Mercurial > repos > immport-devteam > check_fcs_headers
changeset 1:a5609a84ed16 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit e5be067c50262354a028bd03b77beb8369fb6fb1"
| author | azomics |
|---|---|
| date | Thu, 23 Jul 2020 08:14:29 -0400 |
| parents | d3957a51cc51 |
| children | |
| files | check_fcs_headers/getFCSheader.R check_fcs_headers/getFCSheaders.py check_fcs_headers/getFCSheaders.xml check_fcs_headers/test-data/input1.fcs check_fcs_headers/test-data/input2.fcs check_fcs_headers/test-data/input3.fcs check_fcs_headers/test-data/output.tabular getFCSheader.R getFCSheaders.xml test-data/input1.fcs test-data/input2.fcs test-data/input3.fcs test-data/output.tabular |
| diffstat | 13 files changed, 166 insertions(+), 203 deletions(-) [+] |
line wrap: on
line diff
--- a/check_fcs_headers/getFCSheader.R Mon Feb 27 12:16:44 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -# FCS Headers Module for Galaxy -# FlowCore -###################################################################### -# Copyright (c) 2016 Northrop Grumman. -# All rights reserved. -###################################################################### -# -# Version 1 -# Cristel Thomas -# -# - -library(flowCore) - -getFCSMarkerNames <- function(input, output) { - fcs <- read.FCS(input, transformation=F) - ## marker names - channels <- colnames(fcs) - markers <- as.vector(pData(parameters(fcs))$desc) - df <- data.frame(channels, markers) - fcs_markers <- capture.output(df) - - write.table(df, output, sep="\t") -} - -checkFCS <- function(input_file, output_file) { - isValid <- F - # Check file beginning matches FCS standard - tryCatch({ - isValid = isFCSfile(input_file) - }, error = function(ex) { - print (paste(" ! Error in isFCSfile", ex)) - }) - - if (isValid) { - getFCSMarkerNames(input_file, output_file) - } else { - print (paste(input_file, "does not meet FCS standard")) - } -} - -args <- commandArgs(trailingOnly = TRUE) -checkFCS(args[2], args[3])
--- a/check_fcs_headers/getFCSheaders.py Mon Feb 27 12:16:44 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -#!/usr/bin/env python -###################################################################### -# Copyright (c) 2016 Northrop Grumman. -# All rights reserved. -###################################################################### -from __future__ import print_function -import sys -import os - -from argparse import ArgumentParser - - -def get_fcs_marker_list(marker_file): - with open(marker_file, "r") as mrkrs: - useless_first_line = mrkrs.readline() - channels = [] - markers = [] - for lines in mrkrs: - stuff = lines.strip().split("\t") - channels.append(stuff[1].strip("\"")) - markers.append(stuff[2].strip("\"")) - fcs_markers = [ - "\t".join(channels), - "\t".join(markers) - ] - return(fcs_markers) - - -def print_fcs_headers(files, filenames, outfile, tool_dir): - headers = {} - tool = "/".join([tool_dir, "getFCSheader.R"]) - for eachfile in files: - tmp_output = "tmp_fcs_headers.txt" - run_command = " ". join(["Rscript --slave --vanilla", tool, "--args", eachfile, tmp_output]) - os.system(run_command) - headers[eachfile] = get_fcs_marker_list(tmp_output) - - with open(outfile, "w") as outf: - for i, flc in enumerate(files): - outf.write("\t".join([filenames[i], "channels", headers[flc][0]]) + "\n") - for j, flm in enumerate(files): - outf.write("\t".join([filenames[j], "markers", headers[flm][1]]) + "\n") - return - - -if __name__ == "__main__": - parser = ArgumentParser( - prog="GetFCSHeaders", - description="Gets the headers of all files in given set.") - - parser.add_argument( - '-i', - dest="input_files", - required=True, - action='append', - help="File location for the text files.") - - parser.add_argument( - '-n', - dest="file_names", - required=True, - action='append', - help="File names.") - - parser.add_argument( - '-t', - dest="tool_dir", - required=True, - help="Path to the tool directory") - - parser.add_argument( - '-o', - dest="output_file", - required=True, - help="Name of the output file.") - - args = parser.parse_args() - input_files = [f for f in args.input_files] - file_names = [fn for fn in args.file_names] - print_fcs_headers(input_files, file_names, args.output_file, args.tool_dir) - sys.exit(0)
