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view ukseed.xml @ 5:fec5b295004d draft

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author cropgeeks
date Tue, 17 Apr 2018 11:18:52 -0400
parents 4e2b3a96fee1
children 2a49f0396e8b
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<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></help>

    <citations>
    </citations>
</tool>