annotate qiime2__composition__da_barplot.xml @ 1:c2690db851b5 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 da-barplot" id="qiime2__composition__da_barplot" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Differential abundance bar plots</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 da_barplot '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance]" help="[required]  The ANCOM-BC output to be plotted.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[DifferentialAbundance]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DifferentialAbundance]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="effect_size_label" type="text" value="lfc" label="effect_size_label: Str" help="[default: 'lfc']  Label for effect sizes in `data`.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
            <param name="feature_id_label" type="text" value="id" label="feature_id_label: Str" help="[default: 'id']  Label for feature ids in `data`.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
            <param name="error_label" type="text" value="se" label="error_label: Str" help="[default: 'se']  Label for effect size errors in `data`.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
            <param name="significance_label" type="text" value="q_val" label="significance_label: Str" help="[default: 'q_val']  Label for statistical significance level in `data`.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
            <param name="significance_threshold" type="float" min="0.0" max="1.0" value="1.0" label="significance_threshold: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 1.0]  Exclude features with statistical significance level greater (i.e., less significant) than this threshold."/>
            <param name="effect_size_threshold" type="float" min="0.0" value="0.0" label="effect_size_threshold: Float % Range(0.0, None)" help="[default: 0.0]  Exclude features with an absolute value of effect size less than this threshold."/>
            <repeat name="feature_ids" help="[optional]  Exclude features if their ids are not included in this index." title="feature_ids: Metadata">
                <conditional name="__q2galaxy__GUI__conditional__feature_ids__">
                    <param name="type" type="select" label="feature_ids: 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>
            <conditional name="__q2galaxy__GUI__conditional__level_delimiter__" label="level_delimiter: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="level_delimiter: Str" help="[optional]  If feature ids encode hierarchical information, split the levels when generating feature labels in the visualization using this delimiter.">
                    <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="level_delimiter" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="level_delimiter" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <param name="label_limit" type="integer" optional="true" label="label_limit: Int" help="[optional]  Set the maximum length that will be viewable for axis labels. You can set this parameter if your axis labels are being cut off."/>
        </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 da-barplot
===============================
Differential abundance bar plots


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

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Description:
------------
Generate bar plot views of ANCOM-BC output. One plot will be present per column in the ANCOM-BC output. The `significance_threshold`, `effect_size_threshold` and `feature_ids` filter results are intersected, such that only features that remain after all three filters have been applied will be present in the output.


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