Mercurial > repos > sblanck > smagexp

comparison MetaRNASeq.R @ 39:07ac07715f22 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 7026b0fbe3611962c37c7f9b5f001434f059e32c
author sblanck
date Tue, 26 Jun 2018 04:14:25 -0400
parents a99bbda3cf1f
children
comparison
equal deleted inserted replaced
38:c08b824e40cc 39:07ac07715f22
36 36
37 listfiles <- trimws( unlist( strsplit(trimws(opt$input), ";") ) ) 37 listfiles <- trimws( unlist( strsplit(trimws(opt$input), ";") ) )
38 listfilenames <- trimws( unlist( strsplit(trimws(opt$inputName), ";") ) ) 38 listfilenames <- trimws( unlist( strsplit(trimws(opt$inputName), ";") ) )
39 nbreplicates <- as.numeric(trimws( unlist( strsplit(trimws(opt$nbreplicates), ";") ) )) 39 nbreplicates <- as.numeric(trimws( unlist( strsplit(trimws(opt$nbreplicates), ";") ) ))
40 40
41 listfiles
42 listfilenames
43 nbreplicates
44
45
46
47 #for (i in 1:length(listInput)) 41 #for (i in 1:length(listInput))
48 #{ 42 #{
49 # inputFileInfo <- unlist( strsplit( listInput[i], ';' ) ) 43 # inputFileInfo <- unlist( strsplit( listInput[i], ';' ) )
50 # listfiles=c(listfiles,inputFileInfo[1]) 44 # listfiles=c(listfiles,inputFileInfo[1])
51 # listfilenames=c(listfilenames,inputFileInfo[2]) 45 # listfilenames=c(listfilenames,inputFileInfo[2])
55 49
56 outputfile <- opt$result 50 outputfile <- opt$result
57 result.html = opt$htmloutput 51 result.html = opt$htmloutput
58 html.files.path=opt$htmloutputpath 52 html.files.path=opt$htmloutputpath
59 result.template=opt$htmltemplate 53 result.template=opt$htmltemplate
60
61
62 html.files.path
63 54
64 alpha=as.numeric(opt$fdr) 55 alpha=as.numeric(opt$fdr)
65 56
66 listData=lapply(listfiles,read.table) 57 listData=lapply(listfiles,read.table)
67 orderData=lapply(listData, function(x) x[order(x[1]), ]) 58 orderData=lapply(listData, function(x) x[order(x[1]), ])