Mercurial > repos > immport-devteam > convert_fcs_to_text
changeset 1:99bf034c674d draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/convert_fcs_to_text commit 5ac9759a4f1850b200cd7a301e6662ef8adca55d"
| author | azomics |
|---|---|
| date | Mon, 22 Jun 2020 17:26:06 -0400 |
| parents | 8e10184368a0 |
| children | |
| files | FCSConvert.R convertFCSToText.xml convert_fcs_to_text/FCSConvert.R convert_fcs_to_text/convertFCSToText.xml convert_fcs_to_text/test-data/nocomp.flowtext convert_fcs_to_text/test-data/testfcs1.fcs convert_fcs_to_text/test-data/withcomp.flowtext test-data/nocomp.flowtext test-data/testfcs1.fcs test-data/withcomp.flowtext |
| diffstat | 10 files changed, 231 insertions(+), 230 deletions(-) [+] |
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--- /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])
--- /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 @@ +<tool id="convert_fcs_to_text" name="Convert FCS to Text" version="1.0+galaxy1"> + <description>with no transformation</description> + <requirements> + <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + Rscript $__tool_directory__/FCSConvert.R '${input}' '${output_file}' $compensate + ]]> + </command> + <inputs> + <param format="fcs" name="input" type="data" label="FCS file"/> + <param name="compensate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"> + </param> + </inputs> + <outputs> + <data format="flowtext" name="output_file" label="No Transformation ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="compensate" value="FALSE"/> + <output name="output_file" file="nocomp.flowtext" compare="sim_size"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="compensate" value="TRUE"/> + <output name="output_file" file="withcomp.flowtext" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + This tool converts FCS files to text format with no tranformation. + +----- + +**Input files** + +This tool requires valid FCS files as input. Files are processed serially. Applying compensation is an option for FCS files including a compensation matrix. + +**Output file** + +The output is tab-separated text, containing the fluorescence intensity values for each marker. + +----- + +**Example**:: + + Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4 ... + 449 157 551 129 169 292 ... + 894 1023 199 277 320 227 ... + 262 73 437 69 0 146 ... + 340 115 509 268 0 74 ... + ... ... ... ... ... ... ... + ]]> + </help> +</tool>
--- 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])
--- 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 @@ -<tool id="convert_fcs_to_text" name="Convert FCS to Text" version="1.0"> - <description>with no transformation.</description> - <requirements> - <requirement type="package" version="3.3.0">r</requirement> - <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command><![CDATA[ - Rscript --slave --vanilla $__tool_directory__/FCSConvert.R --args "${input}" "${output_file}" $compensate - ]]> - </command> - <inputs> - <param format="fcs" name="input" type="data" label="FCS file"/> - <param name="compensate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"> - </param> - </inputs> - <outputs> - <data format="flowtext" name="output_file" label="No Transformation ${input.name}"/> - </outputs> - <tests> - <test> - <param name="input" value="testfcs1.fcs"/> - <param name="compensate" value="FALSE"/> - <output name="output_file" file="nocomp.flowtext"/> - </test> - <test> - <param name="input" value="testfcs1.fcs"/> - <param name="compensate" value="TRUE"/> - <output name="output_file" file="withcomp.flowtext"/> - </test> - </tests> - <help><![CDATA[ - This tool converts FCS files to text format with no tranformation. - ------ - -**Input files** - -This tool requires valid FCS files as input. Files are processed serially. Applying compensation is an option for FCS files including a compensation matrix. - -**Output file** - -The output is tab-separated text, containing the fluorescence intensity values for each marker. - ------ - -**Example**:: - - Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4 - 449 157 551 129 169 292 - 894 1023 199 277 320 227 - 262 73 437 69 0 146 - 340 115 509 268 0 74 - ]]> - </help> -</tool>
