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view find_qPCR_regions.xml @ 2:6f5ce4e865a5 draft

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author kyost
date Sat, 28 Apr 2018 19:45:57 -0400
parents fd3ea97a96bc
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<tool id="find_qPCR_regions" name="Find ATAC qPCR regions" version="0.1.0">
    <description> Determines optimal regions for designing ATAC-qPCR primers.</description>
    <requirements>
        <requirement type="package" version="3.4.2" >r-base</requirement>
    </requirements>
    <command><![CDATA[
        Rscript --vanilla $__tool_directory__/find_qPCR_regions.R $input1 $input2 $input3 $input4 $input5 $output
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="tabular" label="Coverage Bed File"/>
        <param type="data" name="input2" format="tabular" label="Spanning Fragment Coverage Bed File"/>
        <param type="data" name="input3" format="tabular" label="Total Read Counts"/>
        <param type="float" name="input4" value="0.8" label="Correlation Cutoff"/>
        <param type="integer" name="input5" value="3" label="Coverage Cutoff"/>
    </inputs>
    <outputs>
	<data name="output" format="bed" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="combined.o.bed.coverage"/>
            <param name="input2" value="combined.f9.bed.coverage"/>
            <param name="input3" value="lib_sizes.txt"/>
            <param name="input4" value="0.7"/>
            <param name="input5" value="2"/>
            <output name="output" file="qPCR_regions.bed"/>
        </test>
    </tests>
    <help><![CDATA[
        Determines optimal regions for designing ATAC-qPCR primers based on correlation between spanning fragments and total peak height. 
    ]]></help>
    <citations>
        <citation type="doi">doi:10.1038/nmeth.4663</citation>
    </citations>
</tool>