view qiime2__diversity__alpha.xml @ 3:a731d77cdb3b draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 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 diversity alpha" id="qiime2__diversity__alpha" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Alpha diversity</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity alpha '$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[PresenceAbsence]"/>
                <filter type="add_value" value="FeatureTable[Frequency]"/>
                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
            </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="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', 'observed_features', 'osd', 'pielou_e', 'robbins', 'shannon', '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="observed_features">observed_features</option>
            <option value="osd">osd</option>
            <option value="pielou_e">pielou_e</option>
            <option value="robbins">robbins</option>
            <option value="shannon">shannon</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="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
========================
Alpha diversity


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

|  

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


|  

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