comparison pipe-t.R @ 4:e248cd7769e8 draft

planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit fe7763760d58ae2b51441b67162bb5f86cffa91e

3:e2fcf5a4609c

	file.header <- readLines(con=readfile, n=100)
	n.header	<- grep("^#", file.header)
	if (length(n.header)==0) 
		n.header	<- 0
	# Read data, skip the required lines
	out	<- read.delim(file=readfile, header=FALSE, colClasses="character", nrows=nspots*n.data[i], skip=n.header, strip.white=TRUE, ...)
	# Return
	out
} # .readCtSDS

.readCtLightCycler	<- 

        !missing(position) | !missing(Ct)) {
        warning("Please use 'column.info' for providing a list of column numbers containing particular information. The use of 'flag', 'feature', 'type', 'position' and 'Ct' is deprecated and will be removed in future versions.")
    }
    if (missing(column.info)) {
        column.info <- switch(format, EDS = list(flag="EXPFAIL", feature="Target.Name",  position="Well.Position", Ct="CT"),
          plain = list(flag = 4,
            feature = 6, type = 7, position = 3, Ct = 8), SDS = list(flag = 4,
            feature = 6, type = 7, position = 3, Ct = 8), LightCycler = list(feature = "Name",
            position = "Pos", Ct = "Cp"), CFX = list(feature = "Content",
            position = "Well", Ct = "Cq.Mean"), OpenArray = list(flag = "ThroughHole.Outlier",
            feature = "Assay.Assay.ID", type = "Assay.Assay.Type",
            position = "ThroughHole.Address", Ct = "ThroughHole.Ct"),
            BioMark = list(flag = "Call", feature = "Name.1",

4:e248cd7769e8

	file.header <- readLines(con=readfile, n=100)
	n.header	<- grep("^#", file.header)
	if (length(n.header)==0) 
		n.header	<- 0
	# Read data, skip the required lines
	out	<- read.delim(file=readfile, header=TRUE, colClasses="character", nrows=nspots*n.data[i], skip=n.header-1, strip.white=TRUE, ...)
	# Return
	out
} # .readCtSDS

.readCtLightCycler	<- 

        !missing(position) | !missing(Ct)) {
        warning("Please use 'column.info' for providing a list of column numbers containing particular information. The use of 'flag', 'feature', 'type', 'position' and 'Ct' is deprecated and will be removed in future versions.")
    }
    if (missing(column.info)) {
        column.info <- switch(format, EDS = list(flag="EXPFAIL", feature="Target.Name",  position="Well.Position", Ct="CT"),
          plain = list(flag = 4, feature = 6, type = 7, position = 3, Ct = 8), 
            #SDS = list(flag = 4,feature = 6, type = 7, position = 3, Ct = 8), 
            SDS = list(flag = "Omit",feature = "Detector", type = "Task", position = "Wells", Ct = "Ct"), 
            LightCycler = list(feature = "Name",
            position = "Pos", Ct = "Cp"), CFX = list(feature = "Content",
            position = "Well", Ct = "Cq.Mean"), OpenArray = list(flag = "ThroughHole.Outlier",
            feature = "Assay.Assay.ID", type = "Assay.Assay.Type",
            position = "ThroughHole.Address", Ct = "ThroughHole.Ct"),
            BioMark = list(flag = "Call", feature = "Name.1",