Mercurial > repos > immport-devteam > profile_cl

comparison getOntology.R @ 1:62d8985a41e2 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
author azomics
date Thu, 23 Jul 2020 08:58:29 -0400
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0:8547aedf1350 1:62d8985a41e2
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)