<tool id="vegan_diversity" name="Vegan Diversity" version="@TOOL_VERSION@">
    <description>
        index
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio.tools_xrefs" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
    <![CDATA[
        Rscript "${vegan_diversity_script}"
    ]]>
    </command>
    <configfiles>
        <configfile name="vegan_diversity_script"><![CDATA[
@RSCRIPT_PREAMBLE@
@RSCRIPT_LOAD_TABULAR_FILE@

write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", quote=FALSE, col.names=NA, sep = "\t")
    ]]>
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="params_load_tabular_file" />
        <conditional name="index_type">
            <param name="index_type_selector" type="select" label="Diversity index to use">
                <option value="shannon" selected="True">Shannon or Shannon–Weaver (or Shannon–Wiener)</option>
                <option value="simpson">Simpson</option>
                <option value="invsimpson">Inverse Simpson</option>
            </param>
            <when value="shannon">
                <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
                <param name="base" type="select" label="The logarithm base">
                    <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
                    <option value="2" selected="False">2</option>
                </param>
            </when>
            <when value="simpson">
                <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
                <param name="base" type="select" label="The logarithm base">
                    <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
                    <option value="2" selected="False">2</option>
                </param>
            </when>
            <when value="invsimpson">
                <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
                <param name="base" type="select" label="The logarithm base">
                    <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
                    <option value="2" selected="False">2</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="output_diversity_index" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
            <param name="species_column" value="6"/>
            <param name="sample_columns" value="2"/>
            <param name="index_type_selector" value="shannon"/>
            <param name="margin" value="1"/>
            <param name="base" value="exp(1)"/>
            <output name="output_diversity_index" ftype="tabular" file="output_diversity_index.tabular" />
        </test>
    </tests>
    <help>
        <![CDATA[
Calculate Diversity index using vegan and selected method.
        ]]>
    </help>
    <expand macro="citations" />
</tool>