Mercurial > repos > mvdbeek > deseq_normalization

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author mvdbeek
date Mon, 29 Jun 2015 05:50:30 -0400
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1 <tool id="DESeq_normalization" name="DESeq Normalization" version="1.0.2">
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2 <description>of hit lists (geometric method)</description>
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3 <requirements>
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4 <requirement type="package" version="3.1.2">R</requirement>
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5 <requirement type="package" version="2.14">biocbasics</requirement>
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6 </requirements>
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7 <command interpreter="Rscript"> $normalizationDESeq </command>
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8 <inputs>
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9 <param name="input" type="data" format="tabular" label="Hit lists of items"/>
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10 </inputs>
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11 <outputs>
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12 <data name="output_factors" format="tabular" label="Normalization Factors (Geometric mean method)" />
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13 <data name="norm_hit_table" format="tabular" label="Normalized Hit Table (Geometric mean method)" />
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input" value="counts.tab" ftype="tabular"/>
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18 <output name="output_factors" file="norm_factors.tab" ftype="tabular"/>
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19 <output name="norm_hit_table" file="norm_table.tab" ftype="tabular"/>
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20 </test>
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21 </tests>
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22 <configfiles>
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23 <configfile name="normalizationDESeq">
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24 ## Setup R error handling to go to stderr
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25 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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26 suppressMessages(require(DESeq))
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27 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE)
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28 rownames( countsTable )= countsTable[,1]
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29 countsTable= countsTable[ , -1 ]
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30 conds = c(rep ("C", length(countsTable[1,])-1 ), "T")
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31 cds = newCountDataSet( countsTable, conds )
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32 cds = estimateSizeFactors( cds )
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33 write.table (as.data.frame(sizeFactors(cds)), file="${output_factors}", row.names=TRUE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
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34 norm_table = as.data.frame(counts( cds, normalized=TRUE ))
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35 norm_table = cbind(rownames(norm_table), norm_table)
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36 colnames(norm_table) = c("gene", colnames(countsTable) )
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37 write.table (norm_table, file="${norm_hit_table}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
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38 </configfile>
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39 </configfiles>
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40 <help>
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41
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42 **What it does**
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43
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44 DESeq Normalization Factors (geometic mean method)
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45 and
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46 Normalized hit lists
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47
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48 </help>
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49 </tool>