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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
author mvdbeek
date Sat, 05 Mar 2016 07:05:06 -0500
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a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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1 <tool id="DESeq2" name="DESeq2 Profiling" version="1.0.2" hidden="true">
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2 <description>of readcount lists</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>Rscript $DESeq2 </command>
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8 <inputs>
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9 <param name="input" type="data" format="tabular" label="miR hit lists, more thant 2 samples"/>
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10 <param name="expPlan" type="text" label="experimental plan" help="Use a string of Cs and Ts. exemple: CCCTTT means 3 control samples versus 3 test samples"/>
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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11 </inputs>
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12 <outputs>
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13 <data name="output" format="tabular" label="DESeq2 differential calling" />
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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 <param name="expPlan" value="CCTTT"/>
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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19 <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="50"/>
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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="DESeq2">
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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 ) } )
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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26 suppressMessages(require(DESeq2))
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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27 ## suppressMessages(require(ReportingTools))
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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28 countData = read.delim("${input}", header=TRUE, check.names=FALSE)
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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29 rownames( countData )= countData[,1]
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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30 countData= countData[ , -1 ]
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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31 stringconds = "${expPlan}"
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32 conds = unlist(strsplit(stringconds, split=""))
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33 colData=data.frame(row.names=colnames(countData), condition=conds)
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34 dds = DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition)
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35 colData(dds)\$condition = factor(colData(dds)\$condition, levels=c("C","T"))
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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36 dds = DESeq(dds, quiet=TRUE)
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37 res = results(dds)
a903407e3ca0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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38 res = res[order(res\$padj),]
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39 baseMeanA = rowMeans(counts(dds, normalized=TRUE)[rownames(res),colData(dds)\$condition== "C"])
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40 baseMeanB = rowMeans(counts(dds, normalized=TRUE)[rownames(res),colData(dds)\$condition== "T"])
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41 res2 = data.frame (gene=rownames(res), baseMeanA=baseMeanA, baseMeanB=baseMeanB, res)
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42 ## resNA = res[-which(is.na(res[,8])),] ## omit the NA lignes
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43 write.table ( res2, file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
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44 ## write.csv(as.data.frame(res), file="${output}")
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45 </configfile>
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46 </configfiles>
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47 <help>
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48
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49 **What it does**
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50
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51 DESeq2 differential calling (order by padj, ascending).
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52 Still in development and testing for replicates/no replicates
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53
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54
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55 </help>
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56 </tool>