--- a/check_fcs_headers/getFCSheaders.xml Mon Feb 27 12:16:44 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -<tool id="get_fcs_headers" name="Get list of markers" version="1.0"> - <description>in FCS files.</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="2:" level="fatal" description="See stderr for more details." /> - </stdio> - <command><![CDATA[ - python $__tool_directory__/getFCSheaders.py -o "${output_file}" -t $__tool_directory__ - #for $f in $input# - -i "${f}" - -n "${f.name}" - #end for# - ]]> - </command> - <inputs> - <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/> - </inputs> - <outputs> - <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/> - </outputs> - <tests> - <test> - <param name="input"> - <collection type="list"> - <element name="input1.fcs" value="input1.fcs"/> - <element name="input2.fcs" value="input2.fcs"/> - <element name="input3.fcs" value="input3.fcs"/> - </collection> - </param> - <output name="output_file" file="output.tabular"/> - </test> - </tests> - <help><![CDATA[ - This tool returns a table of the headers of a set of FCS files. - ------ - -**Input files** - -This tool requires collections of FCS files as input. - -**Output file** - -The output file is a table listing the markers and channels for each file. - ------ - -**Example** - -*File1*:: - - Marker1 Marker2 Marker3 - 34 45 12 - 33 65 10 - -*File2*:: - - Marker4 Marker5 Marker3 - 19 62 98 - 12 36 58 - -*Output*:: - - File1 channels Channel1 Channel2 Channel3 - File2 channels Channel4 Channel5 Channel3 - File1 markers Marker1 Marker2 Marker3 - File2 markers Marker4 Marker5 Marker3 - ]]> - </help> -</tool>
--- a/check_fcs_headers/test-data/output.tabular Mon Feb 27 12:16:44 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -input3.fcs channels FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H -input1.fcs channels FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H -input2.fcs channels FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H -input3.fcs markers Forward Scatter Side Scatter FITC CD4 PE CCR3 PP CD8 APC CCR4 -input1.fcs markers Forward Scatter Side Scatter FITC CD4 PE CD25 PP CD3 APC CD45RA -input2.fcs markers Forward Scatter Side Scatter FITC CD4 PE CXCR3 PP CD8 APC CCR5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getFCSheader.R Thu Jul 23 08:14:29 2020 -0400 @@ -0,0 +1,87 @@ +#!/usr/bin/Rscript --vanilla +# FCS Headers Module for Galaxy +# FlowCore +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 2 +# May 2018 +# Cristel Thomas +# +# + +library(flowCore) + +getFCSChannels <- function(input_fcs) { + fcs <- read.FCS(input_fcs, transformation=F) + return(colnames(fcs)) +} + +getFCSMarkers <- function(input_fcs){ + ffcs <- read.FCS(input_fcs, transformation=F) + fmarkers <- as.vector(pData(parameters(ffcs))$desc) + return(fmarkers) +} + +getFCSMarkerNames <- function(output_file="", file_paths=vector(), + fcs_names=vector()) { + check_files <- sapply(file_paths, isFCSfile) + channels <- lapply(file_paths[check_files], getFCSChannels) + markers <- lapply(file_paths[check_files], getFCSMarkers) + + nb_col <- max(lengths(channels)) + nc <- lapply(channels, `length<-`, nb_col) + ct <- t(as.data.frame(nc)) + + nm <- lapply(markers, `length<-`, nb_col) + mt <- t(as.data.frame(nm)) + + nb_files <- sum(check_files) + Index <- rep(c("channels", "markers"), each=nb_files) + Filename <- rep(fcs_names[check_files], 2) + + idx_nb <- seq(nb_col) + ttt <- rbind(ct,mt) + finalt <- cbind(Filename, Index, ttt) + colnames(finalt)[3:length(colnames(finalt))] <- idx_nb + + + if (nb_files != length(file_paths)){ + not_fcs <- fcs_names[!check_files] + new_df <- cbind(not_fcs, "Not a valid FCS file") + empty_frame <- data.frame(matrix("", nrow=length(not_fcs), ncol=nb_col), + stringsAsFactors = F) + not_fcs_files <- cbind(new_df, empty_frame) + colnames(not_fcs_files) <- colnames(finalt) + new_final <- rbind(finalt, not_fcs_files) + write.table(new_final, file=output_file, quote=F, row.names=F, col.names=T, + sep='\t', append=F) + quit(save = "no", status = 10, runLast = FALSE) + } else { + # output file + write.table(finalt, file=output_file, quote=F, row.names=F, col.names=T, + sep='\t', + append=F) + } +} + +################################################################################ +################################################################################ + +args <- commandArgs(trailingOnly = TRUE) + +i <- 1 +nb_files <- (length(args)-1) / 2 +fcs_files <- character(nb_files) +fcs_names <- character(nb_files) +for (j in 1:length(args)){ + if (!j%%2){ + fcs_files[[i]] <- args[[j]] + fcs_names[[i]]<- args[[j+1]] + i <- i + 1 + } +} + +getFCSMarkerNames(args[1], fcs_files, fcs_names)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getFCSheaders.xml Thu Jul 23 08:14:29 2020 -0400 @@ -0,0 +1,72 @@ +<tool id="get_fcs_headers" name="Get list of markers" version="2.0+galaxy0"> + <description>in FCS files.</description> + <requirements> + <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> + </requirements> + <stdio> + <exit_code range="10" level="warning" description="Not all files are valid FCS files, see output for details." /> + </stdio> + <command><![CDATA[ + Rscript '$__tool_directory__/getFCSheader.R' '${output_file}' + #for $f in $input + '${f}' '${f.name}' + #end for + ]]> + </command> + <inputs> + <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/> + </inputs> + <outputs> + <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input"> + <collection type="list"> + <element name="input1.fcs" value="input1.fcs"/> + <element name="input2.fcs" value="input2.fcs"/> + <element name="input3.fcs" value="input3.fcs"/> + </collection> + </param> + <output name="output_file" file="output.tabular" lines_diff="8"/> + </test> + </tests> + <help><![CDATA[ + This tool returns a table of the headers of a set of FCS files. + +----- + +**Input files** + +This tool requires collections of FCS files as input. + +**Output file** + +The output file is a table listing the markers and channels for each file. + +----- + +**Example** + +*File1*:: + + Marker1 Marker2 Marker3 + 34 45 12 + 33 65 10 + +*File2*:: + + Marker4 Marker5 Marker3 + 19 62 98 + 12 36 58 + +*Output*:: + + Filename Index 1 2 3 + File1 channels Channel1 Channel2 Channel3 + File2 channels Channel4 Channel5 Channel3 + File1 markers Marker1 Marker2 Marker3 + File2 markers Marker4 Marker5 Marker3 + ]]> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tabular Thu Jul 23 08:14:29 2020 -0400 @@ -0,0 +1,7 @@ +Filename Index 1 2 3 4 5 6 +input3.fcs channels FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H +input2.fcs channels FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H +input1.fcs channels FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H +input3.fcs markers Forward Scatter Side Scatter FITC CD4 PE CCR3 PP CD8 APC CCR4 +input2.fcs markers Forward Scatter Side Scatter FITC CD4 PE CXCR3 PP CD8 APC CCR5 +input1.fcs markers Forward Scatter Side Scatter FITC CD4 PE CD25 PP CD3 APC CD45RA