annotate qiime2__longitudinal__anova.xml @ 3:5141cd08458f draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

<?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: 2024.2.1)
for:
    qiime2 (version: 2024.2.0)
-->
<tool name="qiime2 longitudinal anova" id="qiime2__longitudinal__anova" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>ANOVA test</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version longitudinal</version_command>
    <command detect_errors="exit_code">q2galaxy run longitudinal anova '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <repeat name="metadata" min="1" help="[required]  Sample metadata containing formula terms." 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="formula" type="text" label="formula: Str" help="[required]  R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format &quot;a ~ b + c&quot;, where &quot;a&quot; is the metric (dependent variable) and &quot;b&quot; and &quot;c&quot; are independent covariates. Use &quot;+&quot; to add a variable; &quot;+ a:b&quot; to add an interaction between variables a and b; &quot;*&quot; to include a variable and all interactions; and &quot;-&quot; to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises.">
            <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="sstype" type="select" label="sstype: Str % Choices('I', 'II', 'III')" display="radio">
                <option value="I">I</option>
                <option value="II" selected="true">II</option>
                <option value="III">III</option>
            </param>
            <param name="repeated_measures" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="repeated_measures: Bool" help="[default: No]  Perform ANOVA as a repeated measures ANOVA. Implemented via statsmodels, which has the following limitations: Currently, only fully balanced within-subject designs are supported. Calculation of between-subject effects and corrections for violation of sphericity are not yet implemented."/>
            <conditional name="__q2galaxy__GUI__conditional__individual_id_column__" label="individual_id_column: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="individual_id_column: Str" help="[optional]  The column containing individual ID with repeated measures to account for.This should not be included in the formula.">
                    <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="individual_id_column" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="individual_id_column" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <param name="rm_aggregate" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="rm_aggregate: Bool" help="[default: No]  If the data set contains more than a single observation per individual id and cell of the specified model, this function will be used to aggregate the data by the mean before running the ANOVA. Only applicable for repeated measures ANOVA. "/>
        </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: longitudinal anova
===========================
ANOVA test


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

|  

Description:
------------
Perform an ANOVA test on any factors present in a metadata file and/or metadata-transformable artifacts. This is followed by pairwise t-tests to examine pairwise differences between categorical sample groups.


|  

</help>
    <citations>
        <citation type="doi">10.1128/mSystems.00219-18</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>