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1 <tool id="minfi_getbeta" name="Minfi Get Beta" version="@MINFI_VERSION@">
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2 <description>obtain Beta value matrix</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 Rscript '$minfi_beta_script'
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10 ]]>
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11 </command>
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12 <configfiles>
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13 <configfile name="minfi_beta_script"><![CDATA[
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14 require("minfi", quietly = TRUE)
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15
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16 MSet <- get(load('$mset'))
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17
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18 beta <- getBeta(MSet)
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19
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20 write.table(beta, file = '$matrix', quote = FALSE, sep = "\t")
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21 ]]>
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22 </configfile>
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23 </configfiles>
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24 <inputs>
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25 <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
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26 location."/>
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27 </inputs>
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28 <outputs>
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29 <data name="matrix" format="bedgraph" label="Beta Values Matrix"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="mset" value="MethylSet.rdata"/>
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34 <output name="matrix" file="Beta_Values_Matrix.bedgraph"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 This tools outputs an interval file 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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39 ]]></help>
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40 <expand macro="citations" />
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41 </tool>
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