| Previous changeset 28:018a9771de28 (2021-04-07) Next changeset 30:444e3ed135e3 (2024-07-15) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e |
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modified:
abims_xcms_summary.xml lib.r macros_xcms.xml test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html xcms_summary.r |
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added:
static/images/msnbase_readmsdata_workflow.png static/images/xcms_fillpeaks_workflow.png static/images/xcms_group.png static/images/xcms_group_workflow.png static/images/xcms_merge_workflow.png static/images/xcms_plot_chromatogram_workflow.png static/images/xcms_retcor.png static/images/xcms_retcor_workflow.png static/images/xcms_tics.png static/images/xcms_xcmsset_workflow.png test-data/BPIs.pdf test-data/MM14.mzML test-data/TICs.pdf test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.dataMatrix.NAless.tsv test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.variableMetadata.tsv test-data/faahKO-single-class.xset.merged.RData test-data/faahKO-single-class.xset.merged.group.RData test-data/faahKO-single-class.xset.merged.group.retcor.RData test-data/faahKO-single-class.xset.merged.group.retcor.group.RData test-data/faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData test-data/faahKO.xset.group.dataMatrix.tsv test-data/faahKO.xset.group.variableMetadata.tsv test-data/faahKO_reduce.zip test-data/ko15-raw.RData test-data/ko15-xset.RData test-data/ko15.CDF test-data/ko16-raw.RData test-data/ko16-xset.RData test-data/ko16.CDF test-data/noclass.merged.sampleMetadata.tsv test-data/roiList.txt test-data/sampleMetadata.tab test-data/sampleMetadata.tsv test-data/sampleMetadata_missing.tab test-data/wt15-raw.RData test-data/wt15-xset.RData test-data/wt15.CDF test-data/wt16-raw.RData test-data/wt16-xset.RData test-data/wt16.CDF |
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removed:
README.rst repository_dependencies.xml |
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| diff -r 018a9771de28 -r 2a2850fdf29e README.rst --- a/README.rst Wed Apr 07 16:46:50 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,54 +0,0 @@ - -Changelog/News --------------- - -.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS - -**Version 3.12.0+galaxy* - 03/03/2020** - -- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_) - -**Version 3.6.1+galaxy1 - 05/04/2020** - -- UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0 - -- BUGFIX: "Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds" - -**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 3.4.4.0 - 08/02/2019** - -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) - -**Version 3.0.0.0 - 14/02/2018** - -- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods - -- IMPROVEMENT: the tool now shows all the parameters and not only those which were setted. - - -**Version 1.0.4 - 13/02/2018** - -- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 - - -**Version 1.0.3 - 03/02/2017** - -- IMPROVEMENT: xcms.summary can deal with merged individual data - - -**Version 1.0.2 - 06/07/2016** - -- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 - - -**Version 1.0.1 - 04/04/2016** - -- TEST: refactoring to pass planemo test using conda dependencies - - -**Version 1.0.0 - 10/02/2016** - -- NEW: Create a summary of XCMS analysis |
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| diff -r 018a9771de28 -r 2a2850fdf29e abims_xcms_summary.xml --- a/abims_xcms_summary.xml Wed Apr 07 16:46:50 2021 +0000 +++ b/abims_xcms_summary.xml Mon Sep 11 09:23:36 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy0"> +<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Create a summary of XCMS analysis</description> @@ -41,7 +41,7 @@ </test>--> <test> <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/> - <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" /> + <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" lines_diff="2"/> </test> </tests> @@ -82,6 +82,8 @@ .. image:: xcms_summary_workflow.png +@HELP_XCMS_MANUAL@ + --------------------------------------------------- Changelog/News |
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| diff -r 018a9771de28 -r 2a2850fdf29e lib.r --- a/lib.r Wed Apr 07 16:46:50 2021 +0000 +++ b/lib.r Mon Sep 11 09:23:36 2023 +0000 |
