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1 # Cell Ontology Module for Galaxy
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2 # FlowCL
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3 ######################################################################
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4 # Copyright (c) 2016 Northrop Grumman.
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5 # All rights reserved.
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6 ######################################################################
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7 #
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8 # Version 1
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9 # Cristel Thomas
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10 #
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11 #
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12
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13 library(flowCL)
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14 library(base)
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15
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16 getOntology <- function(output_file, markers) {
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17 res <- flowCL(markers, ResetArch = TRUE)
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18 if (length(res) == 6) {
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19 report <- capture.output(res$Table)
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20 sink(output_file)
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21 cat(report, sep = "\n")
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22 sink()
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23 }
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24 }
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25
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26 args <- commandArgs(trailingOnly = TRUE)
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27 markers <- paste(args[3:length(args)], collapse="")
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28 getOntology(args[2], markers)
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