| Previous changeset 12:f6b2750ea32e (2020-01-07) Next changeset 14:11ab2081bd4a (2021-04-12) |
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Commit message:
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" |
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modified:
lib.r msnbase_readmsdata.r msnbase_readmsdata.xml |
| b |
| diff -r f6b2750ea32e -r 226fb89cacc4 lib.r --- a/lib.r Tue Jan 07 04:30:02 2020 -0500 +++ b/lib.r Wed Feb 12 08:27:38 2020 -0500 |
| [ |
| b'@@ -42,16 +42,16 @@\n chromBPI <- NULL\n chromTIC_adjusted <- NULL\n chromBPI_adjusted <- NULL\n+ md5sumList <- NULL\n for(image in args$images) {\n \n load(image)\n # Handle infiles\n if (!exists("singlefile")) singlefile <- NULL\n if (!exists("zipfile")) zipfile <- NULL\n- rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)\n+ rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)\n zipfile <- rawFilePath$zipfile\n singlefile <- rawFilePath$singlefile\n- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)\n \n if (exists("raw_data")) xdata <- raw_data\n if (!exists("xdata")) stop("\\n\\nERROR: The RData doesn\'t contain any object called \'xdata\'. This RData should have been created by an old version of XMCS 2.*")\n@@ -149,7 +149,7 @@\n \n par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))\n \n- group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]\n+ group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")\n names(group_colors) <- unique(xdata$sample_group)\n \n xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))\n@@ -170,7 +170,7 @@\n pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)\n \n # Color by group\n- group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]\n+ group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")\n if (length(group_colors) > 1) {\n names(group_colors) <- unique(xdata$sample_group)\n plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])\n@@ -239,15 +239,15 @@\n pdf(pdfname, width=16, height=10)\n \n # Color by group\n- group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]\n+ group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")\n if (length(group_colors) > 1) {\n names(group_colors) <- unique(xdata$sample_group)\n- plot(chrom, col = group_colors[chrom$sample_group], main=main)\n+ plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none")\n legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)\n }\n \n # Color by sample\n- plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)\n+ plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none")\n legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)\n \n dev.off()\n@@ -317,142 +317,43 @@\n }\n \n \n-# This function check if xcms will found all the files\n-#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM\n-checkFilesCompatibilityWithXcms <- function(directory) {\n- cat("Checking files filenames compatibilities with xmcs...\\n")\n- # WHAT XCMS WILL FIND\n- filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")\n- filepattern <- paste(paste("\\\\.", filepattern, "$", sep=""),collapse="|")\n- info <- file.info(directory)\n- listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)\n- files <- c(directory[!info$isdir], listed)\n- files_abs <- file.path(getwd(), files)\n- exists <- file.exists(files_abs)\n- files[exists] <- files_abs[exists]\n- files[exists] <- sub("//","/",files[exists])\n-\n- # WHAT IS ON THE FILESYSTEM\n- filesystem_filepaths <- system(paste0("find \\"",getwd(),"/",directory,"\\" -not -name \'\\\\.*\' -not -path \'*conda-env*\' -type f -name \\"*\\""), intern=T)\n- filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]\n-\n- # COMPARISON\n- if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {\n- write("\\n\\nERROR: List of the files which will not be imported by xcmsSet",stderr())\n- write(files'..b'ames <- unlist(strsplit(singlefile_sampleNames,"\\\\|"))\n-\n- singlefile <- NULL\n- for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {\n- singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]\n- singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]\n- # In case, an url is used to import data within Galaxy\n- singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)\n- singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath\n- }\n- }\n- return(list(zipfile=zipfile, singlefile=singlefile))\n-}\n-\n # This function retrieve the raw file in the working