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| b'@@ -4,12 +4,12 @@\n #@author G. Le Corguille\n # solve an issue with batch if arguments are logical TRUE/FALSE\n parseCommandArgs <- function(...) {\n- args <- batch::parseCommandArgs(...)\n- for (key in names(args)) {\n- if (args[key] %in% c("TRUE", "FALSE"))\n- args[key] <- as.logical(args[key])\n- }\n- return(args)\n+ args <- batch::parseCommandArgs(...)\n+ for (key in names(args)) {\n+ if (args[key] %in% c("TRUE", "FALSE"))\n+ args[key] <- as.logical(args[key])\n+ }\n+ return(args)\n }\n \n #@author G. Le Corguille\n@@ -17,237 +17,247 @@\n # - load the packages\n # - display the sessionInfo\n loadAndDisplayPackages <- function(pkgs) {\n- for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))\n+ for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))\n \n- sessioninfo <- sessionInfo()\n- cat(sessioninfo$R.version$version.string, "\\n")\n- cat("Main packages:\\n")\n- for (pkg in names(sessioninfo$otherPkgs)) {\n- cat(paste(pkg, packageVersion(pkg)), "\\t")\n- }\n- cat("\\n")\n- cat("Other loaded packages:\\n")\n- for (pkg in names(sessioninfo$loadedOnly)) {\n- cat(paste(pkg, packageVersion(pkg)), "\\t")\n- }\n- cat("\\n")\n+ sessioninfo <- sessionInfo()\n+ cat(sessioninfo$R.version$version.string, "\\n")\n+ cat("Main packages:\\n")\n+ for (pkg in names(sessioninfo$otherPkgs)) {\n+ cat(paste(pkg, packageVersion(pkg)), "\\t")\n+ }\n+ cat("\\n")\n+ cat("Other loaded packages:\\n")\n+ for (pkg in names(sessioninfo$loadedOnly)) {\n+ cat(paste(pkg, packageVersion(pkg)), "\\t")\n+ }\n+ cat("\\n")\n }\n \n #@author G. Le Corguille\n # This function merge several chromBPI or chromTIC into one.\n mergeChrom <- function(chrom_merged, chrom) {\n- if (is.null(chrom_merged)) return(NULL)\n- chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)\n- return(chrom_merged)\n+ if (is.null(chrom_merged)) return(NULL)\n+ chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)\n+ return(chrom_merged)\n }\n \n #@author G. Le Corguille\n # This function merge several xdata into one.\n mergeXData <- function(args) {\n- chromTIC <- NULL\n- chromBPI <- NULL\n- chromTIC_adjusted <- NULL\n- chromBPI_adjusted <- NULL\n- md5sumList <- NULL\n- for (image in args$images) {\n+ chromTIC <- NULL\n+ chromBPI <- NULL\n+ chromTIC_adjusted <- NULL\n+ chromBPI_adjusted <- NULL\n+ md5sumList <- NULL\n+ for (image in args$images) {\n \n- load(image)\n- # Handle infiles\n- if (!exists("singlefile")) singlefile <- NULL\n- if (!exists("zipfile")) zipfile <- NULL\n- rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)\n- zipfile <- rawFilePath$zipfile\n- singlefile <- rawFilePath$singlefile\n+ load(image)\n+ # Handle infiles\n+ if (!exists("singlefile")) singlefile <- NULL\n+ if (!exists("zipfile")) zipfile <- NULL\n+ rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)\n+ zipfile <- rawFilePath$zipfile\n+ singlefile <- rawFilePath$singlefile\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+ 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 \n- cat(sampleNamesList$sampleNamesOrigin, "\\n")\n+ cat(sampleNamesList$sampleNamesOrigin, "\\n")\n \n- if (!exists("xdata_merged")) {\n- xdata_merged <- xdata\n- singlefile_merged <- singlefile\n- md5sumList_merged <- md5sumList\n- sampleNamesList_merged <- sampleNamesList\n- chromTIC_merged <- chromTIC\n- chromBPI_merged <- c'..b'e_galaxyPath, singlefile_sampleName)\n- files <- c(files, singlefile_sampleName)\n- }\n+ if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))\n+ file.copy(singlefile_galaxyPath, singlefile_sampleName)\n+ files <- c(files, singlefile_sampleName)\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- suppressWarnings(unzip(zipfile, unzip = "unzip"))\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+ suppressWarnings(unzip(zipfile, unzip = "unzip"))\n \n- #get the directory name\n- suppressWarnings(filesInZip <- unzip(zipfile, list = T))\n- directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))\n- directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]\n- directory <- "."\n- if (length(directories) == 1) directory <- directories\n+ #get the directory name\n+ suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))\n+ directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))\n+ directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]\n+ directory <- "."