<?xml version="1.0" ?>
<tool id="qiime_diversity_alpha" name="qiime diversity alpha"
      version="2020.8">
  <description>Alpha diversity</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity alpha

--i-table=$itable

--p-metric=$pmetric

--o-alpha-diversity=oalphadiversity

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp oalphadiversity.qza $oalphadiversity

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]   The feature table containing the samples for which alpha diversity should be computed.          [required]" name="itable" optional="False" type="data" />
    <param label="--p-metric: " name="pmetric" optional="False" type="select">
      <option value="strong">strong</option>
      <option value="observed_features">observed_features</option>
      <option value="heip_e">heip_e</option>
      <option value="dominance">dominance</option>
      <option value="goods_coverage">goods_coverage</option>
      <option value="ace">ace</option>
      <option value="gini_index">gini_index</option>
      <option value="simpson_e">simpson_e</option>
      <option value="osd">osd</option>
      <option value="pielou_e">pielou_e</option>
      <option value="mcintosh_e">mcintosh_e</option>
      <option value="esty_ci">esty_ci</option>
      <option value="berger_parker_d">berger_parker_d</option>
      <option value="shannon">shannon</option>
      <option value="enspie">enspie</option>
      <option value="mcintosh_d">mcintosh_d</option>
      <option value="chao1_ci">chao1_ci</option>
      <option value="lladser_pe">lladser_pe</option>
      <option value="brillouin_d">brillouin_d</option>
      <option value="menhinick">menhinick</option>
      <option value="simpson">simpson</option>
      <option value="margalef">margalef</option>
      <option value="robbins">robbins</option>
      <option value="doubles">doubles</option>
      <option value="chao1">chao1</option>
      <option value="michaelis_menten_fit">michaelis_menten_fit</option>
      <option value="singles">singles</option>
      <option value="kempton_taylor_q">kempton_taylor_q</option>
      <option value="fisher_alpha">fisher_alpha</option>
    </param>
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity" />
    
  </outputs>

  <help><![CDATA[
Alpha diversity
###############################################################

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

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples for which alpha diversity
    should be computed.
metric : Str % Choices('mcintosh_e', 'esty_ci', 'chao1', 'observed_features', 'ace', 'margalef', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'heip_e', 'michaelis_menten_fit', 'enspie', 'menhinick', 'shannon', 'pielou_e', 'singles', 'simpson', 'chao1_ci', 'strong', 'fisher_alpha', 'osd', 'dominance', 'robbins', 'lladser_pe', 'kempton_taylor_q', 'mcintosh_d', 'brillouin_d', 'goods_coverage')
    The alpha diversity metric to be computed.

Returns
-------
alpha_diversity : SampleData[AlphaDiversity]
    Vector containing per-sample alpha diversities.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>