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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author mvdbeek
date Mon, 29 Jun 2015 05:50:30 -0400
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1 <tool id="DESeq_normalization" name="DESeq Normalization" version="1.0.2">
2 <description>of hit lists (geometric method)</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"> $normalizationDESeq </command>
8 <inputs>
9 <param name="input" type="data" format="tabular" label="Hit lists of items"/>
10 </inputs>
11 <outputs>
12 <data name="output_factors" format="tabular" label="Normalization Factors (Geometric mean method)" />
13 <data name="norm_hit_table" format="tabular" label="Normalized Hit Table (Geometric mean method)" />
14 </outputs>
15 <tests>
16 <test>
17 <param name="input" value="counts.tab" ftype="tabular"/>
18 <output name="output_factors" file="norm_factors.tab" ftype="tabular"/>
19 <output name="norm_hit_table" file="norm_table.tab" ftype="tabular"/>
20 </test>
21 </tests>
22 <configfiles>
23 <configfile name="normalizationDESeq">
24 ## Setup R error handling to go to stderr
25 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
26 suppressMessages(require(DESeq))
27 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE)
28 rownames( countsTable )= countsTable[,1]
29 countsTable= countsTable[ , -1 ]
30 conds = c(rep ("C", length(countsTable[1,])-1 ), "T")
31 cds = newCountDataSet( countsTable, conds )
32 cds = estimateSizeFactors( cds )
33 write.table (as.data.frame(sizeFactors(cds)), file="${output_factors}", row.names=TRUE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
34 norm_table = as.data.frame(counts( cds, normalized=TRUE ))
35 norm_table = cbind(rownames(norm_table), norm_table)
36 colnames(norm_table) = c("gene", colnames(countsTable) )
37 write.table (norm_table, file="${norm_hit_table}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
38 </configfile>
39 </configfiles>
40 <help>
41
42 **What it does**
43
44 DESeq Normalization Factors (geometic mean method)
45 and
46 Normalized hit lists
47
48 </help>
49 </tool>