Mercurial > repos > pavlo-lutsik > rnbeads

comparison RnBeadsGalaxy.R @ 8:7bc6e673c8e8 draft

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author pavlo-lutsik
date Thu, 18 Apr 2013 07:36:36 -0400
parents a1c96ef6c111
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7:a1c96ef6c111 8:7bc6e673c8e8
39 # string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\"/>\n", opt.name, opt.type, opt.lab, opt.def.val) 39 # string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\"/>\n", opt.name, opt.type, opt.lab, opt.def.val)
40 # } 40 # }
41 # string 41 # string
42 # }) 42 # })
43 # 43 #
44 #cat(xml.strings, sep="", file="C:\\Users\\User\\workspace\\RnBeads\\Supplement\\galaxy\\automated.settings.xml.txt") 44 #cat(xml.strings, sep="", file="automated.settings.xml.txt")
45 # 45 #
46 #opt.def.strings<-apply(rnb.opt.spec,1, function(row){ 46 #opt.def.strings<-apply(rnb.opt.spec,1, function(row){
47 # 47 #
48 # opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE) 48 # opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
49 # opt.long<-row[1] 49 # opt.long<-row[1]
50 # opt.short<-row[2] 50 # opt.short<-row[2]
51 # 51 #
52 # if(row[4]=="logical"){ 52 # if(row[4]=="logical"){
53 # def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long) 53 # def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long)
54 # }else{ 54 # }else{
55 # def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s = \"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name) 55 # def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s=\"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name)
56 # } 56 # }
57 # def.string 57 # def.string
58 # 58 #
59 # }) 59 # })
60 #cat(opt.def.strings, sep="", file="C:\\Users\\User\\workspace\\RnBeads\\Supplement\\galaxy\\automated.option.assignments.txt") 60 #cat(opt.def.strings, sep="", file="automated.option.assignments.txt")
61 61
62 62
63 rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type) 63 rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type)
64 rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type) 64 rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type)
65 rnb.opt.spec<-rbind(data.frame( 65 rnb.opt.spec<-rbind(data.frame(