# HG changeset patch # User azomics # Date 1592861166 14400 # Node ID 99bf034c674d35ccc7bd0d5a691bc64c36f3468b # Parent 8e10184368a0e8e9a8c00a5efe5619f81cf31e8e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/convert_fcs_to_text commit 5ac9759a4f1850b200cd7a301e6662ef8adca55d" diff -r 8e10184368a0 -r 99bf034c674d FCSConvert.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FCSConvert.R Mon Jun 22 17:26:06 2020 -0400 @@ -0,0 +1,151 @@ +#!/usr/bin/env Rscript +# ImmPort FCSConvert +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Converts the FCS file to text without transformaton +# To run in R +# 1) library(flowCore) +# 2) source("FCSConvert.R") +# 3) transformFCS("filename") +# +# Version 1.4.1 +# March 2016 -- added lines to run directly from command line +# + +library(flowCore) + +convertFCS <- function(fcs,compensate=FALSE,debug=FALSE) { + # Check file type and FCS version + if (class(fcs)[1] != "flowFrame") { + print("convertFCS requires flowFrame object as input") + return(FALSE) + } + + keywords <- keyword(fcs) + markers <- colnames(fcs) + print_markers <- as.vector(pData(parameters(fcs))$desc) + # Update print_markers if the $P?S not in the FCS file + for (i in 1:length(print_markers)) { + if (is.na(print_markers[i])) { + print_markers[i] <- markers[i] + } + } + + if (debug) { + print("****Inside convertFCS") + print(paste(" FCS version:", keywords$FCSversion)) + print(paste(" DATATYPE:", keywords['$DATATYPE'])) + } + + if (keywords$FCSversion == "2" || + keywords$FCSversion == "3" || + keywords$FCSversion == "3.1" ) { + datatype = unlist(keywords['$DATATYPE']) + if (datatype == 'F') { + # Apply compensation if available and requested + spill <- keyword(fcs)$SPILL + if (is.null(spill) == FALSE && compensate == TRUE) { + if (debug) { + print("Attempting compensation") + } + tryCatch({ fcs = compensate(fcs, spill) }, + error = function(ex) { str(ex); }) + } + # Process fcs expression data, using transformation + # based on category of the marker. + fcs_exprs <- exprs(fcs) + colnames(fcs_exprs) <- print_markers + } else if (datatype == 'I') { + fcs_exprs <- exprs(fcs) + colnames(fcs_exprs) = print_markers + } else { + print(paste("Data type", datatype, "in FCS 3 is not supported")) + fcs_exprs <- FALSE + } + } else { + print(paste("FCS version", keyword(fcs)$FCSversion, "is not supported")) + fcs_exprs <- FALSE + } + fcs_exprs +} + + +# +# Starting function for processing a FCS file +# +processFCSFile <- function(input_file, output_file="", + keyword_file="",compensate=FALSE, debug=FALSE) { + + # + # Generate the file names for the output_file and keyword_file + # + pieces <- unlist(strsplit(input_file, .Platform$file.sep)) + filename <- pieces[length(pieces)] + + if (output_file == "") { + filepieces = unlist(strsplit(filename, '\\.')) + #replace .fcs with .txt; append .txt if not ending in .fcs + if (filepieces[length(filepieces)] == 'fcs') { + filepieces[length(filepieces)] <- 'txt' + } else { + filepieces[length(filepieces)+1] <- 'txt' + } + output_file <- paste(filepieces, collapse = '.') + } + + if (keyword_file == "") { + filepieces <- unlist(strsplit(filename, '\\.')) + #replace .fcs with .keyword; append .keyword if not ending in .fcs + if (filepieces[length(filepieces)] == 'fcs') { + filepieces[length(filepieces)] <- 'keyword' + } else { + filepieces[length(filepieces)+1] <- 'keyword' + } + keyword_file <- paste(filepieces, collapse = '.') + } + + if (debug) { + print (paste("Converting file: ",input_file)) + print (paste("Original file name: ",filename)) + print (paste("Output file name: ",output_file)) + print (paste("Keyword file name: ",keyword_file)) + } + fcs <- read.FCS(input_file, transformation=F) + keywords <- keyword(fcs) + write.table(as.matrix(keywords),file=keyword_file, quote=F, + row.names=T, col.names=F, sep='=', append=F) + + transformed_data <- convertFCS(fcs,compensate,debug) + write.table(transformed_data, file=output_file, quote=F, + row.names=F,col.names=T, sep='\t', append=F) +} + +# Convert FCS file without transformation +# @param input_file FCS file to be transformed +# @param output_file FCS file transformed ".txt" extension +# @param keyword_file FCS file keywords ".keywords" extension" +# @param compensate Flag indicating whether to apply compensation +# matrix if it exists. +transformFCS <- function(input_file, output_file="", + compensate=FALSE, keyword_file="", debug=FALSE) { + + isValid <- F + # Check file beginning matches FCS standard + tryCatch({ + isValid <- isFCSfile(input_file) + }, error = function(ex) { + print (paste(" ! Error in isFCSfile", ex)) + }) + + if (isValid) { + processFCSFile(input_file, output_file, keyword_file, compensate, debug) + } else { + print (paste(input_file, "does not meet FCS standard")) + } +} + +args <- commandArgs(trailingOnly = TRUE) +transformFCS(args[1], args[2], args[3]) diff -r 8e10184368a0 -r 99bf034c674d convertFCSToText.