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1 #!/usr/bin/env Rscript
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2
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3 #sink(file("/dev/null", "w"), type = "message");
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4
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5 library(pathprint);
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6
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7 # Figure out the relative path to the galaxy-pathprint.r library.
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8 script.args <- commandArgs(trailingOnly = FALSE);
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9 script.name <- sub("--file=", "", script.args[grep("--file=", script.args)])
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10 script.base <- dirname(script.name)
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11 library.path <- file.path(script.base, "galaxy-pathprint.r");
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12 source(library.path)
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13
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14 usage <- function() {
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15 stop("Usage: heatmap.r <fingerprint> <sdev> <output>", call. = FALSE)
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16 }
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17
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18 ## Get the command line arguments.
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19 args <- commandArgs(trailingOnly = TRUE)
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20
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21 input <- ifelse(! is.na(args[1]), args[1], usage())
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22 sdev <- ifelse(! is.na(args[2]), as.numeric(args[2]), usage())
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23 output <- ifelse(! is.na(args[3]), args[3], usage())
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24
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25
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26 fingerprint <- loadFingerprint(input);
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27 fingerprint <- data.frame(fingerprint[complete.cases(fingerprint),]);
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28
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29 generateHeatmap(fingerprint, sdev, output);
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30
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31 quit("no", 0)
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