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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/vegan_diversity commit 37144be811dd587897dd9dcb652de0854f049b9a

<tool id="vegan_diversity" name="Vegan Diversity" version="0.0.1">
    <description>
        index
    </description>
    <requirements>
        <requirement type="package" version="3.2.1">R</requirement>
        <requirement type="package" version="2.3-0">vegan</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <command><![CDATA[
        Rscript "${vegan_diversity_script}"
    ]]>
    </command>
    <configfiles>
        <configfile name="vegan_diversity_script"><![CDATA[
#set $int_species_column = int( str( $species_column ) )
#set $fixed_sample_columns = []
#for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
#assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
#silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
#end for
library(vegan)
input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=${header} )
input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )

write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", col.names=NA, sep = "\t")
    ]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_abundance" type="data" format="tabular" label="File with abundance values for community" help="Rows are samples; columns are species/phyla/community classifier"/>
        <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
        <param name="sample_columns" label="Sample count columns" type="data_column" multiple="True" value="2" data_ref="input_abundance" help="Select each column that contains counts"/>
        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
        <conditional name="index_type">
            <param name="index_type_selector" type="select" label="Diversity index to use">
                <option value="shannon" selected="True">shannon</option>
                <option value="simpson">simpson</option>
                <option value="invsimpson">invsimpson</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 used in shannon">
                    <option value="exp(1)" selected="True">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 used in shannon">
                    <option value="exp(1)" selected="True">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 used in shannon">
                    <option value="exp(1)" selected="True">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>
            <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_slope" ftype="tabular" file="output_diversity_index.tabular" />
        </test>
    </tests>
    <help>
        <![CDATA[
Calculate Diversity index using vegan and selected method.
        ]]>
    </help>
    <citations>
    </citations>
</tool>