annotate qiime2__diversity__beta_rarefaction.xml @ 5:1506cdb7caad draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 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 diversity beta-rarefaction" id="qiime2__diversity__beta_rarefaction" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Beta diversity rarefaction</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 diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity beta_rarefaction '$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[Frequency]" help="[required]  Feature table upon which to perform beta diversity rarefaction analyses.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'braycurtis', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'generalized_unifrac', 'hamming', 'jaccard', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac', 'yule')">
            <option value="__q2galaxy__::literal::None">Selection required</option>
            <option value="aitchison">aitchison</option>
            <option value="braycurtis">braycurtis</option>
            <option value="canberra">canberra</option>
            <option value="canberra_adkins">canberra_adkins</option>
            <option value="chebyshev">chebyshev</option>
            <option value="cityblock">cityblock</option>
            <option value="correlation">correlation</option>
            <option value="cosine">cosine</option>
            <option value="dice">dice</option>
            <option value="euclidean">euclidean</option>
            <option value="generalized_unifrac">generalized_unifrac</option>
            <option value="hamming">hamming</option>
            <option value="jaccard">jaccard</option>
            <option value="jensenshannon">jensenshannon</option>
            <option value="matching">matching</option>
            <option value="minkowski">minkowski</option>
            <option value="rogerstanimoto">rogerstanimoto</option>
            <option value="russellrao">russellrao</option>
            <option value="seuclidean">seuclidean</option>
            <option value="sokalmichener">sokalmichener</option>
            <option value="sokalsneath">sokalsneath</option>
            <option value="sqeuclidean">sqeuclidean</option>
            <option value="unweighted_unifrac">unweighted_unifrac</option>
            <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
            <option value="weighted_unifrac">weighted_unifrac</option>
            <option value="yule">yule</option>
            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
        </param>
        <param name="clustering_method" type="select" label="clustering_method: Str % Choices('nj', 'upgma')" display="radio">
            <option value="__q2galaxy__::literal::None">Selection required</option>
            <option value="nj">nj</option>
            <option value="upgma">upgma</option>
            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
        </param>
        <repeat name="metadata" min="1" help="[required]  The sample metadata used for the Emperor jackknifed PCoA plot." 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="sampling_depth" type="integer" min="1" value="" label="sampling_depth: Int % Range(1, None)" help="[required]  The total frequency that each sample should be rarefied to prior to computing the diversity metric."/>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="phylogeny" type="data" format="qza" optional="true" label="phylogeny: Phylogeny[Rooted]" help="[optional]  Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics]">
                <options options_filter_attribute="metadata.semantic_type">
                    <filter type="add_value" value="Phylogeny[Rooted]"/>
                </options>
                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
            </param>
            <param name="iterations" type="integer" min="2" value="10" label="iterations: Int % Range(2, None)" help="[default: 10]  Number of times to rarefy the feature table at a given sampling depth."/>
            <param name="correlation_method" type="select" label="correlation_method: Str % Choices('pearson', 'spearman')" display="radio">
                <option value="pearson">pearson</option>
                <option value="spearman" selected="true">spearman</option>
            </param>
            <param name="color_scheme" type="select" label="color_scheme: Str % Choices('BrBG', 'BrBG_r', 'PRGn', 'PRGn_r', 'PiYG', 'PiYG_r', 'PuOr', 'PuOr_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r')">
                <option value="BrBG" selected="true">BrBG</option>
                <option value="BrBG_r">BrBG_r</option>
                <option value="PRGn">PRGn</option>
                <option value="PRGn_r">PRGn_r</option>
                <option value="PiYG">PiYG</option>
                <option value="PiYG_r">PiYG_r</option>
                <option value="PuOr">PuOr</option>
                <option value="PuOr_r">PuOr_r</option>
                <option value="RdBu">RdBu</option>
                <option value="RdBu_r">RdBu_r</option>
                <option value="RdGy">RdGy</option>
                <option value="RdGy_r">RdGy_r</option>
                <option value="RdYlBu">RdYlBu</option>
                <option value="RdYlBu_r">RdYlBu_r</option>
                <option value="RdYlGn">RdYlGn</option>
                <option value="RdYlGn_r">RdYlGn_r</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: diversity beta-rarefaction
===================================
Beta diversity rarefaction


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

|  

Description:
------------
Repeatedly rarefy a feature table to compare beta diversity results within a given rarefaction depth.

For a given beta diversity metric, this visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered by UPGMA or neighbor joining with support calculation, and a heatmap showing the correlation between rarefaction trials of that beta diversity metric.


|  

</help>
    <citations>
        <citation type="bibtex">@article{cite1,
 author = {Mantel, Nathan},
 journal = {Cancer research},
 number = {2 Part 1},
 pages = {209--220},
 publisher = {AACR},
 title = {The detection of disease clustering and a generalized regression approach},
 volume = {27},
 year = {1967}
}
</citation>
        <citation type="doi">https://doi.org/10.1098/rspl.1895.0041</citation>
        <citation type="doi">https://doi.org/10.2307/1422689</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>