directory\n # - if zipfile: unzip the file with its directory tree\n # - if singlefiles: set symlink with the good filename\n #@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n-retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {\n+retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") {\n+\n+ if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either \'\', \'Positive\', \'Negative\', \'MS1\' or \'MS2\'")\n+\n+ # single - if the file are passed in the command arguments -> refresh singlefile\n+ if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {\n+ singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\\\|"))\n+ singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\\\|"))\n+\n+ singlefile <- NULL\n+ for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {\n+ singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]\n+ singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]\n+ # In case, an url is used to import data within Galaxy\n+ singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)\n+ singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath\n+ }\n+ }\n+ # zipfile - if the file are passed in the command arguments -> refresh zipfile\n+ if (!is.null(args[[paste0("zipfile",prefix)]]))\n+ zipfile <- args[[paste0("zipfile",prefix)]]\n+\n+ # single\n if(!is.null(singlefile) && (length("singlefile")>0)) {\n+ files <- vector()\n for (singlefile_sampleName in names(singlefile)) {\n singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]\n if(!file.exists(singlefile_galaxyPath)){\n@@ -462,22 +363,16 @@\n \n if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))\n file.copy(singlefile_galaxyPath, singlefile_sampleName)\n-\n+ files <- c(files, singlefile_sampleName)\n }\n- directory <- "."\n-\n }\n+ # zipfile\n if(!is.null(zipfile) && (zipfile != "")) {\n if(!file.exists(zipfile)){\n error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")\n print(error_message)\n stop(error_message)\n }\n-\n- #list all file in the zip file\n- #zip_files <- unzip(zipfile,list=T)[,"Name"]\n-\n- #unzip\n suppressWarnings(unzip(zipfile, unzip="unzip"))\n \n #get the directory name\n@@ -489,8 +384,17 @@\n \n cat("files_root_directory\\t",directory,"\\n")\n \n+ filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")\n+ filepattern <- paste(paste("\\\\.", filepattern, "$", sep=""),collapse="|")\n+ info <- file.info(directory)\n+ listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)\n+ files <- c(directory[!info$isdir], listed)\n+ exists <- file.exists(files)\n+ files <- files[exists]\n+\n }\n- return (directory)\n+ return(list(zipfile=zipfile, singlefile=singlefile, files=files))\n+\n }\n \n \n' |
| b |
| diff -r f6b2750ea32e -r 226fb89cacc4 msnbase_readmsdata.r --- a/msnbase_readmsdata.r Tue Jan 07 04:30:02 2020 -0500 +++ b/msnbase_readmsdata.r Wed Feb 12 08:27:38 2020 -0500 |
| b |
| @@ -38,16 +38,12 @@ # Handle infiles if (!exists("singlefile")) singlefile <- NULL if (!exists("zipfile")) zipfile <- NULL -rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) +rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) zipfile <- rawFilePath$zipfile singlefile <- rawFilePath$singlefile -directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) +files <- rawFilePath$files -# Check some character issues -md5sumList <- list("origin" = getMd5sum(directory)) -checkXmlStructure(directory) -checkFilesCompatibilityWithXcms(directory) - +md5sumList <- list("origin" = getMd5sum(files)) cat("\n\n") @@ -58,9 +54,6 @@ cat("\t\tCOMPUTE\n") -## Get the full path to the files -files <- getMSFiles(directory) - cat("\t\t\tCreate a phenodata data.frame\n") s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1)) s_name <- tools::file_path_sans_ext(basename(files)) |
| b |
| diff -r f6b2750ea32e -r 226fb89cacc4 msnbase_readmsdata.xml --- a/msnbase_readmsdata.xml Tue Jan 07 04:30:02 2020 -0500 +++ b/msnbase_readmsdata.xml Wed Feb 12 08:27:38 2020 -0500 |
| b |
| @@ -58,11 +58,11 @@ <test> <param name="input" value="ko15.CDF" ftype="netcdf" /> <assert_stdout> - <has_text text="rowNames: ./ko15.CDF" /> + <has_text text="rowNames: ko15.CDF" /> <has_text text="ko15.CDF" /> <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" /> <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" /> - <has_text text="./ko15.CDF ko15 ." /> + <has_text text="ko15.CDF ko15 ." /> </assert_stdout> </test> <!-- DISABLE FOR TRAVIS |