annotate qiime2__diversity_lib__alpha_passthrough.xml @ 6:93509f4b48aa draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit b1fccfb38b4873cd4699743033449014a2978e7d

<?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: 2025.4.0)
for:
    qiime2 (version: 2025.4.0)
-->
<tool name="qiime2 diversity-lib alpha-passthrough" id="qiime2__diversity_lib__alpha_passthrough" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
    <description>Alpha Passthrough (non-phylogenetic)</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
    </requirements>
    <version_command>q2galaxy version diversity_lib</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity_lib alpha_passthrough '$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]  The feature table containing the samples for which a selected metric should be computed.">
            <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('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong')">
            <option value="__q2galaxy__::literal::None">Selection required</option>
            <option value="ace">ace</option>
            <option value="berger_parker_d">berger_parker_d</option>
            <option value="brillouin_d">brillouin_d</option>
            <option value="chao1">chao1</option>
            <option value="chao1_ci">chao1_ci</option>
            <option value="dominance">dominance</option>
            <option value="doubles">doubles</option>
            <option value="enspie">enspie</option>
            <option value="esty_ci">esty_ci</option>
            <option value="fisher_alpha">fisher_alpha</option>
            <option value="gini_index">gini_index</option>
            <option value="goods_coverage">goods_coverage</option>
            <option value="heip_e">heip_e</option>
            <option value="kempton_taylor_q">kempton_taylor_q</option>
            <option value="lladser_pe">lladser_pe</option>
            <option value="margalef">margalef</option>
            <option value="mcintosh_d">mcintosh_d</option>
            <option value="mcintosh_e">mcintosh_e</option>
            <option value="menhinick">menhinick</option>
            <option value="michaelis_menten_fit">michaelis_menten_fit</option>
            <option value="osd">osd</option>
            <option value="robbins">robbins</option>
            <option value="simpson">simpson</option>
            <option value="simpson_e">simpson_e</option>
            <option value="singles">singles</option>
            <option value="strong">strong</option>
            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
        </param>
    </inputs>
    <outputs>
        <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="table" value="alpha_passthrough.test0.feature-table.qza" ftype="qza"/>
            <param name="metric" value="simpson"/>
            <output name="vector" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: diversity-lib alpha-passthrough
========================================
Alpha Passthrough (non-phylogenetic)


Outputs:
--------
:vector.qza: Vector containing per-sample values for the chosen metric.

|  

Description:
------------
Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.

Examples:
---------

basic
*****
Using the ``qiime2 diversity-lib alpha-passthrough`` tool:
 #. Set *"table"* to ``#: feature-table.qza``
 #. Set *"metric"* to ``simpson``
 #. Press the ``Execute`` button.

Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
 (Renaming is optional, but it will make any subsequent steps easier to complete.)

 .. list-table::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza``
      - ``simpson-vector.qza``


|  

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