Mercurial > repos > mvdbeek > simple_deseq
comparison 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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| -1:000000000000 | 0:d00e0214e517 |
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| 1 <tool id="simpleDESeq" name="DESeq Profiling" version="1.0.2" hidden="true"> | |
| 2 <description>2 samples / no replicates</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 interpreter="Rscript">$simpleDESeq </command> | |
| 8 <inputs> | |
| 9 <param name="input" type="data" format="tabular" label="readcount lists, 2 samples"/> | |
| 10 </inputs> | |
| 11 <outputs> | |
| 12 <data name="output" format="tabular" label="DESeq differential calling" /> | |
| 13 </outputs> | |
| 14 <tests> | |
| 15 <test> | |
| 16 <param name="input" value="counts.tab" ftype="tabular"/> | |
| 17 <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="5"/> | |
| 18 </test> | |
| 19 </tests> | |
| 20 <configfiles> | |
| 21 <configfile name="simpleDESeq"> | |
| 22 ## Setup R error handling to go to stderr | |
| 23 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 24 suppressMessages(require(DESeq)) | |
| 25 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) | |
| 26 rownames( countsTable )= countsTable[,1] | |
| 27 countsTable= countsTable[ , -1 ] | |
| 28 conds = c("C","T") | |
| 29 cds = newCountDataSet( countsTable, conds ) | |
| 30 cds = estimateSizeFactors( cds ) | |
| 31 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 | |
| 32 res = nbinomTest( cds, "C", "T" ) | |
| 33 resNA = res[-which(is.na(res[,8])),] ## omit the NA lignes | |
| 34 write.table ( resNA[order(resNA[,8]), ], file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") | |
| 35 </configfile> | |
| 36 </configfiles> | |
| 37 <help> | |
| 38 | |
| 39 **What it does** | |
| 40 | |
| 41 DESeq (version 1) differential calling (order by padj, ascending), on two samples, no replicate | |
| 42 </help> | |
| 43 </tool> |