| Previous changeset 29:793f87231d49 (2020-01-07) Next changeset 31:eb15a3841da4 (2020-04-28) |
|
Commit message:
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" |
|
modified:
README.rst abims_xcms_xcmsSet.xml lib.r macros_xcms.xml xcms_xcmsSet.r |
| b |
| diff -r 793f87231d49 -r 14b1c52fae62 README.rst --- a/README.rst Tue Jan 07 08:16:02 2020 -0500 +++ b/README.rst Wed Feb 12 08:30:58 2020 -0500 |
| b |
| @@ -24,6 +24,10 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +**Version 3.6.1.0 - 03/09/2019** + +- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) + **Version 3.4.4.1 - 30/04/2019** - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms. |
| b |
| diff -r 793f87231d49 -r 14b1c52fae62 abims_xcms_xcmsSet.xml --- a/abims_xcms_xcmsSet.xml Tue Jan 07 08:16:02 2020 -0500 +++ b/abims_xcms_xcmsSet.xml Wed Feb 12 08:30:58 2020 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@WRAPPER_VERSION@.2"> +<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0"> <description>Chromatographic peak detection</description> <macros> @@ -224,7 +224,7 @@ <param name="ppm" value="25" /> <param name="peakwidth" value="20,50" /> </conditional> - <expand macro="test_file_load_single_ko15"/> + <expand macro="test_file_load_single_file" filename="ko15"/> <assert_stdout> <has_text text="ppm: 25" /> <has_text text="peakwidth: 20, 50" /> @@ -235,6 +235,7 @@ <has_text text="Peak Groups: 0" /> <has_text text="Sample classes: ." /> </assert_stdout> + <!--<output name="xsetRData" file="ko15-xset.RData" />--> </test> <!-- DISABLE FOR TRAVIS Useful to generate test-data for the further steps @@ -245,6 +246,7 @@ <param name="ppm" value="25" /> <param name="peakwidth" value="20,50" /> </conditional> + <expand macro="test_file_load_single_file" filename="ko16"/> <assert_stdout> <has_text text="object with 1 samples" /> <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" /> @@ -253,6 +255,7 @@ <has_text text="Peak Groups: 0" /> <has_text text="Sample classes: ." /> </assert_stdout> + <output name="xsetRData" file="ko16-xset.RData" /> </test> <test> <param name="image" value="wt15-raw.RData" ftype="rdata" /> @@ -261,6 +264,7 @@ <param name="ppm" value="25" /> <param name="peakwidth" value="20,50" /> </conditional> + <expand macro="test_file_load_single_file" filename="wt15"/> <assert_stdout> <has_text text="object with 1 samples" /> <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" /> @@ -269,6 +273,7 @@ <has_text text="Peak Groups: 0" /> <has_text text="Sample classes: ." /> </assert_stdout> + <output name="xsetRData" file="wt15-xset.RData" /> </test> <test> <param name="image" value="wt16-raw.RData" ftype="rdata" /> @@ -277,6 +282,7 @@ <param name="ppm" value="25" /> <param name="peakwidth" value="20,50" /> </conditional> + <expand macro="test_file_load_single_file" filename="wt16"/> <assert_stdout> <has_text text="object with 1 samples" /> <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" /> @@ -285,6 +291,7 @@ <has_text text="Peak Groups: 0" /> <has_text text="Sample classes: ." /> </assert_stdout> + <output name="xsetRData" file="wt16-xset.RData" /> </test> --> <!-- DISABLE FOR TRAVIS @@ -485,14 +492,13 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +@HELP_XCMS_NEWVERSION_3610@ + **Version 3.4.4.1 - 30/04/2019** - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms. -**Version 3.4.4.0 - 08/02/2019** - -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) - +@HELP_XCMS_NEWVERSION_3440@ **Version 3.0.0.0 - 08/03/2018** |
| b |
| diff -r 793f87231d49 -r 14b1c52fae62 lib.r --- a/lib.r Tue Jan 07 08:16:02 2020 -0500 +++ b/lib.r Wed Feb 12 08:30:58 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 793f87231d49 -r 14b1c52fae62 macros_xcms.xml --- a/macros_xcms.xml Tue Jan 07 08:16:02 2020 -0500 +++ b/macros_xcms.xml Wed Feb 12 08:30:58 2020 -0500 |
| b |
| @@ -1,11 +1,11 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">3.4.4</token> + <token name="@TOOL_VERSION@">3.6.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> + <requirement type="package" version="1.1_5">r-batch</requirement> <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> <requirement type="package" version="6.0">unzip</requirement> <yield /> @@ -69,11 +69,11 @@ </section> </xml> - <xml name="test_file_load_single_ko15"> + <xml name="test_file_load_single_file" token_filename=""> <section name="file_load_section"> <conditional name="file_load_conditional"> <param name="file_load_select" value="yes" /> - <param name="input" value="ko15.CDF" ftype="netcdf" /> + <param name="input" value="@FILENAME@.CDF" ftype="netcdf" /> </conditional> </section> </xml> @@ -246,6 +246,17 @@ </token> + <token name="@HELP_XCMS_NEWVERSION_3440@"> +**Version 3.4.4.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) + </token> + <token name="@HELP_XCMS_NEWVERSION_3610@"> +**Version 3.6.1+galaxy* - 03/09/2019** + +- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) + </token> + <xml name="citation"> <citations> <citation type="doi">10.1021/ac051437y</citation> |
| b |
| diff -r 793f87231d49 -r 14b1c52fae62 xcms_xcmsSet.r --- a/xcms_xcmsSet.r Tue Jan 07 08:16:02 2020 -0500 +++ b/xcms_xcmsSet.r Wed Feb 12 08:30:58 2020 -0500 |
| [ |
| @@ -59,12 +59,9 @@ if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData") # 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) cat("\n\n") @@ -76,9 +73,6 @@ cat("\t\tCOMPUTE\n") -## Get the full path to the files -files <- getMSFiles(directory) - cat("\t\t\tApply filter[s] (if asked)\n") if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2]) if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam) @@ -99,9 +93,6 @@ # Check if there are no peaks if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings") -# Transform the files absolute pathways into relative pathways -xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files) - # Create a sampleMetada file sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv") |