<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">r-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>
    
    <xml name="bio.tools_xrefs">
        <xrefs>
            <xref type="bio.tools">vegan</xref>
        </xrefs>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @Manual{,
                    title = {vegan: Community Ecology Package},
                    author = {Jari Oksanen and Gavin L. Simpson and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R.B. O'Hara and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner and Matt Barbour and Michael Bedward and Ben Bolker and Daniel Borcard and Gustavo Carvalho and Michael Chirico and Miquel {De Caceres} and Sebastien Durand and Heloisa Beatriz Antoniazi Evangelista and Rich FitzJohn and Michael Friendly and Brendan Furneaux and Geoffrey Hannigan and Mark O. Hill and Leo Lahti and Dan McGlinn and Marie-Helene Ouellette and Eduardo {Ribeiro Cunha} and Tyler Smith and Adrian Stier and Cajo J.F. {Ter Braak} and James Weedon},
                    year = {2024},
                    note = {R package version 2.6-5},
                    url = {https://github.com/vegandevs/vegan},
                  }
            </citation>
        </citations>
    </xml>

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

    <token name="@TOOL_VERSION@">2.4-3</token>

</macros>