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• Taxa_Quality_Control.xml

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net.maizegenetics.analysis.workflow.Taxa_Quality_Control.xml Maven / Gradle / Ivy

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<TasselPipeline>
    <citation>
        Romay, M, Wang Y., Casstevens T. (2015) First Annual Tassel Hackathon.
    </citation>
    <workflow>
        Quality Control.
    </workflow>
    <fork1>
        <importGuess>
            filename
            <workflow> 
                Load Genotype File. (example: mdp_genotype.hmp.txt)
            </workflow>
        </importGuess>
        <FilterTaxaNames>
            <workflow> 
                Filter Taxa Names. (example: select lines which contains "NC" and capture the selection)
            </workflow>
        </FilterTaxaNames>
        <filterAlign>
            <filterAlignMinFreq>0.0005</filterAlignMinFreq>
            <workflow>
                Filter out mono-morphic sites. (example: Minimum Count: 1, Minimum Frequency: 0.0005, Maximum Frequency: 1.0)
            </workflow>
        </filterAlign>
        <FilterTaxaPropertiesPlugin>
            <minNotMissing>0.1</minNotMissing>
            <minHeterozygous>0.0</minHeterozygous>
            <maxHeterozygous>0.05</maxHeterozygous>
            <workflow>
                Filter to remove Taxa with low coverage. (example: Min Proportion of Sites Present: 0.1, Min Heterozygous Proportion: 0.0, Max Heterozygous Proportion: 0.05)
            </workflow>
        </FilterTaxaPropertiesPlugin>
    </fork1>
    <runfork1/>
    <fork2>
        <genotypeSummary>
            taxa
            <workflow>
                Generate taxa summary. (exmaple: only select taxa)
            </workflow>
        </genotypeSummary>
        <input1/>
    </fork2>
    <fork4>
        <tree>
            Neighbor
            <workflow>
                Generate phylogenetic tree and distance matrix.
            </workflow>
        </tree>
        <input1/>
    </fork4>
    <fork5>
        <MultiDimensionalScalingPlugin/>
        <input4/>
    </fork5>
    <fork6>
        <archaeopteryx>
            <workflow>
                View phylogenetic tree.
            </workflow>
        </archaeopteryx>
        <input4/>
    </fork6>
</TasselPipeline>