--- 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 19.1100006103516 3.83999991416931 146.879989624023 125.440002441406 942.760009765625 0 -13879.5 11372 76400.875 66800 -70.6800003051758 167.959991455078 157.43000793457 80.0800018310547 51.8400001525879 83.5199966430664 -4.90000009536743 -11.7600002288818 0 -53197.5 49698 32821.8828125 30290 243.959991455078 1424.23999023438 212.940002441406 66.4300003051758 731.519958496094 822.719970703125 -8.81999969482422 40.1800003051758 0 -94011.75 85861 46558.33203125 45425 -55.4799995422363 178.599990844727 600.600036621094 103.740005493164 546.239990234375 13994.8798828125 42.1399993896484 34.2999992370605 0.100000001490116 -56965.5 51060 42377.79296875 41492 2128.76000976562 12543.0400390625 239.330001831055 9038.1201171875 2529.59985351562 2429.76000976562 620.340026855469 1694.42004394531 0.100000001490116 -102877.5 91646 74486.234375 70382 2954.8798828125 8467.919921875 346.710021972656 276.640014648438 12951.359375 9643.2001953125 353.779998779297 209.720001220703 0.200000002980232 -170482.5 135955 126331.6640625 106115 196.839996337891 4349.47998046875 1876.42004394531 1431.43005371094 919.679992675781 12119.0400390625 265.580017089844 941.780029296875 0.200000002980232 -140555.25 100224 108512.046875 72196 173.279998779297 1068.55993652344 1397.76000976562 447.720001220703 1393.919921875 24694.080078125 210.699996948242 183.260009765625 0.200000002980232 -46518.75 37218 138006.046875 113970 74.4799957275391 1400.67993164062 2420.60009765625 755.300048828125 435.839996337891 7570.56005859375 211.68000793457 242.059997558594 0.200000002980232 -11892.75 11583 10502.310546875 10123 -37.2399978637695 220.399993896484 55.5100021362305 49.1400032043457 -7.67999982833862 7.67999982833862 -12.7399997711182 65.6600036621094 0.300000011920929
--- a/convert_fcs_to_text/test-data/withcomp.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 -87.0409478040183 1862.84642436843 271.401077855461 -21.5928234634463 -3.8953788307554 128.962897543941 -105.49762363372 883.862950370797 0 -13879.5 11372 76400.875 66800 -78.6039894593431 181.219255881273 155.837498648 65.4989955303374 49.1162320405613 34.35089684109 -93.9379731423774 -20.2250618932269 0 -53197.5 49698 32821.8828125 30290 230.052594687552 1373.99921235714 197.676575400523 43.2961600914911 719.022620194678 260.803809001924 -123.26357251272 -7.84948514046658 0 -94011.75 85861 46558.33203125 45425 -71.9173894410761 175.966101207251 32.020003628979 59.0097517206453 -16.3262596884212 14004.8608140457 19.4103482134535 26.3251000552498 0.100000001490116 -56965.5 51060 42377.79296875 41492 1141.7755127904 10749.6103892967 198.722094418903 8932.67673912722 2473.54527111587 532.454297443733 422.911926152405 942.872373887256 0.100000001490116 -102877.5 91646 74486.234375 70382 2882.43278670468 7885.97842835489 269.438114676268 171.646872288934 12954.6785962761 -229.3446155909 202.938466043071 -74.2736739022447 0.200000002980232 -170482.5 135955 126331.6640625 106115 36.6180435027011 3913.39806836873 1398.12822721842 1227.24406134117 435.463239428049 11681.3109026932 -612.66079632735 757.567147469633 0.200000002980232 -140555.25 100224 108512.046875 72196 118.194682368212 954.043993675198 406.120956366245 316.018805963466 412.280494784593 24349.6063726745 -40.2882648979737 135.879221006295 0.200000002980232 -46518.75 37218 138006.046875 113970 10.0578231845294 1267.0939533411 2123.37003323943 495.398550791435 125.007577719306 7314.15255846409 -1039.4176032792 173.430016675029 0.200000002980232 -11892.75 11583 10502.310546875 10123 -43.2553273261776 203.396825762157 55.0774261065933 45.3952130843187 -8.67869816746458 10.0850033972805 -49.5506216433673 57.4240755386454 0.300000011920929
