Mercurial > repos > immport-devteam > flowcl
diff 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 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getOntology.R Thu Jul 23 08:50:18 2020 -0400 @@ -0,0 +1,29 @@ +#!/usr/bin/Rscript --vanilla +# Cell Ontology Module for Galaxy +# FlowCL +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 1 +# Cristel Thomas +# +# + +suppressWarnings(suppressMessages(library(flowCL))) +suppressWarnings(suppressMessages(library(base))) + +getOntology <- function(output_file, markers) { + res <- flowCL(markers, ResetArch = TRUE) + if (length(res) == 6) { + report <- capture.output(res$Table) + sink(output_file) + cat(report, sep = "\n") + sink() + } +} + +args <- commandArgs(trailingOnly = TRUE) +markers <- paste(args[2:length(args)], collapse="") +getOntology(args[1], markers)