Mercurial > repos > immport-devteam > fcs_summary
comparison FCSstats.R @ 1:d2749aa59d20 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_summary commit 72efaa6d006ddda6c8eed10ec9ba541cbdecf3a8"
| author | azomics |
|---|---|
| date | Mon, 22 Jun 2020 17:33:38 -0400 |
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| children |
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| 0:1d926a8daa92 | 1:d2749aa59d20 |
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| 1 #!/usr/bin/Rscript --vanilla | |
| 2 # FCS Summary Statistic Module for Galaxy | |
| 3 # FlowCore | |
| 4 ###################################################################### | |
| 5 # Copyright (c) 2016 Northrop Grumman. | |
| 6 # All rights reserved. | |
| 7 ###################################################################### | |
| 8 # | |
| 9 # Version 1 | |
| 10 # Cristel Thomas | |
| 11 # | |
| 12 # | |
| 13 | |
| 14 library(flowCore) | |
| 15 | |
| 16 getMarkerNames <- function(input, output) { | |
| 17 fcs <- read.FCS(input, transformation=F) | |
| 18 | |
| 19 ## marker names | |
| 20 channels <- colnames(fcs) | |
| 21 markers <- as.vector(pData(parameters(fcs))$desc) | |
| 22 df <- data.frame(channels, markers) | |
| 23 fcs_summary <- capture.output(summary(fcs)) | |
| 24 fcs_dim <- capture.output(dim(fcs)) | |
| 25 fcs_markers <- capture.output(df) | |
| 26 | |
| 27 | |
| 28 sink(output) | |
| 29 cat(fcs_dim, sep="\n") | |
| 30 cat("\n\n=========================\n") | |
| 31 cat("== FCS SUMMARY ==\n") | |
| 32 cat("=========================\n") | |
| 33 cat(fcs_summary, sep="\n") | |
| 34 cat("\n\n=========================\n") | |
| 35 cat("== MARKERS IN FCS ==\n") | |
| 36 cat("=========================\n") | |
| 37 cat(fcs_markers, sep="\n") | |
| 38 sink() | |
| 39 } | |
| 40 | |
| 41 checkFCS <- function(input_file, output_file) { | |
| 42 isValid <- F | |
| 43 # Check file beginning matches FCS standard | |
| 44 tryCatch({ | |
| 45 isValid <- isFCSfile(input_file) | |
| 46 }, error = function(ex) { | |
| 47 print (paste(" ! Error in isFCSfile", ex)) | |
| 48 }) | |
| 49 | |
| 50 if (isValid) { | |
| 51 getMarkerNames(input_file, output_file) | |
| 52 } else { | |
| 53 print (paste(input_file, "does not meet FCS standard")) | |
| 54 } | |
| 55 } | |
| 56 | |
| 57 args <- commandArgs(trailingOnly = TRUE) | |
| 58 checkFCS(args[1], args[2]) |