<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.2.1">R</requirement>
            <requirement type="package" version="2.3-0">vegan</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command><![CDATA[Rscript -e 'library(vegan)' 2>&1 > /dev/null | grep 'This is vegan']]></version_command>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
        </stdio>
    </xml>

    <xml name="params_load_tabular_file">
        <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"/>
    </xml>

    <token name="@RSCRIPT_LOAD_TABULAR_FILE@"><![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 $sample_col-1 ) )
#end for
input_abundance <- read.delim("${input_abundance}", header=${header}, sep="\t", row.names=${ species_column })
input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )

]]>
    </token>

    <token name="@RSCRIPT_PREAMBLE@"><![CDATA[
options(bitmapType='cairo')## No X11, so we'll use cairo
library(vegan)
]]>
    </token>

    <token name="@VERSION@">2.3-0</token>

</macros>