<tool id="vegan_fisher_alpha" name="Vegan Fisher Alpha" version="0.0.3">
    <description>
        index
    </description>
    <macros>
        <import>vegan_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        Rscript "${vegan_fisher_alpha_script}"
    ]]>
    </command>
    <configfiles>
        <configfile name="vegan_fisher_alpha_script"><![CDATA[
@RSCRIPT_PREAMBLE@
@RSCRIPT_LOAD_TABULAR_FILE@

write.table( fisher.alpha( input_abundance, MARGIN = ${margin} ), "${output_fisher_alpha}", quote=FALSE, col.names=NA, sep = "\t")
    ]]>
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="params_load_tabular_file" />
        <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output_fisher_alpha" />
    </outputs>
    <tests>
        <test>
            <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
            <param name="species_column" value="6"/>
            <param name="sample_columns" value="2"/>
            <param name="margin" value="1"/>
            <output name="output_fisher_alpha" ftype="tabular" file="output_fisher_alpha.tabular" />
        </test>
    </tests>
    <help>
        <![CDATA[
Calculate Diversity index using vegan and selected method.
        ]]>
    </help>
    <citations>
    </citations>
</tool>