Mercurial > repos > immport-devteam > flowcl
comparison getOntology.R @ 1:f70f75e89890 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowcl commit d59d95d2bc6a64eb5c37b8291a7c314754c2067f"
| author | azomics |
|---|---|
| date | Thu, 23 Jul 2020 08:50:18 -0400 |
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| children |
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| 0:fb0ee82f686d | 1:f70f75e89890 |
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| 1 #!/usr/bin/Rscript --vanilla | |
| 2 # Cell Ontology Module for Galaxy | |
| 3 # FlowCL | |
| 4 ###################################################################### | |
| 5 # Copyright (c) 2016 Northrop Grumman. | |
| 6 # All rights reserved. | |
| 7 ###################################################################### | |
| 8 # | |
| 9 # Version 1 | |
| 10 # Cristel Thomas | |
| 11 # | |
| 12 # | |
| 13 | |
| 14 suppressWarnings(suppressMessages(library(flowCL))) | |
| 15 suppressWarnings(suppressMessages(library(base))) | |
| 16 | |
| 17 getOntology <- function(output_file, markers) { | |
| 18 res <- flowCL(markers, ResetArch = TRUE) | |
| 19 if (length(res) == 6) { | |
| 20 report <- capture.output(res$Table) | |
| 21 sink(output_file) | |
| 22 cat(report, sep = "\n") | |
| 23 sink() | |
| 24 } | |
| 25 } | |
| 26 | |
| 27 args <- commandArgs(trailingOnly = TRUE) | |
| 28 markers <- paste(args[2:length(args)], collapse="") | |
| 29 getOntology(args[1], markers) |