Mercurial > repos > mvdbeek > simple_deseq
diff simpleDESeq.xml @ 0:d00e0214e517 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
| author | mvdbeek |
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| date | Sat, 05 Mar 2016 07:00:59 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/simpleDESeq.xml Sat Mar 05 07:00:59 2016 -0500 @@ -0,0 +1,43 @@ +<tool id="simpleDESeq" name="DESeq Profiling" version="1.0.2" hidden="true"> + <description>2 samples / no replicates</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2.14">biocbasics</requirement> + </requirements> + <command interpreter="Rscript">$simpleDESeq </command> + <inputs> + <param name="input" type="data" format="tabular" label="readcount lists, 2 samples"/> + </inputs> + <outputs> + <data name="output" format="tabular" label="DESeq differential calling" /> + </outputs> + <tests> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="5"/> + </test> + </tests> + <configfiles> + <configfile name="simpleDESeq"> + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + suppressMessages(require(DESeq)) + countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) + rownames( countsTable )= countsTable[,1] + countsTable= countsTable[ , -1 ] + conds = c("C","T") + cds = newCountDataSet( countsTable, conds ) + cds = estimateSizeFactors( cds ) + cds = estimateDispersions( cds, method="blind", sharingMode="fit-only" ) #fitType="local" when dispersion fucks the test. Otherwise DESeq performs a parametric fit using a gamma-family GLM + res = nbinomTest( cds, "C", "T" ) + resNA = res[-which(is.na(res[,8])),] ## omit the NA lignes + write.table ( resNA[order(resNA[,8]), ], file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + </configfile> + </configfiles> + <help> + +**What it does** + +DESeq (version 1) differential calling (order by padj, ascending), on two samples, no replicate + </help> +</tool>