Mercurial > repos > immport-devteam > profile_cl
comparison profile_cl/getOntology.R @ 0:8547aedf1350 draft
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| author | immport-devteam |
|---|---|
| date | Mon, 27 Feb 2017 13:03:19 -0500 |
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| -1:000000000000 | 0:8547aedf1350 |
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| 1 # Cell Ontology Module for Galaxy | |
| 2 # FlowCL | |
| 3 ###################################################################### | |
| 4 # Copyright (c) 2016 Northrop Grumman. | |
| 5 # All rights reserved. | |
| 6 ###################################################################### | |
| 7 # | |
| 8 # Version 1 | |
| 9 # Cristel Thomas | |
| 10 # | |
| 11 # | |
| 12 | |
| 13 library(flowCL) | |
| 14 library(base) | |
| 15 | |
| 16 getOntology <- function(output_file, markers) { | |
| 17 res <- flowCL(markers, ResetArch = TRUE) | |
| 18 if (length(res) == 6) { | |
| 19 report <- capture.output(res$Table) | |
| 20 sink(output_file) | |
| 21 cat(report, sep = "\n") | |
| 22 sink() | |
| 23 } | |
| 24 } | |
| 25 | |
| 26 args <- commandArgs(trailingOnly = TRUE) | |
| 27 markers <- paste(args[3:length(args)], collapse="") | |
| 28 getOntology(args[2], markers) |