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nocomp.flowtext Mon Jun 22 17:26:06 2020 -0400 @@ -0,0 +1,11 @@ +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 19.1100006103516 3.83999991416931 146.879989624023 125.440002441406 942.760009765625 0 +13879.5 11372 76400.875 66800 -70.6800003051758 167.959991455078 157.43000793457 80.0800018310547 51.8400001525879 83.5199966430664 -4.90000009536743 -11.7600002288818 0 +53197.5 49698 32821.8828125 30290 243.959991455078 1424.23999023438 212.940002441406 66.4300003051758 731.519958496094 822.719970703125 -8.81999969482422 40.1800003051758 0 +94011.75 85861 46558.33203125 45425 -55.4799995422363 178.599990844727 600.600036621094 103.740005493164 546.239990234375 13994.8798828125 42.1399993896484 34.2999992370605 0.100000001490116 +56965.5 51060 42377.79296875 41492 2128.76000976562 12543.0400390625 239.330001831055 9038.1201171875 2529.59985351562 2429.76000976562 620.340026855469 1694.42004394531 0.100000001490116 +102877.5 91646 74486.234375 70382 2954.8798828125 8467.919921875 346.710021972656 276.640014648438 12951.359375 9643.2001953125 353.779998779297 209.720001220703 0.200000002980232 +170482.5 135955 126331.6640625 106115 196.839996337891 4349.47998046875 1876.42004394531 1431.43005371094 919.679992675781 12119.0400390625 265.580017089844 941.780029296875 0.200000002980232 +140555.25 100224 108512.046875 72196 173.279998779297 1068.55993652344 1397.76000976562 447.720001220703 1393.919921875 24694.080078125 210.699996948242 183.260009765625 0.200000002980232 +46518.75 37218 138006.046875 113970 74.4799957275391 1400.67993164062 2420.60009765625 755.300048828125 435.839996337891 7570.56005859375 211.68000793457 242.059997558594 0.200000002980232 +11892.75 11583 10502.310546875 10123 -37.2399978637695 220.399993896484 55.5100021362305 49.1400032043457 -7.67999982833862 7.67999982833862 -12.7399997711182 65.6600036621094 0.300000011920929
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/withcomp.flowtext Mon Jun 22 17:26:06 2020 -0400 @@ -0,0 +1,11 @@ +FSC-A FSC-H SSC-A SSC-H CD127 CD45RO LIVE CD4 CD3 HLA-DR CD25 CCR4 Time +9081 8811 19575.009765625 18578 -87.0409478040183 1862.84642436843 271.401077855461 -21.5928234634463 -3.8953788307554 128.96289754394 -105.49762363372 883.862950370797 0 +13879.5 11372 76400.875 66800 -78.6039894593431 181.219255881273 155.837498648 65.4989955303373 49.1162320405613 34.35089684109 -93.9379731423774 -20.2250618932269 0 +53197.5 49698 32821.8828125 30290 230.052594687552 1373.99921235714 197.676575400523 43.2961600914911 719.022620194678 260.803809001924 -123.26357251272 -7.84948514046658 0 +94011.75 85861 46558.33203125 45425 -71.9173894410761 175.966101207251 32.020003628979 59.0097517206453 -16.326259688421 14004.8608140457 19.4103482134534 26.3251000552498 0.100000001490116 +56965.5 51060 42377.79296875 41492 1141.7755127904 10749.6103892967 198.722094418903 8932.67673912722 2473.54527111587 532.454297443732 422.911926152405 942.872373887256 0.100000001490116 +102877.5 91646 74486.234375 70382 2882.43278670468 7885.9784283549 269.438114676268 171.646872288934 12954.6785962761 -229.3446155909 202.938466043071 -74.2736739022447 0.200000002980232 +170482.5 135955 126331.6640625 106115 36.6180435027011 3913.39806836873 1398.12822721842 1227.24406134117 435.463239428049 11681.3109026932 -612.66079632735 757.567147469633 0.200000002980232 +140555.25 100224 108512.046875 72196 118.194682368212 954.043993675198 406.120956366245 316.018805963466 412.280494784594 24349.6063726745 -40.2882648979739 135.879221006295 0.200000002980232 +46518.75 37218 138006.046875 113970 10.0578231845294 1267.0939533411 2123.37003323943 495.398550791435 125.007577719306 7314.15255846409 -1039.4176032792 173.430016675029 0.200000002980232 +11892.75 11583 10502.310546875 10123 -43.2553273261776 203.396825762157 55.0774261065933 45.3952130843187 -8.67869816746458 10.0850033972805 -49.5506216433673 57.4240755386454 0.300000011920929