Mercurial > repos > mvdbeek > deseq_with_replicates
comparison replicateDESeq.xml @ 0:da2dbe13adc2 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
| author | mvdbeek |
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| date | Sat, 05 Mar 2016 07:02:52 -0500 |
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| -1:000000000000 | 0:da2dbe13adc2 |
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| 1 <tool id="replicateDESeq" name="DESeq1 Profiling (replicates)" version="1.0.1"> | |
| 2 <description>with sample 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>Rscript $replicateDESeq </command> | |
| 8 <inputs> | |
| 9 <param name="input" type="data" format="tabular" label="gene readcount list, more than 2 samples"/> | |
| 10 <param name="expPlan" type="text" label="experimental plan" help="Use a string of Cs and Ts. exemple: CCCTTT means 3 control samples versus 3 test samples"/> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data name="output" format="tabular" label="DESeq differential calling" /> | |
| 14 </outputs> | |
| 15 <tests> | |
| 16 <test> | |
| 17 <param name="input" value="counts.tab" ftype="tabular"/> | |
| 18 <param name="expPlan" value="CCTTT"/> | |
| 19 <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="5"/> | |
| 20 </test> | |
| 21 </tests> | |
| 22 <configfiles> | |
| 23 <configfile name="replicateDESeq"> | |
| 24 ## Setup R error handling to go to stderr | |
| 25 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 26 suppressMessages(require(DESeq)) | |
| 27 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) | |
| 28 rownames( countsTable )= countsTable[,1] | |
| 29 countsTable= countsTable[ , -1 ] | |
| 30 stringconds = "${expPlan}" | |
| 31 conds = unlist(strsplit(stringconds, split="")) | |
| 32 cds = newCountDataSet( countsTable, conds ) | |
| 33 cds = estimateSizeFactors( cds ) | |
| 34 cds = estimateDispersions( cds, method="per-condition", sharingMode="maximum") ## was fit-only before 9-12-2013 !! tried for RNAseq - Actually does not change anything ! | |
| 35 ## Attention: fitType="local" is added when parametricDispersionFit fails. remove after use ! | |
| 36 res = nbinomTest( cds, "C", "T" ) | |
| 37 # resNA = res[-which(is.na(res[,8])),] ## omitted the NA lignes, but this was causing a full delete of the table completely devoid of NA !! (not logical but true) | |
| 38 write.table ( res[order(res[,8]), ], file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") | |
| 39 </configfile> | |
| 40 </configfiles> | |
| 41 <help> | |
| 42 | |
| 43 **What it does** | |
| 44 | |
| 45 DESeq differential calling (order by padj, ascending), on more than two samples, with replicates. | |
| 46 | |
| 47 | |
| 48 </help> | |
| 49 </tool> |