annotate qiime2__composition__ancom.xml @ 3:e3fdc3dc9fcc draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 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 composition ancom" id="qiime2__composition__ancom" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Apply ANCOM to identify features that differ in abundance.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version composition</version_command>
    <command detect_errors="exit_code">q2galaxy run composition ancom '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Composition]" help="[required]  The feature table to be used for ANCOM computation.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Composition]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]']</validator>
        </param>
        <conditional name="metadata">
            <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required]  The categorical sample metadata column to test for differential abundance across.">
                <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"/>
                <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
                    <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
                </param>
            </when>
            <when value="qza">
                <param name="source" type="data" format="qza" label="Metadata Source"/>
                <param name="column" type="text" label="Column Name">
                    <validator type="empty_field"/>
                </param>
            </when>
        </conditional>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="transform_function" type="select" label="transform_function: Str % Choices('sqrt', 'log', 'clr')" display="radio">
                <option value="sqrt">sqrt</option>
                <option value="log">log</option>
                <option value="clr" selected="true">clr</option>
            </param>
            <param name="difference_function" type="select" label="difference_function: Str % Choices('mean_difference', 'f_statistic')" display="radio">
                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
                <option value="mean_difference">mean_difference</option>
                <option value="f_statistic">f_statistic</option>
            </param>
            <param name="filter_missing" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="filter_missing: Bool" help="[default: No]  If True, samples with missing metadata values will be filtered from the table prior to analysis. If False, an error will be raised if there are any missing metadata values."/>
        </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: composition ancom
==========================
Apply ANCOM to identify features that differ in abundance.


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

|  

Description:
------------
Apply Analysis of Composition of Microbiomes (ANCOM) to identify features that are differentially abundant across groups.


|  

</help>
    <citations>
        <citation type="doi">10.3402/mehd.v26.27663</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>