comparison extract_fcs_keywords/FCSKeyword.R @ 1:1d5e530c8a5e draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
author azomics
date Mon, 22 Jun 2020 17:22:21 -0400
parents dc00746654dc
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0:dc00746654dc 1:1d5e530c8a5e
1 # ImmPort FCSKeywords
2 ######################################################################
3 # Copyright (c) 2016 Northrop Grumman.
4 # All rights reserved.
5 ######################################################################
6 #
7 # Converts the FCS file to text without transformaton
8 # To run in R
9 # 1) library(flowCore)
10 # 2) source("FCSKeyword.R")
11 # 3) transformFCS("filename")
12 #
13 # Version 1.4.1
14 # March 2016 -- added lines to run directly from command line
15 #
16
17 library(flowCore)
18
19 #
20 # Starting function for processing a FCS file
21 #
22 extractKeywords <- function(input_file, keyword_file="", debug=FALSE) {
23 #
24 # Generate the file names for the output_file and keyword_file
25 #
26 pieces <- unlist(strsplit(input_file, .Platform$file.sep))
27 filename <- pieces[length(pieces)]
28
29 if (keyword_file == "") {
30 filepieces <- unlist(strsplit(filename, '\\.'))
31 #replace .fcs with .keyword; append .keyword if not ending in .fcs
32 if (filepieces[length(filepieces)] == 'fcs') {
33 filepieces[length(filepieces)] = 'keyword'
34 } else {
35 filepieces[length(filepieces)+1] = 'keyword'
36 }
37 keyword_file <- paste(filepieces, collapse = '.')
38 }
39
40 if (debug) {
41 print (paste("Converting file: ", input_file))
42 print (paste("Original file name: ", filename))
43 print (paste("Output file name: ", output_file))
44 print (paste("Keyword file name: ", keyword_file))
45 }
46 fcs <- read.FCS(input_file, transformation=F)
47 keywords <- keyword(fcs)
48 write.table(as.matrix(keywords), file=keyword_file, quote=F,
49 row.names=T, col.names=F, sep='=', append=F)
50 }
51
52 # Extract Keywords
53 # @param input_file FCS file to be transformed
54 # @param keyword_file FCS file keywords ".keywords" extension"
55 transformFCS <- function(input_file, keyword_file="", debug=FALSE) {
56 isValid <- F
57 # Check file beginning matches FCS standard
58 tryCatch({
59 isValid = isFCSfile(input_file)
60 }, error = function(ex) {
61 print (paste(" ! Error in isFCSfile", ex))
62 })
63
64 if (isValid) {
65 extractKeywords(input_file, keyword_file, debug)
66 } else {
67 print (paste(input_file, "does not meet FCS standard"))
68 }
69 }
70
71 args <- commandArgs(TRUE)
72 transformFCS(args[2], args[3])