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convertFCSToText.xml Mon Jun 22 17:26:06 2020 -0400 @@ -0,0 +1,58 @@ + + with no transformation + + bioconductor-flowcore + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 8e10184368a0 -r 99bf034c674d convert_fcs_to_text/FCSConvert.R --- a/convert_fcs_to_text/FCSConvert.R Mon Feb 27 12:45:51 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,150 +0,0 @@ -# ImmPort FCSConvert -###################################################################### -# Copyright (c) 2016 Northrop Grumman. -# All rights reserved. -###################################################################### -# -# Converts the FCS file to text without transformaton -# To run in R -# 1) library(flowCore) -# 2) source("FCSConvert.R") -# 3) transformFCS("filename") -# -# Version 1.4.1 -# March 2016 -- added lines to run directly from command line -# - -library(flowCore) - -convertFCS <- function(fcs,compensate=FALSE,debug=FALSE) { - # Check file type and FCS version - if (class(fcs)[1] != "flowFrame") { - print("convertFCS requires flowFrame object as input") - return(FALSE) - } - - keywords <- keyword(fcs) - markers <- colnames(fcs) - print_markers <- as.vector(pData(parameters(fcs))$desc) - # Update print_markers if the $P?S not in the FCS file - for (i in 1:length(print_markers)) { - if (is.na(print_markers[i])) { - print_markers[i] <- markers[i] - } - } - - if (debug) { - print("****Inside convertFCS") - print(paste(" FCS version:", keywords$FCSversion)) - print(paste(" DATATYPE:", keywords['$DATATYPE'])) - } - - if (keywords$FCSversion == "2" || - keywords$FCSversion == "3" || - keywords$FCSversion == "3.1" ) { - datatype = unlist(keywords['$DATATYPE']) - if (datatype == 'F') { - # Apply compensation if available and requested - spill <- keyword(fcs)$SPILL - if (is.null(spill) == FALSE && compensate == TRUE) { - if (debug) { - print("Attempting compensation") - } - tryCatch({ fcs = compensate(fcs, spill) }, - error = function(ex) { str(ex); }) - } - # Process fcs expression data, using transformation - # based on category of the marker. - fcs_exprs <- exprs(fcs) - colnames(fcs_exprs) <- print_markers - } else if (datatype == 'I') { - fcs_exprs <- exprs(fcs) - colnames(fcs_exprs) = print_markers - } else { - print(paste("Data type", datatype, "in FCS 3 is not supported")) - fcs_exprs <- FALSE - } - } else { - print(paste("FCS version", keyword(fcs)$FCSversion, "is not supported")) - fcs_exprs <- FALSE - } - fcs_exprs -} - - -# -# Starting function for processing a FCS file -# -processFCSFile <- function(input_file, output_file="", - keyword_file="",compensate=FALSE, debug=FALSE) { - - # - # Generate the file names for the output_file and keyword_file - # - pieces <- unlist(strsplit(input_file, .Platform$file.sep)) - filename <- pieces[length(pieces)] - - if (output_file == "") { - filepieces = unlist(strsplit(filename, '\\.')) - #replace .fcs with .txt; append .txt if not ending in .fcs - if (filepieces[length(filepieces)] == 'fcs') { - filepieces[length(filepieces)] <- 'txt' - } else { - filepieces[length(filepieces)+1] <- 'txt' - } - output_file <- paste(filepieces, collapse = '.') - } - - if (keyword_file == "") { - filepieces <- unlist(strsplit(filename, '\\.')) - #replace .fcs with .keyword; append .keyword if not ending in .fcs - if (filepieces[length(filepieces)] == 'fcs') { - filepieces[length(filepieces)] <- 'keyword' - } else { - filepieces[length(filepieces)+1] <- 'keyword' - } - keyword_file <- paste(filepieces, collapse = '.') - } - - if (debug) { - print (paste("Converting file: ",input_file)) - print (paste("Original file name: ",filename)) - print (paste("Output file name: ",output_file)) - print (paste("Keyword file name: ",keyword_file)) - } - fcs <- read.FCS(input_file, transformation=F) - keywords <- keyword(fcs) - write.table(as.matrix(keywords),file=keyword_file, quote=F, - row.names=T, col.names=F, sep='=', append=F) - - transformed_data <- convertFCS(fcs,compensate,debug) - write.table(transformed_data, file=output_file, quote=F, - row.names=F,col.names=T, sep='\t', append=F) -} - -# Convert FCS file without transformation -# @param input_file FCS file to be transformed -# @param output_file FCS file transformed ".txt" extension -# @param keyword_file FCS file keywords ".keywords" extension" -# @param compensate Flag indicating whether to apply compensation -# matrix if it exists. -transformFCS <- function(input_file, output_file="", - compensate=FALSE, keyword_file="", debug=FALSE) { - - isValid <- F - # Check file beginning matches FCS standard - tryCatch({ - isValid <- isFCSfile(input_file) - }, error = function(ex) { - print (paste(" ! Error in isFCSfile", ex)) - }) - - if (isValid) { - processFCSFile(input_file, output_file, keyword_file, compensate, debug) - } else { - print (paste(input_file, "does not meet FCS standard")) - } -} - -args <- commandArgs(trailingOnly = TRUE) -transformFCS(args[2], args[3], args[4]) diff -r 8e10184368a0 -r 99bf034c674d convert_fcs_to_text/convertFCSToText.xml --- a/convert_fcs_to_text/convertFCSToText.xml Mon Feb 27 12:45:51 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ - - with no transformation. - - r - bioconductor-flowcore - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 8e10184368a0 -r 99bf034c674d convert_fcs_to_text/test-data/nocomp.flowtext --- a/convert_fcs_to_text/test-data/nocomp.flowtext Mon Feb 27 12:45:51 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -FSC-A FSC-H SSC-A SSC-H CD127 CD45RO LIVE CD4 CD3 HLA-DR CD25 CCR4 Time -9081 8811 19575.009765625 18578 -76 2140.15991210938 278.460021972656 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