annotate qiime2__diversity__alpha_phylogenetic.xml @ 7:8454d1802ed2 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.7.0)
for:
    qiime2 (version: 2025.7.0)
-->
<tool name="qiime2 diversity alpha-phylogenetic" id="qiime2__diversity__alpha_phylogenetic" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
    <description>Alpha diversity (phylogenetic)</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity alpha_phylogenetic '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which alpha diversity should be computed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
        </param>
        <param name="phylogeny" type="data" format="qza" label="phylogeny: Phylogeny[Rooted]" help="[required]  Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="Phylogeny[Rooted]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
        </param>
        <param name="metric" type="select" label="metric: Str % Choices('faith_pd')" display="radio">
            <option value="faith_pd">faith_pd</option>
        </param>
    </inputs>
    <outputs>
        <data name="alpha_diversity" format="qza" label="${tool.name} on ${on_string}: alpha_diversity.qza" from_work_dir="alpha_diversity.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: diversity alpha-phylogenetic
=====================================
Alpha diversity (phylogenetic)


Outputs:
--------
:alpha_diversity.qza: Vector containing per-sample alpha diversities.

|  

Description:
------------
Computes a user-specified phylogenetic alpha diversity metric for all samples in a feature table.


|  

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