\n+ if (length(directories) == 1) directory <- directories\n \n- cat("files_root_directory\\t", directory, "\\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$isdir], listed)\n- exists <- file.exists(files)\n- files <- files[exists]\n+ filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")\n+ filepattern <- paste(paste("\\\\.", filepattern, "$", 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(list(zipfile = zipfile, singlefile = singlefile, files = files))\n-\n+ }\n+ return(list(zipfile = zipfile, singlefile = singlefile, files = files))\n }\n \n \n # This function retrieve a xset like object\n #@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n getxcmsSetObject <- function(xobject) {\n- # XCMS 1.x\n- if (class(xobject) == "xcmsSet")\n- return(xobject)\n- # XCMS 3.x\n- if (class(xobject) == "XCMSnExp") {\n- # Get the legacy xcmsSet object\n- suppressWarnings(xset <- as(xobject, "xcmsSet"))\n- if (!is.null(xset@phenoData$sample_group))\n- sampclass(xset) <- xset@phenoData$sample_group\n- else\n- sampclass(xset) <- "."\n- return(xset)\n- }\n+ # XCMS 1.x\n+ if (class(xobject) == "xcmsSet")\n+ return(xobject)\n+ # XCMS 3.x\n+ if (class(xobject) == "XCMSnExp") {\n+ # Get the legacy xcmsSet object\n+ suppressWarnings(xset <- as(xobject, "xcmsSet"))\n+ if (!is.null(xset@phenoData$sample_group))\n+ sampclass(xset) <- xset@phenoData$sample_group\n+ else\n+ sampclass(xset) <- "."\n+ return(xset)\n+ }\n }\n' |
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| diff -r 018a9771de28 -r 2a2850fdf29e macros_xcms.xml --- a/macros_xcms.xml Wed Apr 07 16:46:50 2021 +0000 +++ b/macros_xcms.xml Mon Sep 11 09:23:36 2023 +0000 |
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| @@ -2,6 +2,8 @@ <macros> <token name="@TOOL_VERSION@">3.12.0</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">21.09</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> @@ -17,7 +19,7 @@ #if $file_load_section.file_load_conditional.file_load_select == "yes": #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) - #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = '|'.join( [ str( $single_file.element_identifier ) for $single_file in $file_load_section.file_load_conditional.input ] ) singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' #else @@ -36,7 +38,7 @@ <when value="no"> </when> <when value="yes"> - <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: zip. See the help section below." /> </when> </conditional> </section> @@ -80,7 +82,7 @@ <!-- PEAKLIST --> <token name="@COMMAND_PEAKLIST@"> - #if $peaklist.peaklistBool + #if $peaklist.peaklistBool == 'true' convertRTMinute $peaklist.convertRTMinute numDigitsMZ $peaklist.numDigitsMZ numDigitsRT $peaklist.numDigitsRT @@ -103,14 +105,17 @@ <xml name="input_peaklist_section"> <section name="peaklist" title="Peak List" expanded="True"> - <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" /> + <param name="peaklistBool" type="hidden" label="Get the Peak List" value="true" /> <expand macro="input_peaklist"/> </section> </xml> <xml name="input_peaklist_conditional"> <conditional name="peaklist"> - <param name="peaklistBool" type="boolean" label="Get the Peak List" /> + <param name="peaklistBool" type="select" label="Get the Peak List"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> <when value="true"> <expand macro="input_peaklist"/> </when> @@ -120,10 +125,10 @@ <xml name="output_peaklist" token_function=""> <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" > - <filter>(peaklist['peaklistBool'])</filter> + <filter>peaklist['peaklistBool'] == 'true'</filter> </data> <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" > - <filter>(peaklist['peaklistBool'])</filter> + <filter>peaklist['peaklistBool'] == 'true'</filter> </data> </xml> @@ -243,24 +248,24 @@ .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html -.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +.. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS </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_) +- 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_) +- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS news_) </token> <token name="@HELP_XCMS_NEWVERSION_31200@"> **Version 3.12.0+galaxy* - 03/03/2020** -- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_) +- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS news_) </token> <xml name="citation"> |
