Mercurial > repos > pavlo-lutsik > rnbeads
comparison RnBeadsGalaxy.R @ 8:7bc6e673c8e8 draft
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author | pavlo-lutsik |
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date | Thu, 18 Apr 2013 07:36:36 -0400 |
parents | a1c96ef6c111 |
children |
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7:a1c96ef6c111 | 8:7bc6e673c8e8 |
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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( |