net.maizegenetics.analysis.workflow.MLM_(PCA+K).xml Maven / Gradle / Ivy

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<TasselPipeline>
    <citation>
        Casstevens T, Wang Y. (2015) First Annual Tassel Hackathon.
    </citation>
    <workflow>
        Association analysis using GLM.
    </workflow>
    <fork1>
        <importGuess>
            filename
            <workflow> 
                Load Genotype File. (example: mdp_genotype.hmp.txt)
            </workflow>
        </importGuess>
        <filterAlign>
            <filterAlignMinFreq>0.05</filterAlignMinFreq>
            <workflow>
                Filter out mono-morphic sites. (example: Minimum Count: 150, Minimum Frequency: 0.05, Maximum Frequency: 1.0)
            </workflow>
        </filterAlign>
    </fork1>
    <runfork1/>
    <fork2>
        <pca>
            <workflow>
                Using PCA method to calculate the populations structure. (example: number of components: 3)
            </workflow>
        </pca>
        <input1/>
    </fork2>
    <fork3>
        <ck>
            <workflow>
                Calculate the kinship data.
            </workflow>
        </ck>
        <input1/>
    </fork3>
    <fork4>
        <importGuess>
            filename
            <workflow> 
                Load Phenotypes File. (example: mdp_traits.txt)
            </workflow>
        </importGuess>
    </fork4>
    <runfork4/>
    <combine5>
        <input1/>
        <input2/>
        <input4/>
        <intersect/> 
    </combine5>
    <combine6>
        <input5/>
        <input3/>
        <mlm>
            <workflow>
                Association analysis using MLM.
            </workflow>
        </mlm>
        <mhd>
            <workflow>
                Manhattan Plot
                (example: select dpoll to draw the Manhattan plot)
            </workflow>
        </mhd>
    </combine6>
</TasselPipeline>