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| diff -r 018a9771de28 -r 2a2850fdf29e repository_dependencies.xml --- a/repository_dependencies.xml Wed Apr 07 16:46:50 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -<?xml version="1.0" ?> -<repositories> - <repository name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="544f6d2329ac"/> - <repository name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="4a51ab3d8ecf"/> -</repositories> \ No newline at end of file |
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| diff -r 018a9771de28 -r 2a2850fdf29e test-data/MM14.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM14.mzML Mon Sep 11 09:23:36 2023 +0000 |
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| b'@@ -0,0 +1,3667 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1">\n+\t<cvList count="2">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t</fileContent>\n+\t\t<sourceFileList count="1">\n+\t\t\t<sourceFile id="sf_ru_0" name="analysis.baf" location="MM14_20uM_2-A%2c4_01_1745.d/">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="" 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| Binary file test-data/TICs.pdf has changed |
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| diff -r 018a9771de28 -r 2a2850fdf29e test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.dataMatrix.NAless.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.dataMatrix.NAless.tsv Mon Sep 11 09:23:36 2023 +0000 |
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|
| b |
| diff -r 018a9771de28 -r 2a2850fdf29e test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.variableMetadata.tsv Mon Sep 11 09:23:36 2023 +0000 |
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| @@ -13,6 +13,8 @@ </HEAD> <BODY> <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1> +By: planemo@galaxyproject.org - +Date: 230525-08:53:25 </div> <h2>Samples used:</h2> <div><table> |
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|
| b |
| diff -r 018a9771de28 -r 2a2850fdf29e test-data/faahKO.xset.group.variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.variableMetadata.tsv Mon Sep 11 09:23:36 2023 +0000 |
| b |
| b'@@ -0,0 +1,8373 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| diff -r 018a9771de28 -r 2a2850fdf29e xcms_summary.r --- a/xcms_summary.r Wed Apr 07 16:46:50 2021 +0000 +++ b/xcms_summary.r Mon Sep 11 09:23:36 2023 +0000 |
| [ |
| b'@@ -14,13 +14,15 @@\n \n #Import the different functions\n source_local <- function(fname) {\n- argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))\n+ argv <- commandArgs(trailingOnly = FALSE)\n+ base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))\n+ source(paste(base_dir, fname, sep = "/"))\n }\n source_local("lib.r")\n \n pkgs <- c("CAMERA", "batch")\n loadAndDisplayPackages(pkgs)\n-cat("\\n\\n");\n+cat("\\n\\n")\n \n \n # ----- FUNCTION -----\n@@ -28,29 +30,29 @@\n cat(..., "\\n", file = htmlOutput, append = TRUE, sep = "")\n }\n writeraw <- function(htmlOutput, object, open = "at") {\n- log_file <- file(htmlOutput, open = open)\n- sink(log_file)\n- sink(log_file, type = "output")\n- print(object)\n- sink()\n- close(log_file)\n+ log_file <- file(htmlOutput, open = open)\n+ sink(log_file)\n+ sink(log_file, type = "output")\n+ print(object)\n+ sink()\n+ close(log_file)\n }\n getSampleNames <- function(xobject) {\n- if (class(xobject) == "xcmsSet")\n- return(sampnames(xobject))\n- if (class(xobject) == "XCMSnExp")\n- return(xobject@phenoData@data$sample_name)\n+ if (class(xobject) == "xcmsSet")\n+ return(sampnames(xobject))\n+ if (class(xobject) == "XCMSnExp")\n+ return(xobject@phenoData@data$sample_name)\n }\n getFilePaths <- function(xobject) {\n- if (class(xobject) == "xcmsSet")\n- return(xobject@filepaths)\n- if (class(xobject) == "XCMSnExp")\n- return(fileNames(xobject))\n+ if (class(xobject) == "xcmsSet")\n+ return(xobject@filepaths)\n+ if (class(xobject) == "XCMSnExp")\n+ return(fileNames(xobject))\n }\n equalParams <- function(param1, param2) {\n- writeraw("param1.txt", param1, open = "wt")\n- writeraw("param2.txt", param2, open = "wt")\n- return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt"))\n+ writeraw("param1.txt", param1, open = "wt")\n+ writeraw("param2.txt", param2, open = "wt")\n+ return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt"))\n }\n \n \n@@ -62,29 +64,29 @@\n # ----- ARGUMENTS PROCESSING -----\n \n #image is an .RData file necessary to use xset variable given by previous tools\n-load(args$image);\n+load(args$image)\n \n htmlOutput <- "summary.html"\n-if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput;\n+if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput\n \n user_email <- NULL\n-if (!is.null(args$user_email)) user_email <- args$user_email;\n+if (!is.null(args$user_email)) user_email <- args$user_email\n \n # if the RData come from XCMS 1.x\n if (exists("xset")) {\n- xobject <- xset\n- # retrocompatability\n- if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject)))\n+ xobject <- xset\n+ # retrocompatability\n+ if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject)))\n }\n # if the RData come from CAMERA\n if (exists("xa")) {\n- xobject <- xa@xcmsSet\n- if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name))\n+ xobject <- xa@xcmsSet\n+ if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name))\n }\n # if the RData come from XCMS 3.x\n if (exists("xdata")) {\n- xobject <- xdata\n- if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name))\n+ xobject <- xdata\n+ if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name))\n }\n \n if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")\n@@ -95,143 +97,141 @@\n writehtml("<HTML lang=\'en\'>")\n \n writehtml("<HEAD>")\n- writehtml("<meta http-equiv=\'Content-Type\' content=\'text/html; charset=UTF-8\' />")\n+writehtml("<meta http-equiv=\'Content-Type\' content=\'text/html; charset=UTF-8\' />")\n \n- '..b'\n+ writehtml("</div>")\n+}\n \n- writehtml("<h2>Citations:</h2>")\n- writehtml("<div><ul>")\n- writehtml("<li>To cite the <b>XCMS</b> package in publications use:")\n- writehtml("<ul>")\n- writehtml("<li>", "Smith, C.A. and Want, E.J. and O\'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)", "</li>")\n- writehtml("<li>", "Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)", "</li>")\n- writehtml("<li>", "H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)", "</li>")\n- writehtml("</ul>")\n- writehtml("</li>")\n+writehtml("<h2>Citations:</h2>")\n+writehtml("<div><ul>")\n+writehtml("<li>To cite the <b>XCMS</b> package in publications use:")\n+writehtml("<ul>")\n+writehtml("<li>", "Smith, C.A. and Want, E.J. and O\'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)", "</li>")\n+writehtml("<li>", "Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)", "</li>")\n+writehtml("<li>", "H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)", "</li>")\n+writehtml("</ul>")\n+writehtml("</li>")\n \n- writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")\n- writehtml("<ul>")\n- writehtml("<li>", "Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)", "</li>")\n- writehtml("</ul>")\n- writehtml("</li>")\n+writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")\n+writehtml("<ul>")\n+writehtml("<li>", "Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)", "</li>")\n+writehtml("</ul>")\n+writehtml("</li>")\n \n- writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")\n- writehtml("<ul>")\n- writehtml("<li>", "Franck Giacomoni, Gildas Le Corguill\xc3\xa9, Misharl Monsoor, Marion Landi, Pierre Pericard, M\xc3\xa9lanie P\xc3\xa9t\xc3\xa9ra, Christophe Duperier, Marie Tremblay-Franco, Jean-Fran\xc3\xa7ois Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Th\xc3\xa9venot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813", "</li>")\n- writehtml("</ul>")\n- writehtml("</li>")\n- writehtml("</ul></div>")\n+writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")\n+writehtml("<ul>")\n+writehtml("<li>", "Franck Giacomoni, Gildas Le Corguill\xc3\xa9, Misharl Monsoor, Marion Landi, Pierre Pericard, M\xc3\xa9lanie P\xc3\xa9t\xc3\xa9ra, Christophe Duperier, Marie Tremblay-Franco, Jean-Fran\xc3\xa7ois Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Th\xc3\xa9venot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813", "</li>")\n+writehtml("</ul>")\n+writehtml("</li>")\n+writehtml("</ul></div>")\n \n writehtml("</BODY>")\n \n' |
