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author kpbioteam
date Wed, 27 Jun 2018 14:34:55 -0400
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1 <tool id="minfi_getbeta" name="minfi_getbeta" version="0.1.0">
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2 <description>obtain Beta value matrix</description>
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3 <requirements>
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4 <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 Rscript ${__tool_directory__}/minfi_getbeta.R "$input1" "$output1"
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="input1" format="rdata" label="MethylSet"/>
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11 </inputs>
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12 <outputs>
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13 <data name="output1" format="bedgraph" label="Beta Value"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input1" value="RSet.rdata"/>
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18 <output name="output1" file="getbeta.bedgraph"/>
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19 </test>
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20 </tests>
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21 <help><![CDATA[
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22 This tools outputs a matrix of methylation indices (beta values), which are continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site.
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23 ]]></help>
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24 <citations>
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25 <citation type="doi">10.1093/bioinformatics/btu049</citation>
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26 </citations>
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27 </tool>