Mercurial > repos > azomics > check_fcs_header

comparison getFCSheader.R @ 0:2227def10ea4 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
author azomics
date Wed, 24 Jun 2020 17:36:27 -0400
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-1:000000000000 0:2227def10ea4
1 #!/usr/bin/Rscript --vanilla
2 # FCS Headers Module for Galaxy
3 # FlowCore
4 ######################################################################
5 # Copyright (c) 2016 Northrop Grumman.
6 # All rights reserved.
7 ######################################################################
8 #
9 # Version 2
10 # May 2018
11 # Cristel Thomas
12 #
13 #
14
15 library(flowCore)
16
17 getFCSChannels <- function(input_fcs) {
18 fcs <- read.FCS(input_fcs, transformation=F)
19 return(colnames(fcs))
20 }
21
22 getFCSMarkers <- function(input_fcs){
23 ffcs <- read.FCS(input_fcs, transformation=F)
24 fmarkers <- as.vector(pData(parameters(ffcs))$desc)
25 return(fmarkers)
26 }
27
28 getFCSMarkerNames <- function(output_file="", file_paths=vector(),
29 fcs_names=vector()) {
30 check_files <- sapply(file_paths, isFCSfile)
31 channels <- lapply(file_paths[check_files], getFCSChannels)
32 markers <- lapply(file_paths[check_files], getFCSMarkers)
33
34 nb_col <- max(lengths(channels))
35 nc <- lapply(channels, `length<-`, nb_col)
36 ct <- t(as.data.frame(nc))
37
38 nm <- lapply(markers, `length<-`, nb_col)
39 mt <- t(as.data.frame(nm))
40
41 nb_files <- sum(check_files)
42 Index <- rep(c("channels", "markers"), each=nb_files)
43 Filename <- rep(fcs_names[check_files], 2)
44
45 idx_nb <- seq(nb_col)
46 ttt <- rbind(ct,mt)
47 finalt <- cbind(Filename, Index, ttt)
48 colnames(finalt)[3:length(colnames(finalt))] <- idx_nb
49
50
51 if (nb_files != length(file_paths)){
52 not_fcs <- fcs_names[!check_files]
53 new_df <- cbind(not_fcs, "Not a valid FCS file")
54 empty_frame <- data.frame(matrix("", nrow=length(not_fcs), ncol=nb_col),
55 stringsAsFactors = F)
56 not_fcs_files <- cbind(new_df, empty_frame)
57 colnames(not_fcs_files) <- colnames(finalt)
58 new_final <- rbind(finalt, not_fcs_files)
59 write.table(new_final, file=output_file, quote=F, row.names=F, col.names=T,
60 sep='\t', append=F)
61 quit(save = "no", status = 10, runLast = FALSE)
62 } else {
63 # output file
64 write.table(finalt, file=output_file, quote=F, row.names=F, col.names=T,
65 sep='\t',
66 append=F)
67 }
68 }
69
70 ################################################################################
71 ################################################################################
72
73 args <- commandArgs(trailingOnly = TRUE)
74
75 i <- 1
76 nb_files <- (length(args)-1) / 2
77 fcs_files <- character(nb_files)
78 fcs_names <- character(nb_files)
79 for (j in 1:length(args)){
80 if (!j%%2){
81 fcs_files[[i]] <- args[[j]]
82 fcs_names[[i]]<- args[[j+1]]
83 i <- i + 1
84 }
85 }
86
87 getFCSMarkerNames(args[1], fcs_files, fcs_names)