test1.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="x_measure" value="x"/>
            <param name="y_measure" value="y"/>
            <param name="replicate_method" value="mean"/>
            <param name="group_by" value="group"/>
            <param name="title" value="Lineplot with mean replicate method__comma__ grouped by `group`."/>
            <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="lineplot.test2.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="x_measure" value="x"/>
            <param name="y_measure" value="y"/>
            <param name="replicate_method" value="median"/>
            <param name="title" value="Lineplot with median replicate method (no grouping)."/>
            <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="lineplot.test3.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="x_measure" value="x"/>
            <param name="y_measure" value="y"/>
            <param name="replicate_method" value="mean"/>
            <param name="title" value="Lineplot with mean replicate method (no grouping)."/>
            <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="lineplot.test4.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="x_measure" value="a"/>
            <param name="y_measure" value="y"/>
            <param name="group_by" value="group"/>
            <param name="title" value="Lineplot with no replicate method__comma__ grouped by `group`."/>
            <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="lineplot.test5.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="x_measure" value="b"/>
            <param name="y_measure" value="y"/>
            <param name="title" value="Lineplot with no replicate method (no grouping)."/>
            <output name="visualization" ftype="qzv"/>
        </test>
    </tests>
    <help>
QIIME 2: vizard lineplot
========================
Lineplot


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

|  

Description:
------------
Basic lineplot for visualizing two numeric Metadata measures with optional grouping. All numeric columns present in the Metadata will be available as drop-down options on the Y-axis, but the chosen `x_measure` remains fixed.

Examples:
---------

lineplot_median_replicates_with_grouping
****************************************
Using the ``qiime2 vizard lineplot`` 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``
 #. Expand the ``additional options`` section

    #. Set *"replicate_method"* to ``median``
    #. Set *"group_by"* to ``group``
    #. Set *"title"* to ``Lineplot with median replicate method, grouped by `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 lineplot [...] : visualization.qzv``
      - ``lineplot.qzv``

lineplot_mean_replicates_with_grouping
**************************************
Using the ``qiime2 vizard lineplot`` 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``
 #. Expand the ``additional options`` section

    #. Set *"replicate_method"* to ``mean``
    #. Set *"group_by"* to ``group``
    #. Set *"title"* to ``Lineplot with mean replicate method, grouped by `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 lineplot [...] : visualization.qzv``
      - ``lineplot.qzv``

lineplot_median_replicates_no_grouping
**************************************
Using the ``qiime2 vizard lineplot`` 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``
 #. Expand the ``additional options`` section

    #. Set *"replicate_method"* to ``median``
    #. Set *"title"* to ``Lineplot with median replicate method (no grouping).``

 #. 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 lineplot [...] : visualization.qzv``
      - ``lineplot.qzv``

lineplot_mean_replicates_no_grouping
************************************
Using the ``qiime2 vizard lineplot`` 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``
 #. Expand the ``additional options`` section

    #. Set *"replicate_method"* to ``mean``
    #. Set *"title"* to ``Lineplot with mean replicate method (no grouping).``

 #. 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 lineplot [...] : visualization.qzv``
      - ``lineplot.qzv``

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

    - Perform the following steps.

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


 #. Set *"x_measure"* to ``a``
 #. Set *"y_measure"* to ``y``
 #. Expand the ``additional options`` section

    #. Set *"group_by"* to ``group``
    #. Set *"title"* to ``Lineplot with no replicate method, grouped by `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 lineplot [...] : visualization.qzv``
      - ``lineplot.qzv``

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

    - Perform the following steps.

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


 #. Set *"x_measure"* to ``b``
 #. Set *"y_measure"* to ``y``
 #. Expand the ``additional options`` section

    - Set *"title"* to ``Lineplot with no replicate method (no grouping).``

 #. 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 lineplot [...] : visualization.qzv``
      - ``lineplot.qzv``


|  

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