<tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="@WRAPPER_VERSION@.0">
    <description> on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>alpha_diversity.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
#set $chosen_metrics = str( $metrics ).split( "," )
alpha_diversity.py
    --input_path '$input_path'
    -o alphadiv
    --metrics '$metrics'
    #if "PD_whole_tree" in $chosen_metrics:
        --tree_path '$tree_path'
    #end if
    ]]></command>
    <inputs>
        <param argument="--input_path" type="data" format="tabular,txt,tsv,biom" multiple="True"  label="OTU table"/>
        <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Alpha-diversity metric(s) to use">
            <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option>
            <option value="berger_parker_d">Berger-Parker dominance</option>
            <option value="brillouin_d">Brillouin index of alpha diversity</option>
            <option value="chao1" selected="true">chao1 richness estimator</option>
            <option value="chao1_ci">chao1 confidence interval</option>
            <option value="dominance">Dominance</option>
            <option value="doubles">Number of double occurrences (doubletons)</option>
            <option value="enspie">ENS_pie alpha diversity measure</option>
            <option value="equitability">Equitability</option>
            <option value="esty_ci">Esty’s CI</option>
            <option value="fisher_alpha">Fisher’s alpha</option>
            <option value="gini_index">Gini index</option>
            <option value="goods_coverage">Good’s coverage of counts</option>
            <option value="heip_e">Heip’s evenness measure</option>
            <option value="kempton_taylor_q">Kempton-Taylor Q index of alpha diversity</option>
            <option value="margalef">Margalef’s richness index</option>
            <option value="mcintosh_d">McIntosh dominance index D</option>
            <option value="mcintosh_e">McIntosh’s evenness measure E</option>
            <option value="menhinick">Menhinick’s richness index</option>
            <option value="michaelis_menten_fit">Michaelis-Menten fit to rarefaction curve of observed OTUs</option>
            <option value="observed_otus">Number of distinct OTUs</option>
            <option value="observed_species" selected="true">Number of distinct species</option>
            <option value="osd">Observed OTUs, singles, and doubles</option>
            <option value="simpson_reciprocal">simpson_reciprocal</option>
            <option value="robbins">Robbins’ estimator for the probability of unobserved outcomes</option>
            <option value="shannon">Shannon entropy of counts</option>
            <option value="simpson">Simpson’s index</option>
            <option value="simpson_e">Simpson’s evenness measure E</option>
            <option value="singles">Number of single occurrencesles</option>
            <option value="strong"> Strong’s dominance index</option>
            <option value="PD_whole_tree">Phylogenetic diversity</option>
        </param>
        <param argument="--tree_path" type="data" format="nhx" optional="true" label="Newick tree (optional, except for PD_whole_tree metric)"/>
    </inputs>
    <outputs>
        <data name="alpha_diversity" format="tabular" from_work_dir="alphadiv" label="${tool.name} on ${on_string}: Alpha diversity"/>
    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="input_path" value="alpha_diversity/otu_table.biom"/>
            <output name="alpha_diversity" file="alpha_diversity/alphadiv"/>
        </test>
        <test><!-- test with all metrics and tree file -->
            <param name="input_path" value="alpha_diversity/otu_table.biom"/>
            <param name="metrics" value="ace,berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,michaelis_menten_fit,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree"/>
            <param name="tree_path" value="alpha_diversity/rep_set.tre"/>
            <output name="alpha_diversity" ftype="tabular">
                <assert_contents>
                    <has_text text="ace"/>
                    <has_text text="simpson"/>
                    <has_text text="PD_whole_tree"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool calculates alpha diversity, or within-sample diversity, using an
OTU table.

The resulting file(s) is a tab-delimited text file, where the columns correspond
to alpha diversity metrics and the rows correspond to samples and their calculated
diversity measurements. When a folder is given as input (-i), the script processes
every otu table file in the given folder, and creates a corresponding file in the
output directory.

More information about this tool is available on
`QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_.
    ]]></help>
    <citations>
        <expand macro="citations"/>
    </citations>
</tool>