annotate qiime2__longitudinal__pairwise_differences.xml @ 2:b56e60e6c6e0 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 65e4952f33eb335528e8553150e9097e5ea8f556

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, 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: 2023.5.0)
for:
    qiime2 (version: 2023.5.1)
-->
<tool name="qiime2 longitudinal pairwise-differences" id="qiime2__longitudinal__pairwise_differences" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Paired difference testing and boxplots</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version longitudinal</version_command>
    <command detect_errors="exit_code">q2galaxy run longitudinal pairwise_differences '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <repeat name="metadata" min="1" help="[required]  Sample metadata file containing individual_id_column." 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="metric" type="text" label="metric: Str" help="[required]  Numerical metadata or artifact column to test.">
            <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="state_column" type="text" label="state_column: Str" help="[required]  Metadata column containing state (e.g., Time) across which samples are paired.">
            <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="state_1" type="text" label="state_1: Str" help="[required]  Baseline state column value.">
            <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="state_2" type="text" label="state_2: Str" help="[required]  State column value to pair with baseline.">
            <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="individual_id_column" type="text" label="individual_id_column: Str" help="[required]  Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state_1 or state_2, that subject will be dropped and reported in standard output by default. Set replicate_handling=&quot;random&quot; to instead randomly select one member.">
            <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="table" type="data" format="qza" optional="true" label="table: FeatureTable[RelativeFrequency]" help="[optional]  Feature table to optionally use for paired comparisons.">
                <options options_filter_attribute="metadata.semantic_type">
                    <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                </options>
                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
            </param>
            <conditional name="__q2galaxy__GUI__conditional__group_column__" label="group_column: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="group_column: Str" help="[optional]  Metadata column on which to separate groups for comparison">
                    <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_column" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="group_column" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <param name="parametric" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parametric: Bool" help="[default: No]  Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests."/>
            <param name="palette" type="select" label="palette: Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis')">
                <option value="Set1" selected="true">Set1</option>
                <option value="Set2">Set2</option>
                <option value="Set3">Set3</option>
                <option value="Pastel1">Pastel1</option>
                <option value="Pastel2">Pastel2</option>
                <option value="Paired">Paired</option>
                <option value="Accent">Accent</option>
                <option value="Dark2">Dark2</option>
                <option value="tab10">tab10</option>
                <option value="tab20">tab20</option>
                <option value="tab20b">tab20b</option>
                <option value="tab20c">tab20c</option>
                <option value="viridis">viridis</option>
                <option value="plasma">plasma</option>
                <option value="inferno">inferno</option>
                <option value="magma">magma</option>
                <option value="terrain">terrain</option>
                <option value="rainbow">rainbow</option>
                <option value="cividis">cividis</option>
            </param>
            <param name="replicate_handling" type="select" label="replicate_handling: Str % Choices('error', 'random', 'drop')" display="radio">
                <option value="error" selected="true">error</option>
                <option value="random">random</option>
                <option value="drop">drop</option>
            </param>
        </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 pairwise-differences
==========================================
Paired difference testing and boxplots


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

|  

Description:
------------
Performs paired difference testing between samples from each subject. Sample pairs may represent a typical intervention study (e.g., samples collected pre- and post-treatment), paired samples from two different timepoints (e.g., in a longitudinal study design), or identical samples receiving different treatments. This action tests whether the change in a numeric metadata value "metric" differs from zero and differs between groups (e.g., groups of subjects receiving different treatments), and produces boxplots of paired difference distributions for each group. Note that "metric" can be derived from a feature table or metadata.


|  

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