Mercurial > repos > mvdbeek > deseq2
comparison deseq2.xml @ 0:a903407e3ca0 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
| author | mvdbeek |
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| date | Sat, 05 Mar 2016 07:05:06 -0500 |
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| -1:000000000000 | 0:a903407e3ca0 |
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| 1 <tool id="DESeq2" name="DESeq2 Profiling" version="1.0.2" hidden="true"> | |
| 2 <description>of readcount lists</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.1.2">R</requirement> | |
| 5 <requirement type="package" version="2.14">biocbasics</requirement> | |
| 6 </requirements> | |
| 7 <command>Rscript $DESeq2 </command> | |
| 8 <inputs> | |
| 9 <param name="input" type="data" format="tabular" label="miR hit lists, more thant 2 samples"/> | |
| 10 <param name="expPlan" type="text" label="experimental plan" help="Use a string of Cs and Ts. exemple: CCCTTT means 3 control samples versus 3 test samples"/> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data name="output" format="tabular" label="DESeq2 differential calling" /> | |
| 14 </outputs> | |
| 15 <tests> | |
| 16 <test> | |
| 17 <param name="input" value="counts.tab" ftype="tabular"/> | |
| 18 <param name="expPlan" value="CCTTT"/> | |
| 19 <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="50"/> | |
| 20 </test> | |
| 21 </tests> | |
| 22 <configfiles> | |
| 23 <configfile name="DESeq2"> | |
| 24 ## Setup R error handling to go to stderr | |
| 25 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 26 suppressMessages(require(DESeq2)) | |
| 27 ## suppressMessages(require(ReportingTools)) | |
| 28 countData = read.delim("${input}", header=TRUE, check.names=FALSE) | |
| 29 rownames( countData )= countData[,1] | |
| 30 countData= countData[ , -1 ] | |
| 31 stringconds = "${expPlan}" | |
| 32 conds = unlist(strsplit(stringconds, split="")) | |
| 33 colData=data.frame(row.names=colnames(countData), condition=conds) | |
| 34 dds = DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition) | |
| 35 colData(dds)\$condition = factor(colData(dds)\$condition, levels=c("C","T")) | |
| 36 dds = DESeq(dds, quiet=TRUE) | |
| 37 res = results(dds) | |
| 38 res = res[order(res\$padj),] | |
| 39 baseMeanA = rowMeans(counts(dds, normalized=TRUE)[rownames(res),colData(dds)\$condition== "C"]) | |
| 40 baseMeanB = rowMeans(counts(dds, normalized=TRUE)[rownames(res),colData(dds)\$condition== "T"]) | |
| 41 res2 = data.frame (gene=rownames(res), baseMeanA=baseMeanA, baseMeanB=baseMeanB, res) | |
| 42 ## resNA = res[-which(is.na(res[,8])),] ## omit the NA lignes | |
| 43 write.table ( res2, file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") | |
| 44 ## write.csv(as.data.frame(res), file="${output}") | |
| 45 </configfile> | |
| 46 </configfiles> | |
| 47 <help> | |
| 48 | |
| 49 **What it does** | |
| 50 | |
| 51 DESeq2 differential calling (order by padj, ascending). | |
| 52 Still in development and testing for replicates/no replicates | |
| 53 | |
| 54 | |
| 55 </help> | |
| 56 </tool> |