<tool id="ukseed_dartseq" name="UK SeeD Dartseq Analysis" version="0.0.1">
    <description>run a dartseq analysis</description>
    <requirements>
        <requirement type="package" version="1.90b4">plink</requirement>
		<requirement type="package" version="1.12.2">bioconductor-snprelate</requirement>
		<requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
		<requirement type="package" version="0.8_14">r-amap</requirement>
		<requirement type="package" version="1.2_16">r-rgdal</requirement>
		
    </requirements>

    <command><![CDATA[
	    Rscript --vanilla $__tool_directory__/dartseq_seeduk_1.R $input
		&&		
		plink --bfile test --recode A 
		&&		
		Rscript --vanilla $__tool_directory__/dartseq_seeduk_2.R $output		
    ]]></command>
	
    <inputs>
        <param format="csv" name="input" type="data" label="Input file"
            help="Input file of genotype data"/>
    </inputs>

    <outputs>
        <data name="output" format="csv" />
    </outputs>
  
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <help>
	In ``UK SeeD``, a BBSRC-Newton funded project, we have deployed an advanced computing hardware and software platform for the 
	analysis of large genomics datasets for wheat varieties. The platform integrates computing resources and bioinformatics expertise to 
    enable crop geneticists to implement sophisticated data analysis algorithms to improve the use of genetic resources for wheat and 
    other important crops. The computing platform is distributed across the partners’ sites with hardware deployed at CIMMYT (Mexico) and 
    the Earlham Institute (UK).  
	
	
	|JHI|
	
	.. |JHI| image:: https://ics.hutton.ac.uk/resources/ukseed/jhi.png
	
	</help>

    <citations>
    </citations>
</tool>